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Enterprise Solutions and Databases including E-Notebook

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User’s Guide
Chem & Bio Office Enterprise 2010
for Windows
Chem & Bio Office Enterprise is an Enterprise and Workgroup solution including:
• Knowledge Management: E-Notebook & CombiChem
• Laboratory Informatics: Workflow LIMS and Compliant SDMS
• Biological Informatics: BioAssay Enterprise, BioSAR and BioViz
• Chemical Informatics: Inventory Enterprise and Registration Enterprise
• Manufacturing Informatics: E-Notebook compliance execution and Inventory
• Scientific Databases: The Merck Index and ChemACX Database
Chem & Bio Office
®
Enterprise Solutions and Databases including E-Notebook

License Information
All resources and application files in ChemBioOffice, ChemOffice, BioOffice, ChemBioDraw,
ChemDraw, BioDraw, ChemBio3D, Chem3D, ChemFinder, BioViz, Inventory, E-Notebook, BioAssay,
ChemINDEX, ChemFinder, and ChemInfo programs, all resources in the ChemOffice,
ChemDraw, Chem3D, ChemFinder, and ChemInfo application files, and this manual are Copyright
© 1986-2009 by CambridgeSoft Corporation (“CS”) with all rights reserved worldwide. MOPAC
2002 is Copyright © 1993-2006 by Fujitsu Limited with all rights reserved.
Information in this document is subject to change without notice and does not represent a commitment
on the part of CS. Both these materials and the right to use them are owned exclusively by CS.
Use of these materials is licensed by CS under the terms of a software license agreement; they may
be used only as provided for in said agreement.
ChemBioOffice, ChemOffice BioOffice, ChemBioDraw, ChemDraw, BioDraw, ChemBio3D,
Chem3D, CS MOPAC, ChemFinder, BioViz, Inventory, E-Notebook, and BioAssay, and ChemInfo
are not supplied with copy protection. Do not duplicate any of the copyrighted materials except for
your personal backups without written permission from CS. To do so would be in violation of federal
and international law, and may result in criminal as well as civil penalties. You may use ChemBioOffice,
ChemOffice BioOffice, ChemBioDraw, ChemDraw, BioDraw, ChemBio3D, Chem3D, CS
MOPAC, ChemFinder, BioViz, Inventory, E-Notebook, and BioAssay ChemOffice, ChemDraw,
Chem3D, CS MOPAC, ChemFinder, Inventory, E-Notebook, BioAssay, and ChemInfo on any computer
owned by you; however, extra copies may not be made for that purpose. Consult the CS
License Agreement for Software and Database Products for further details.
Trademark Notices
ChemBioOffice, ChemOffice, BioOffice, ChemBioDraw. ChemDraw, BioDraw,ChemBio3D,
Chem3D, ChemINDEX, ChemFinder, ChemInfo and ChemACX are registered trademarks of
CambridgeSoft Corporation (Cambridge Scientific Computing, Inc.).
The Merck Index is a registered trademark of Merck & Co., Inc. ©2006 All rights reserved.
MOPAC 2002 is a trademark of Fujitsu Limited.
Microsoft Windows, Windows 2000, Windows XP, and Microsoft Word, Microsoft Excel, Microsoft
PowerPoint, Microsoft Access, and SQL Server 2005 are registered trademarks of Microsoft Corporation.
Apple Events, Macintosh, Laserwriter, Imagewriter, QuickDraw and AppleScript are registered
trademarks of Apple Computer, Inc. Geneva, Monaco, and TrueType are trademarks of Apple Computer,
Inc.
InChI is a trademark of the International Union of Pure and Applied Chemistry.
Jaguar is a trademark of Schrödinger, LLC.
THE MERCK INDEX ® is a trademark of Merck & Company Incorporated, Whitehouse Station,
New Jersey, USA and is registered in the United States Patent and Trademark Office.

Oracle ® is a registered trademark of Oracle Corporation and/or its affiliates. Other names may be
trademarks of their respective owners.
All other trademarks are the property of their respective holders. Any use of the marks in connection
with the sale, offering for sale, distribution or advertising of any goods and services, including any
other Web site, or in connection with labels, signs, prints, packages, wrappers, receptacles or advertisements
used for the sale, offering for sale, distribution or advertising of any goods and services,
including any other Web site, which is likely to cause confusion, to cause mistake or to deceive, is
strictly prohibited.
Copyright Notice
The materials contained in CambridgeSoft Database Products, including but not limited to, ChemACX,
ChemIndex, and The Merck Index, are protected by copyright laws and international copyright
treaties, as well as other intellectual property laws and treaties. Copyright in the materials
contained on the CD and internet subscription products, including, but not limited to, the textual
material, chemical structures representations, artwork, photographs, computer software, audio and
visual elements, is owned or controlled separately by CS.
CS is a distributor (and not a publisher) of information supplied by third parties. Accordingly, CS has
no editorial control over such information. Database Suppliers (“Supplier”) individually own all
right, title, and interest, including copyright, in their database—and retain all such rights in providing
information to Customers.
The materials contained in The Merck Index are protected by copyright laws and international copyright
treaties, as well as other intellectual property laws and treaties. Copyright in the materials contained
on the CD and internet subscription products, including, but not limited to, the textual
material, chemical structures representations, artwork, photographs, computer software, audio and
visual elements, is owned or controlled separately by Merck & Co., Inc., (“Merck”) and
CambridgeSoft Corporation (“CS”).
The ChemReact68, ChemSynth, ChemReact500, and ChemSelect Reaction Database is copyrighted
© by InfoChem GmbH 1997.
AspTear is copyrighted © by Softwing.
InChI is a trademark of the International Union of Pure and Applied Chemistry. InChI Material
in ChemDraw is © IUPAC 2005.
schrödinger ® Jaguar
GAMESS is copyrighted © by Ames Laboratory
Copyright © 1986-2009 CambridgeSoft Corporation (Cambridge Scientific Computing, Inc.) All
Rights Reserved.
Printed in the United States of America.
All other trademarks are the property of their respective holders.
CambridgeSoft End-User License Agreement for Software Products

Important: This CambridgeSoft Software License Agreement (“Agreement”) is a legal agreement
between you, the end user (either an individual or an entity), and CambridgeSoft Corporation (“CS”)
regarding the use of CS Software and Database Products, which may include computer software, the
associated media, any printed materials, and any “online” or electronic documentation. By installing,
copying, or otherwise using any CS Software Product, you signify that you have read the CS End
User License Agreement and agree to be bound by its terms. If you do not agree to the Agreement’s
terms, promptly return the package within 30 days of purchase and all its contents to the place of purchase
for a full refund.
CambridgeSoft Software and Database License
1. Grant of License. CambridgeSoft (CS) Software Products are licensed, not sold. CS grants and
you hereby accept a nonexclusive license to use one copy of the enclosed Software Product (“Software”)
in accordance with the terms of this Agreement. This licensed copy of the Software may only
be used on a single computer, except as provided below.
You may physically transfer the Software from one computer to another for your own use, provided
the Software is in use (or installed) on only one computer at a time. If the Software is permanently
installed on your computer (other than a network server), you may also use the Software on a portable
or home computer, provided that you use the software on only one computer at a time. You may
not (a) electronically transfer the Software from one computer to another, (b) distribute copies of the
Software to others, or (c) modify or translate the Software without the prior written consent of CS,
(d) place the software on a server so that it is accessible via a public network such as the Internet, (e)
sublicense, rent, lease or lend any portion of the Software or Documentation, (f) modify or adapt the
Software or merge it into another program, (g) modify or circumvent the software activation, or (h)
reverse engineer the software activation so as to circumvent it. The Software may be placed on a file
or disk server connected to a network, provided that a license has been purchased for every computer
with access to that server. You may make only those copies of the Software which are necessary to
install and use it as permitted by this agreement, or are for purposes of backup and archival records;
all copies shall bear CS’s copyright and proprietary notices. You may not make copies of any accompanying
written materials.
With a fixed license, the software cannot be installed on more than the number of computers equivalent
to the number of fixed licenses purchased. For example, a 10-user fixed license means the software
can be installed on no more than 10 different computers. A fixed license cannot be installed on
a server. With a concurrent license, the software can be installed on any number of computers at the
organization, but the number of computers using the software at any one time cannot exceed the
number of concurrent licenses purchased. For example, a 10-user concurrent license can be installed
on 20 computers, but no more than 10 users can be using it at any one time. If the number of users of
the software could potentially exceed the number of licensed copies, then Licensee must have a reasonable
mechanism or process in place to assure that the number of persons using the software does
not exceed the number of copies. CambridgeSoft reserves the right to conduct periodic audits no

more than once per year to review the implementation of this agreement at the Licensee’s site. At
CambridgeSoft’s request, Licensee will provide a knowledgeable employee to assist in said audit
2. Ownership. The Software is and at all times shall remain the sole property of CS. This ownership
is protected by the copyright laws of the United States and by international treaty provisions. Upon
expiration or termination of this agreement, you shall promptly return all copies of the Software and
accompanying written materials to CS. You may not modify, decompile, reverse engineer, or disassemble
the Software.
3. Assignment Restrictions. You may not rent, lease, or otherwise sublet the Software or any part
thereof. You may transfer on a permanent basis the rights granted under this license provided you
transfer this Agreement and all copies of the Software, including prior versions, and all accompanying
materials. The recipient must agree to the terms of this Agreement in full and register this transfer
in writing with CS.
4. Use of Included Data. All title and copyrights in and to the Software product, including but not
limited to any images, photographs, animations, video, audio, music, text, applets, Java applets, and
data files and databases (the “Included Data”), are owned by CS or its suppliers.
• You may not copy, distribute or otherwise make the Included Data publicly available.
• Licensed users of ChemOffice Enterprise and Workgroup and the accompanying Plug-in software
products may access, search, and view the Included Data and may transmit the results of any
search of the Included Data to other users of the licensed ChemOffice Enterprise and Workgroup
software products within your organization only, provided that such transmission is via an internal
corporate (or university) network and is not accessible by the public.
• You may not install the Included Data on non-licensed computers nor distribute or otherwise
make the Included Data publicly available.
• You may use the Software to organize personal data, and you may transmit such personal data
over the Internet provided that the transmission does not contain any Included Data.
• All rights not specifically granted under this Agreement are reserved by CS.
5. Limitations on Use. (a) Desktop versions of E-Notebook, Inventory, and BioAssay are licensed
for use with SQL Server Express, and are not licensed for use with SQL Server. Licenses for use with
SQL Server are available separately. (b) Workgroup versions of E-Notebook, Inventory, and BioAssay
are licensed for use with SQL Server and SQL Server Express. (c) Except as expressly provided
by copyright law, copying, redistribution, or publication, whether for commercial or non-commercial
purposes, must be with the express permission of CS, Merck, or other CS partner. In any copying,
redistribution, or publication of copyrighted material, any changes to or deletion of author attribution
or copyright notice, or any other proprietary notice of CS, Merck, or other Database producer are
prohibited.
6. Separation of Components. The Software is licensed as a single product. Its component parts may
not be separated for use on more than one computer, except in the case of ChemBioOffice Enterprise.
ChemBioOffice Enterprise includes licenses for ChemBioDraw ActiveX and licenses for

ChemBio3D ActiveX. The ActiveX software products may be installed on computers other than that
one on which ChemBioOffice Enterprise is installed. However, each copy of the ActiveX is individually
subject to the provisions of Paragraphs 1 through 4 of this Agreement.
7. Educational Use Only of Student Licenses. If you are a student enrolled at an educational institution,
the CS License Agreement grants to you personally a license to use one copy of the enclosed
Software in accordance with the terms of this Agreement. In this case the CS License Agreement
does not permit commercial use of the Software nor does it permit you to allow any other person to
use the Software.
8. Modification of Databases, Web sites, or Subscription Services. CS reserves the right to change,
modify, suspend or discontinue any or all parts of any Paid Subscription Services and databases at
any time.
9. Termination. You may terminate the license at any time by destroying all copies of the Software
and documentation in your possession. Without prejudice to any other rights, CS may terminate this
Agreement if you fail to comply with its terms and conditions. In such event, you must destroy all
copies of the Software Product and all of its component parts.
10. Revocation of Subscription Access. Any use which is commercial and/or non-personal is strictly
prohibited, and may subject the Subscriber making such uses to revocation of access to this Paid Subscription
Service, as well as any other applicable civil or criminal penalties. Similarly, sharing a Subscriber
password with a non-Subscriber or otherwise making this Paid Subscription Service available
to third parties other than the Authorized User as defined above is strictly prohibited, and may subject
the Subscriber participating in such activities to revocation of access to the Paid Subscription
Services; and, the Subscriber and any third party, to any other applicable civil or criminal penalties
under copyright or other laws. In the case of an authorized site license, a Subscriber shall cause any
employee, agent or other third party which the Subscriber allows to use the Paid Subscription Service
materials to abide by all of the terms and conditions of this Agreement. In all other cases, only the
Subscriber is permitted to access the Paid Subscription Service materials. Should CambridgeSoft
become aware of any use that might cause revocation of the license, they shall notify the Subscriber.
The Subscriber shall have 90 days from date of notice to correct such violation before any action will
be taken.
11. Confidentiality. The Software contains trade secrets and proprietary know-how that belong to CS
and are being made available to you in strict confidence. ANY USE OR DISCLOSURE OF THE SOFT-
WARE, OR USE OF ITS ALGORITHMS, PROTOCOLS OR INTERFACES, OTHER THAN IN STRICT
ACCORDANCE WITH THIS LICENSE AGREEMENT, MAY BE ACTIONABLE AS A VIOLATION OF OUR
TRADE SECRET RIGHTS.
CS Limited Warranty
Software Limited Warranty. CS’s sole warranty with respect to the Software is that it shall be free
of errors in program logic or documentation, attributable to CS, which prevent the performance of

the principal computing functions of the Software. CS warrants this for a period of thirty (30) days
from the date of receipt.
CS’s Liability. In no event shall CS be liable for any indirect, special, or consequential damages,
such as, but not limited to, loss of anticipated profits or other economic loss in connection with or
arising out of the use of the software by you or the services provided for in this agreement, even if CS
has been advised of the possibility of such damages.
CS’s entire liability and your exclusive remedy shall be, at CS’s discretion, either (A) return of any
license fee, or (B) correction or replacement of software that does not meet the terms of this limited
warranty and that is returned to CS with a copy of your purchase receipt.
Database Representations and Limited Warranty. The User shall indemnify, defend and hold CS,
Merck, and/or other Supplier harmless from any damages, expenses and costs (including reasonable
attorneys’ fees) arising out of any breach or alleged breach of these Terms and Conditions, representations
and/or warranties herein, by the User or any third party to whom User shares her/his password
or otherwise makes available this Subscription Service. The User shall cooperate in the defense of
any claim brought against CambridgeSoft, Merck, and/or other Database Suppliers. In no event shall
CS, Merck, and/or other Supplier be liable for any indirect, special, or consequential damages, such
as, but not limited to, loss of anticipated profits or other economic loss in connection with or arising
out of the use of the software by you or the services provided for in this agreement, even if CS,
Merck, and/or other Supplier has been advised of the possibility of such damages. CS and/or Merck’s
entire liability and your exclusive remedy shall be, at CS’s discretion a return of any pro-rata portion
of the subscription fee. The failure of either party to assert a right hereunder or to insist upon compliance
with any term or condition of this Agreement shall not constitute a waiver of that right or excuse
a similar subsequent failure to perform any such term or condition by the other party.
NO OTHER WARRANTIES. CS DISCLAIMS OTHER IMPLIED WARRANTIES, INCLUDING, BUT NOT LIM-
ITED TO, IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE,
AND IMPLIED WARRANTIES ARISING BY USAGE OF TRADE, COURSE OF DEALING, OR COURSE OF
PERFORMANCE. NOTWITHSTANDING THE ABOVE, WHERE APPLICABLE, IF YOU QUALIFY AS A
“CONSUMER” UNDER THE MAGNUSONMOSS WARRANTY ACT, THEN YOU MAY BE ENTITLED TO ANY
IMPLIED WARRANTIES ALLOWED BY LAW FOR THE PERIOD OF THE EXPRESS WARRANTY AS SET
FORTH ABOVE. SOME STATES DO NOT ALLOW LIMITATIONS ON IMPLIED WARRANTIES, SO THE
ABOVE LIMITATION MIGHT NOT APPLY TO YOU. THIS WARRANTY GIVES
YOU SPECIFIC LEGAL RIGHTS, AND YOU MAY ALSO HAVE OTHER RIGHTS WHICH VARY FROM
STATE TO STATE.
No Waiver. The failure of either party to assert a right hereunder or to insist upon compliance with
any term or condition of this Agreement shall not constitute a waiver of that right or excuse a similar
subsequent failure to perform any such term or condition by the other party.
Governing Law. This Agreement shall be construed according to the laws of the Commonwealth of
Massachusetts.
Export. You agree that the Software will not be shipped, transferred, or exported into any country or
used in any manner prohibited by the United States Export Administration Act or any other export
laws, restrictions, or regulations.

End-User License Agreement for CambridgeSoft Database
Products
Important: This CambridgeSoft End-User License Agreement is a legal agreement between you
(either an individual or a single entity) and CambridgeSoft Corporation for the CambridgeSoft supplied
database product(s) and may include associated media, printed materials, and “online” or electronic
documentation. By using the database product(s) you agree that you have read, understood and
will be bound by this license agreement.
Database Product License
1. Copyright Notice. The materials contained in CambridgeSoft Database Products, including but
not limited to, ChemACX, ChemIndex, and The Merck Index, are protected by copyright laws and
international copyright treaties, as well as other intellectual property laws and treaties. Copyright in
the materials contained on the CD and internet subscription products, including, but not limited to,
the textual material, chemical structures representations, artwork, photographs, computer software,
audio and visual elements, is owned or controlled separately by CambridgeSoft Corporation (“CS”).
CS is a distributor (and not a publisher) of information supplied by third parties. Accordingly, CS has
no editorial control over such information. Database Suppliers (“Supplier”) individually own all
right, title, and interest, including copyright, in their database—and retain all such rights in providing
information to Customers.
The materials contained in The Merck Index are protected by copyright laws and international copyright
treaties, as well as other intellectual property laws and treaties. Copyright in the materials contained
on the CD and internet subscription products, including, but not limited to, the textual
material, chemical structures representations, artwork, photographs, computer software, audio and
visual elements, is owned or controlled separately by the Merck & Co., Inc., (“Merck”) and
CambridgeSoft Corporation (“CS”).
2. Limitations on Use. Except as expressly provided by copyright law, copying, redistribution, or
publication, whether for commercial or non-commercial purposes, must be with the express permission
of CS and/or Merck. In any copying, redistribution, or publication of copyrighted material, any
changes to or deletion of author attribution or copyright notice, or any other proprietary notice of CS,
Merck, or other Database producer are prohibited.
3. Grant of License, CD/DVD Databases. CambridgeSoft Software Products are licensed, not sold.
CambridgeSoft grants and you hereby accept a nonexclusive license to use one copy of the enclosed
Software Product (“Software”) in accordance with the terms of this Agreement. This licensed copy
of the Software may only be used on a single computer, except as provided below. You may physically
transfer the Software from one computer to another for your own use, provided the Software is
in use (or installed) on only one computer at a time. If the Software is permanently installed on your
computer (other than a network server), you may also use the Software on a portable or home computer,
provided that you use the software on only one computer at a time. You may not (a) electronically
transfer the Software from one computer to another, (b) distribute copies of the Software to

others, or (c) modify or translate the Software without the prior written consent of CambridgeSoft,
(d) place the software on a server so that it is accessible via a public network such as the Internet, (e)
sublicense, rent, lease or lend any portion of the Software or Documentation, or (f) modify or adapt
the Software or merge it into another program. The Software may be placed on a file or disk server
connected to a network, provided that a license has been purchased for every computer with access to
that server. You may make only those copies of the Software which are necessary to install and use it
as permitted by this agreement, or are for purposes of backup and archival records; all copies shall
bear CambridgeSoft’s copyright and proprietary notices. You may not make copies of any accompanying
written materials.
4. Assignment Restrictions for CD/DVD databases. You may not rent, lease, or otherwise sublet the
Software or any part thereof. You may transfer on a permanent basis the rights granted under this
license provided you transfer this Agreement and all copies of the Software, including prior versions,
and all accompanying materials. The recipient must agree to the terms of this Agreement in full and
register this transfer in writing with CambridgeSoft.
5. Revocation of Subscription Access. Any use which is commercial and/or non-personal is strictly
prohibited, and may subject the Subscriber making such uses to revocation of access to this Paid Subscription
Service, as well as any other applicable civil or criminal penalties. Similarly, sharing a Subscriber
password with a non-Subscriber or otherwise making this Paid Subscription Service available
to third parties other than the Authorized User as defined above is strictly prohibited, and may subject
the Subscriber participating in such activities to revocation of access to the Paid Subscription
Services; and, the Subscriber and any third party, to any other applicable civil or criminal penalties
under copyright or other laws. In the case of an authorized site license, a Subscriber shall cause any
employee, agent or other third party which the Subscriber allows to use the Paid Subscription Service
materials to abide by all of the terms and conditions of this Agreement. In all other cases, only the
Subscriber is permitted to access the Paid Subscription Service materials. Should CambridgeSoft
become aware of any use that might cause revocation of the license, they shall notify the Subscriber.
The Subscriber shall have 90 days from date of notice to correct such violation before any action will
be taken.
6. Trademark Notice. THE MERCK INDEX ® is a trademark of Merck & Company Incorporated,
Whitehouse Station, New Jersey, USA and is registered in the United States Patent and Trademark
Office. CambridgeSoft ® and ChemACX are trademarks of CambridgeSoft Corporation, Cambridge,
Massachusetts, USA and are registered in the United States Patent and Trademark Office, the European
Union (CTM), Japan, and other markets.
Any use of the marks in connection with the sale, offering for sale, distribution or advertising of any
goods and services, including any other Web site, or in connection with labels, signs, prints, packages,
wrappers, receptacles or advertisements used for the sale, offering for sale, distribution or
advertising of any goods and services, including any other Web site, which is likely to cause confusion,
to cause mistake or to deceive, is strictly prohibited.

7. Modification of Databases, Web sites, or Subscription Services. CS reserves the right to change,
modify, suspend or discontinue any or all parts of any Paid Subscription Services and databases at
any time.
8. Representations and Warranties. The User shall indemnify, defend and hold CS, Merck, and/or
other Supplier harmless from any damages, expenses and costs (including reasonable attorneys’ fees)
arising out of any breach or alleged breach of these Terms and Conditions, representations and/or
warranties herein, by the User or any third party to whom User shares her/his password or otherwise
makes available this Subscription Service. The User shall cooperate in the defense of any claim
brought against CambridgeSoft, Merck, and/or other Database Suppliers.
In no event shall CS, Merck, and/or other Supplier be liable for any indirect, special, or consequential
damages, such as, but not limited to, loss of anticipated profits or other economic loss in connection
with or arising out of the use of the software by you or the services provided for in this agreement,
even if CS, Merck, and/or other Supplier has been advised of the possibility of such damages. CS
and/or Merck’s entire liability and your exclusive remedy shall be, at CS’s discretion a return of any
pro-rata portion of the subscription fee.
The failure of either party to assert a right hereunder or to insist upon compliance with any term or
condition of this
Agreement shall not constitute a waiver of that right or excuse a similar subsequent failure to perform
any such term or condition by the other party.
This Agreement shall be construed according to the laws of the Commonwealth of Massachusetts,
United States of America.

Q: IS IT OK TO COPY MY COLLEAGUE’S
SOFTWARE?
NO, it’s not okay to copy your colleague’s
software. Software is protected by federal copyright law,
which says that you can't make such additional copies
without the permission of the copyright holder. By
protecting the investment of computer software
companies in software development, the copyright law
serves the cause of promoting broad public availability of
new, creative, and innovative products. These companies
devote large portions of their earnings to the creation of
new software products and they deserve a fair return on
their investment. The creative teams who develop the
software–programmers, writers, graphic artists and
others–also deserve fair compensation for their efforts.
Without the protection given by our copyright laws, they
would be unable to produce the valuable programs that
have become so important to our daily lives: educational
software that teaches us much needed skills; business
software that allows us to save time, effort and money;
and entertainment and personal productivity software
that enhances leisure time.
Q: That makes sense, but what do I get out of
purchasing my own software?
A: When you purchase authorized copies of software
programs, you receive user guides and tutorials, quick
reference cards, the opportunity to purchase
upgrades, and technical support from the software
publishers. For most software programs, you can read
about user benefits in the registration brochure or
upgrade flyer in the product box.
Q: What exactly does the law say about copying
software?
A: The law says that anyone who purchases a copy of
software has the right to load that copy onto a single
computer and to make another copy “for archival
purposes only” or, in limited circumstances, for
“purposes only of maintenance or repair.” It is illegal
to use that software on more than one computer or to
make or distribute copies of that software for any
other purpose unless specific permission has been
obtained from the copyright owner. If you pirate
software, you may face not only a civil suit for
damages and other relief, but criminal liability as well,
including fines and jail terms of up to one year
Q: So I'm never allowed to copy software for any other
reason?
A: That’s correct. Other than copying the software you
purchase onto a single computer and making another
copy “for archival purposes only” or “purposes only of
maintenance or repair,” the copyright law prohibits
you from making additional copies of the software for
any other reason unless you obtain the permission of
the software company.
Q: At my company, we pass disks around all the time.
We all assume that this must be okay since it was
the company that purchased the software in the
first place.
A: Many employees don’t realize that corporations are
bound by the copyright laws, just like everyone else.
Such conduct exposes the company (and possibly the
persons involved) to liability for copyright
infringement. Consequently, more and more
corporations concerned about their liability have
written policies against such “softlifting”. Employees
may face disciplinary action if they make extra copies
of the company’s software for use at home or on
additional computers within the office. A good rule to
remember is that there must be one authorized copy
of a software product for every computer upon which
it is run
Q: Can I take a piece of software owned by my
company and install it on my personal computer at
home if instructed by my supervisor?
A: A good rule of thumb to follow is one software
package per computer, unless the terms of the license
agreement allow for multiple use of the program. But
some software publishers’ licenses allow for “remote”
or “home” use of their software. If you travel or
telecommute, you may be permitted to copy your
software onto a second machine for use when you are
not at your office computer. Check the license carefully
to see if you are allowed to do this.
Q: What should I do if become aware of a company
that is not compliant with the copyright law or its
software licenses?
A: Cases of retail, corporate and Internet piracy or noncompliance
with software licenses can be reported on
the Internet at http://www.siia.net/piracy/report.asp
or by calling the Anti-Piracy Hotline:
(800) 388-7478.

Q: Do the same rules apply to bulletin boards and user
groups? I always thought that the reason they got
together was to share software.
A: Yes. Bulletin boards and user groups are bound by the
copyright law just as individuals and corporations.
However, to the extent they offer shareware or public
domain software, this is a perfectly acceptable
practice. Similarly, some software companies offer
bulletin boards and user groups special demonstration
versions of their products, which in some instances
may be copied. In any event, it is the responsibility of
the bulletin board operator or user group to respect
copyright law and to ensure that it is not used as a
vehicle for unauthorized copying or distribution.
Q: I'll bet most of the people who copy software don't
even know that they're breaking the law.
A: Because the software industry is relatively new, and
because copying software is so easy, many people are
either unaware of the laws governing software use or
choose to ignore them. It is the responsibility of each
and every software user to understand and adhere to
copyright law. Ignorance of the law is no excuse. If
you are part of an organization, see what you an do to
initiate a policy statement that everyone respects.
Also, suggest that your management consider
conducting a software audit. Finally, as an individual,
help spread the word that users should be “software
legal.”
Q: What are the penalties for copyright infringement?
SIIA also offers a number of other materials designed to
help you comply with the Federal Copyright Law. These
materials include:
"It's Just Not Worth the Risk" video.
This 12–minute video, available $10, has helped over
20,000 organizations dramatize to their employees the
implications and consequences of software piracy.
“Don’t Copy that Floppy” video
This 9 minute rap video, available for $10, is designed
to educate students on the ethical use of software.
Other education materials including, “Software Use
and the Law”, a brochure detailing the copyright law
and how software should be used by educational
institutions, corporations and individuals; and several
posters to help emphasize the message that unauthorized
copying of software is illegal.
To order any of these materials, please send your request to:
“SIIA Anti-Piracy Materials”
Software & Information Industry Association
1090 Vermont Ave, Sixth Floor,
Washington, D.C. 20005
(202) 289-7442
We urge you to make as many copies as you would like
in order to help us spread the word that unauthorized
copying of software is illegal.
A: The Copyright Act allows a copyright owner to
recover monetary damages measured either by: (1) its
actual damages plus any additional profits of the
infringer attributable to the infringement, or (2)
statutory damages, of up to $150,000 for each copyrighted
work infringed. The copyright owner also has
the right to permanently enjoin an infringer from
engaging in further infringing activities and may be
awarded costs and attorneys’ fees. The law also
permits destruction or other reasonable disposition of
all infringing copies and devices by which infringing
copies have been made or used in violation of the
copyright owner’s exclusive rights. In cases of willful
infringement, criminal penalties may also be assessed
against the infringer.

A Guide to CambridgeSoft Manuals
Manuals:
Chem & Bio Draw
Chem & Bio Office
Chem & Bio Office
Includes:
Chem & Bio
Drawing Standard
Desktop Software
ChemBio 3D
Finder & BioViz
Workgroup Solutions
and Databases
Including E-Notebook
Chem & Bio Draw
■
Chem & Bio 3D
■
Databases Workgroup Solutions Desktop Applications Software
Chem & Bio Finder
BioAssay Desktop
BioViz Desktop
Inventory Desktop
E-Notebook Desktop
ChemDraw/Excel
Struct = Name
ChemNMR
CombiChem/Excel
ChemFinder/Office
MOPAC, GAMESS, MM2
CS Gaussian, Jaguar Interface
CombiChem/E-Notebook
BioAssay Workgroup
BioSAR Enterprise
Inventory Workgroup
Formulations & Mixtures
Compliant SDMS
The Merck Index
R&D Insight/Chemists
ChemINDEX Database, NCI, AIDS & Cancer
Traditional Chinese Medicines
Drugs: Synonyms & Properties
Nanogens Index; Medicinal Chemistry
■
■
■
■
■
■
■
■
■
■
■
■
■
■
■
■
■
■
■
■
■
■
■
■
ChemACX, ChemMSDS Database
■
Sigma-Aldrich MSDS
■
ChemReact500, ChemReact68 & ChemSynth
■

Contents
Section I
E-Notebook
Desktop & Workgroup
Chapter 1
Getting Started .......................................3
Navigation Overview .................................4
Security Overview ......................................5
Logging into E-Notebook ...........................5
Chapter 2
E-Notebook Desktop & Workgroup ....7
About E-Notebook .....................................7
What’s New ................................................7
About this Guide ........................................8
Chapter 3
Working with E-Notebook ....................9
Notebooks .................................................10
Pages and Reaction Pages ........................10
Folders ......................................................12
Reactants Collections ...............................13
Working with a Table of Contents ...........13
Browsing the Collection Tree ..................14
Chapter 4
Managing Collections ..........................19
Organizing Collections .............................19
Viewing Collection Properties .................22
Importing and Exporting Collections .......23
Templates ................................................ 23
Form Tools .............................................. 24
Changing Collection Security Properties 24
Performing a Collection Transition ......... 25
Exporting to Word ................................... 26
Printing Collections or Sections .............. 26
Chapter 5
Working with Reactions ..................... 29
Pre-configured Sections ........................... 29
Reaction Sections .................................... 29
Batch Explorer ......................................... 42
Chapter 6
Spectra and Other Sections ................ 45
Ancillary Data Sections ........................... 45
Captured Image Sections ......................... 46
Table Sections ......................................... 48
MS Word Sections ................................... 53
MS Excel Sections ................................... 54
Chapter 7
Managing Sections ............................... 55
Creating a Section .................................... 55
Modifying a Section ................................ 55
Removing a Section ................................. 56
Moving a Section ..................................... 56
Cutting and Pasting a Section .................. 56
Renaming a Section ................................. 57
Duplicating a Section .............................. 57
Chapter 8
Saving the Collection Changes ........... 59
Working With Save Icon ......................... 59
Chem & Bio Office 2010 User Guide
i

Administrator
Saving a Collection ..................................59
Chapter 9
Working with Data ..............................61
Chemical Structure Data ..........................61
Styled Text ...............................................62
Subsections ...............................................63
Property Lists ...........................................63
Rendering .................................................66
Chapter 10
Searching ..............................................67
Searching ..................................................67
Working with Query Results ....................68
Saving a Query .........................................69
Refining a Search .....................................69
Chapter 11
Working Offline ...................................73
Creating an offline folder .........................73
Working in the Offline mode ...................73
Limitations to Offline Working ................74
Chapter 12
E-Notebook Batch Import Facility .....75
.....................................................75
...................................................75
....................................................75
.....................................75
.....................................76
...................................................76
........................................................76
......................................................77
..................................................77
Refreshing E-Notebook ........................... 79
Numerical Units ...................................... 79
Using the Session Manager ..................... 81
Appendix B
Glossary ................................................83
Terminology ............................................ 83
Section II
BioAssay
Desktop & Workgroup
BioAssay Desktop & Workgroup .......87
What’s New ............................................. 87
About this Guide ..................................... 87
Logging in to BioAssay ........................... 87
Terminology ............................................ 87
Navigation ............................................... 88
Protocols .................................................. 91
External Analysis .................................. 130
A Sample Protocol - IC50 ..................... 131
Compound Lists .................................... 145
Reporting ............................................... 145
Settings .................................................. 148
Actions Menu ........................................ 154
Prohibited Field Names ......................... 158
Security .................................................. 165
Section III
Inventory
Desktop & Workgroup
Appendix A
System Features ...................................79
Viewing User Information .......................79
Inventory Desktop & Workgroup ....169
What’s new ............................................ 169
Login and Logout .................................. 170
ii
Contents

Terminology ...........................................170
The User Interface ..................................170
Searching CS Inventory .........................184
Printing Labels and Reports ...................186
CS Inventory Tasks ................................190
Securing Structure Files .........................196
Section IV
Chem & Bio Office Enterprise
Chapter 15
Informatics Directions .......................201
Collaboration ..........................................202
Technology and Integration ...................202
Professional Services ..............................203
Summary ................................................204
Chapter 16
Supporting an Informatics Enterprise
Workflow ............................................207
Chapter 17
DocManager Enterprise ....................215
Batch Submission ...................................215
Viewing Recent Activities .....................215
Searching for Documents .......................215
Chapter 18
E-Notebook Enterprise ......................217
Working with Collections ......................220
Reaction Sections ...................................221
Spectra and Other Sections ....................223
Working with Data ................................ 224
Searching ............................................... 224
Chapter 19
CombiChem for E-Notebook ............ 229
Chapter 20
BioAssay Enterprise .......................... 231
Protocols ................................................ 231
Reporting ............................................... 232
Chapter 21
Registration ........................................ 233
Registering Records ............................... 233
Query and Reporting ............................. 233
Chapter 22
BioSAR Enterprise ............................ 235
Terminology .......................................... 235
Schema Management ............................. 236
Form Management ................................. 236
Searching ............................................... 236
Chapter 23
Inventory Enterprise ......................... 237
Overview ............................................... 237
Searching Inventory Enterprise ............. 237
Container Management ......................... 237
Grid Management .................................. 237
Managing Batching Fields ..................... 237
Plate Inventory ....................................... 238
Reports Management ............................. 238
Managing Organizations ....................... 239
Integrating with Registration Enterprise 239
Chem & Bio Office 2010 User Guide
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Administrator
Section V
Databases
Chapter 24
Scientific Databases ...........................243
ChemBioFinder.Com Gateway ..............243
Database Offerings .................................243
Reference Data
Chapter 25
The Merck Index ...............................245
How Is It Useful? ...................................245
About The Merck Index .........................246
Using The Merck Index Online ..............246
Compound Searching .............................247
Organic Name Reactions ........................247
Supplemental Tables ..............................248
Logging Off ............................................249
About Ashgate Drugs ............................ 255
Using Ashgate Drugs ............................. 255
Chapter 29
NCI ......................................................259
Using NCI .............................................. 259
Chapter 30
AIDS ....................................................261
Using AIDS on CD ................................ 261
Chapter 31
Traditional Chinese Medicines .........263
About TCM ........................................... 263
ChemOffice Enterprise .......................... 263
Chapter 32
Nanogens .............................................267
Chapter 33
Off-Label Database ............................269
Chapter 26
R&D Insight/Chemists ......................251
About RDIC ...........................................251
Using RDIC Online ................................251
Chapter 27
ChemINDEX ......................................253
How Is It Useful? ...................................253
About ChemIndex ..................................253
Using ChemINDEX Ultra ......................253
Chem & Bio Office Enterprise ...............254
Chapter 28
Ashgate Drugs ....................................255
Chapter 34
Martindale for Scientists ...................271
Database Contents ................................. 271
Accessibility .......................................... 271
Chapter 35
Encyclopedia of Reagents for Organic
Synthesis .............................................273
Reagents and Catalysts .......................... 273
Searchable Reactions ............................. 273
Database Contents ................................. 273
Ready Accessibility ............................... 273
iv
Contents

Sourcing & Safety Data
Chapter 36
Sourcing & Safety Databases ............275
Chapter 37
ChemACX ...........................................277
ChemACX Database ..............................277
How Is It Useful? ...................................277
Using ChemACX with ChemOffice
Enterprise ...............................................278
Chapter 38
ChemMSDX .......................................287
How is it Useful? ....................................287
Using ChemMSDX ................................287
Chapter 39
Sigma-Aldrich MSDS Collection ......289
Chapter 40
EH&S Enterprise ...............................291
How Is It Useful? ...................................291
Key Benefits ...........................................291
Reaction & Synthesis Data
Chapter 41
Reaction & Synthesis Databases ...... 293
Chapter 42
ChemReact ......................................... 295
About ChemReact ................................. 295
Searching ............................................... 296
Chapter 43
ChemRXN .......................................... 299
How Is It Useful? ................................... 299
ChemPrep .............................................. 299
ChemSelect ............................................ 300
Chapter 44
ChemSynth ......................................... 303
About ChemSynth ................................. 303
Using ChemSynth .................................. 303
Index .................................. 307
Chem & Bio Office 2010 User Guide
v

Administrator
vi
Contents

E-Notebook
Desktop & Workgroup

1
Getting Started
E-Notebook helps you manage numerous types
of data on electronic pages that are much like
the pages of a traditional, paper notebook. This
information is organized into collections —
sets of related items that appear in a tree structure
in the left frame when you are browsing E-
Notebook.
Examples of some common types of E-Notebook
collections are:
• Notebook and Page
• Therapeutic Area
• Project
• Experiment
• Reaction Scheme
• Synthesis
For example, you could create a collection that
contains all of the reaction steps for a specific
synthesis. Typically, primary research data is
stored in Reaction/Pages, which are organized
within Notebooks, just like the paper pages in
paper notebooks. In this case, the synthesis
could be a notebook, and each of the steps
could be a page. Each of the pages may come
from a different notebook and may have been
created by a different chemist, but the notebook
for this, particular synthesis could collect
all of these pages in a single place.
You can organize collections in other ways,
too. For example, you may want to create a
collection of all of the synthesis that lead to a
certain product, or all of the E-Notebook users
who are working on a specific project. E-Notebook
enables you to set up these relationships
easily.
Collections are extremely flexible, because
they are designed to allow you to organize
your information in the way that is best suited
to your workflow. E-Notebook allows you to
browse through collections and to search them
for important information. Also, you can create
references to them, duplicate them, and, to prevent
further changes, you can transition them
to a closed, read-only state.
Just as you would use pages in a paper notebook
for recording various types of data, you
can use sections in E-Notebook for recording
reactions, spectra, or any other kind of information.
For example, within pages/reactions
there may be sections for reactions, notes,
reactants, etc. — whatever you need to record
and display your information the way you
would with a paper notebook. You also have
the option to use templates, so that sections are
Chem & Bio Office 2010 User Guide 3
E-Notebook

set up automatically and uniformly with each
new page/reaction you create. Your system
configuration determines the type of collections
and sections that you can create within E-
Notebook and the rules that define their contents.
The permission to view, edit, and create
collections can be set up on a per-collection
basis.
Navigation Overview
E-Notebook is consists of two major modules:
• Browse
• Search
These modules can be accessed using the
Browse and Search buttons on the main Toolbar.
The Browse area displays the collections organized
in a tree structure. To expand a collection
and view its contents, either double-click it or
click the plus sign next to it. Clicking an individual
collection allows you to view and/or
edit it in the right frame. There are a number of
options for specifying your view of the Collec-
4 Getting Started
Chapter 1

tion Tree. See “Browsing the Collection Tree”
on page 14 for more information.
From within the Search area, you can construct
a query to search for information. For example,
you may want to search for all of the sections
that contain a certain structure, or all of the collections
created by a particular user. When you
run a query, you can see both the results list
and the query itself. Clicking any item in the
results list allows you to browse to that item.
Certain menus in E-Notebook are accessed
when a particular item or icon is right-clicked.
For example, right-clicking a collection in the
Collection Tree will display the collection
menu.
To expand the size of a field in a section:
• Double-click the title bar of the field.
The field expands to take up the entire section
area, increasing your working space.
• To shrink the field:
Double-click the title bar again.
Security Overview
Each user of E-Notebook has a unique username
and password. Thus, only valid users
may log into E-Notebook.
Once a user has logged in, security in E-Notebook
is set up on a collection basis. Security
properties may be set up for any collection in
the Collection Tree — whether it be a User, a
Notebook, a Folder, etc. The security properties
of a collection determine who has Read,
Write, or Full Control access to that collection.
These access privileges may be assigned to
individual E-Notebook users or to user groups.
• Read – permission to view the collection,
but not edit it.
• Read and Write – permission to view the
collection and edit it, if it is in a state that
permits edits.
• Full Control – Read and Write permission,
and also the ability to assign and remove
security permissions for the collection.
By default, each collection inherits the security
properties of its parent in the Collection Tree.
The inherited security option may be disabled,
however, so that the security properties of a
collection can be configured independently of
its parent.
In addition to security at the collection level,
security may also be configured for collection
transitions, specifying which users may or may
not perform certain transitions on collections.
If you have Full Control permission to a collection,
you may determine who has access to
the collection. See “Changing Collection Security
Properties” on page 24.
Logging into E-Notebook
To start E-Notebook, you must first log in.
Then, you can begin to browse or search
through E-Notebook. Follow the instructions
below to log into E-Notebook Desktop.
Instructions for E-Notebook Workgroup are
similar:
1. Go to Start>All Programs>ChemBioOffice
2010>E-Notebook>E-Notebook 12.0.
2. At the log in dialog box, enter your name
and password and click Connect.
Chem & Bio Office 2010 User Guide 5
E-Notebook

6 Getting Started
Chapter 1

2
E-Notebook Desktop & Workgroup
E-Notebook is an electronic notebook specifically
designed to help scientists maintain their
laboratory records. E-Notebook makes it possible
for you to manage diverse types of data on
electronic pages that are much like the pages of
a paper notebook. The electronic pages make it
easy to organize information and streamline
your workflow. With E-Notebook, you can set
up notebooks and pages to manage information
about organic syntheses and related information
such as stoichiometry calculations, reaction
preps, spectra, analytical methods, notes,
and spreadsheets.
About E-Notebook
E-Notebook has many advantages over traditional,
paper notebooks. Since E-Notebook has
electronic rather than paper pages, you can
conduct searches by substructure, key word,
date, and so on. You can set up templates to
avoid reentering information that you often
use. E-Notebook fully automates stoichiometric
calculations. E-Notebook also provides a
full audit trail and change tracking features for
compliance with 21 CFR Part 11.
With E-Notebook, you can create a customized
electronic notebook that matches your workflow.
You can develop new fields to manage
specialized types of data, and configure your
own forms to manage the information that is
important to you. You can also add your own
data analysis tools and customized searches to
E-Notebook.
You can use E-Notebook to organize a wide
variety of other information critical to your
work processes as well. For example, common
reactants used in reaction preparations can be
stored in the E-Notebook database and shared
among researchers.
E-Notebook supports the SQL database format.
What’s New
E-Notebook 12.0 Desktop for Chem & Bio
Office Desktop 2010 introduces a variety of
powerful new features to help you become
more productive and better manage your laboratory
data.
Microsoft ® Office 2007 Support. Chem & Bio
Office 2010 supports Microsoft Excel ® , Word,
and PowerPoint ® . Use E-Notebook and
Microsoft Office 2007 together to manage all
your laboratory data. You can now write
reports, develop spreadsheets, and create presentations
without ever leaving Chem & Bio
Office 2010.
Batch Explorer. With the Batch Explorer, you
can view a reaction tree showing successors
and predecessors of a selected batch or com-
Chem & Bio Office 2010 User Guide 7
E-Notebook

pound.For more information “Batch Explorer”
on page 42.
E-Signature. With E-Signatures, you can electronically
sign a PDF version of your completed
page/reaction page.For more
information “E-Signatures” on page 11.
Work offline. With Offline mode, you can continue
doing work when server or network is not
connected and get the data synchronized when
you work in the online mode. For more information
“Working Offline” on page 73.
Name=Struct. The Name=Struct feature in
ChemDraw 12.0 is now available in E-Notebook
Desktop 12.0. For more information, see
“Name=Struct” on page 31.
NOTE: Name=Struct is available only in the
desktop version of E-Notebook.
Full Text Search. This feature comes with
SQL Server 2005 and is used in E-Notebook
for searching. Earlier, the search was possible
for names of the collections or sections. With
Full Text Search, you can search the contents
of the collections, documents and styled text
fields for a particular word.
Appendix Rendering. Add custom a header
and footer information to your printed
pages.You must have administrator privileges
to use appendix rendering. See “Appendix
Rendering” on page 27.
NOTE: Appendix rendering is available only
in the desktop version of E-Notebook.
About this Guide
Inside this guide, you will find a full description
of E-Notebook Desktop and Workgroup,
their features, and complete instructions on
how to use them. This guide is available in
print, online, and CHM formats.
8 E-Notebook Desktop & Workgroup
Chapter 2

3
Working with E-Notebook
A collection in E-Notebook is a set of similar
or related items that you use in your work. A
collection can be a set of notebooks, reactions,
pages, folders, searches, reactants, etc. The
default collection, called your “user collection”,
is where all your other collections are
listed.
The User Collection
Each E-Notebook user has a user collection
associated with them. Your user collection is
your home collection, and appears at the top of
the Collection Tree when you first log into E-
Notebook.
When you select your user collection in the
Collection Tree, your home page appears in the
right frame. The home page displays information
about you as a user, in addition to summary
information about your open pages/
reactions.
You can add different types of collections
directly to your user collection:
• Notebooks
• Folders
• User Configurations and AutoText Definitions
• Searches - Collection Searches, Section
Searches, Text Searches, Unannotated Version
Searches, Chemical Structure
Searches.
• Pages and Reaction Pages
• References to Notebooks
• References to Folders
• References to Page or Reaction Pages Templates
Adding a New Collection
To add a new collection:
1. In the Collection Tree, right-click your user
collection. A menu appears.
2. Select New, and then a type of collection.
The new collection appears and you are
prompted to rename it.
Adding a Reference
1. In the Collection Tree, click the Notebook,
Folder, or Template to which you wish to
create the reference.
2. While holding the CONTROL and SHIFT
keys, drag the collection until the user collection
(or destination collection) is highlighted.
3. Release the mouse. The Reference appears
in the Collection Tree.
Alternatively, you may right-click the collection
you wish to reference, and select Copy
from the collection menu. Then, right-click the
Chem & Bio Office 2010 User Guide 9
E-Notebook

user collection (or destination collection) and
select Paste Reference.
Browsing up to the User Group
If you have the required security permissions,
you may browse up to the next highest level in
the Collection Tree and view the user group at
that level. To do this, right click your user collection,
and select Go Up To, and then the name
of your user group.
Alternatively, you may select View from the
menu bar, and then Go Up To.
Notebooks
Notebooks contain Page or Reaction Page collections.
Each Notebook has a table of contents
associated with it, which displays summary
information for each collection in the Notebook.
Creating a Notebook
To create a new, Notebook collection:
1. In the Collection Tree, right-click your user
collection. A menu appears.
2. Select New > Notebook.
A new Notebook collection appears and
you are prompted to rename it. The Table
of Contents section of the Notebook
appears in the right frame.
To create a new Page/Reaction Page in the
Notebook, click the New Page and then select
the page/reaction page.
Each Notebook has a Table of Contents associated
with it. The Table of Contents summarizes
all of the Pages/Reaction Pages that the notebook
contains. Clicking on any of the contained
Pages/Reaction Pages listed will allow
you to navigate to that Page/Reaction Pages.
You may also print the Table of Contents to
create a hardcopy of it; See “Printing Collections
or Sections” on page 26.
When you rename a Notebook, the names of
the Pages or Reaction Pages within it change to
match the name of the Notebook.
Pages and Reaction Pages
Pages/Reaction Pages in E-Notebook may contain
several different types of sections for
experimental data.
Creating a Page or Reaction
Page
To create a new Page or Reaction Page collection:
1. In the Collection Tree, right-click the Notebook
collection to which you would like to
add the Page or Reaction Page.
A menu appears.
2. Select New > Page (or Reaction Page).
A new Page or Reaction Page collection
appears in the Notebook. It is numbered
automatically.
You may associate several types of sections
with the Page/Reaction Page:
• Reaction Section
• MS Word Document Section
• Ancillary Data Section
• Spectrum and Spectra Sections
• Table Section
• MS Excel Spreadsheet Section
• Image Section
• MS PowerPoint Slideshow
10 Working with E-Notebook
Chapter 3

• Title Page
NOTE: On selecting a new page, a blank page
is displayed as compared to the reaction page,
reaction section is displayed.
To create a new Page or Reaction Page collection
from a template:
1. In the Collection Tree, select User Configuration>Templates.
2. Drag the template into the Notebook.
A new Page or Reaction Page is created,
based on the template.
Alternatively, you may right-click the template
and select Copy. Then, right-click the Notebook
and select Paste. (See “Templates” on
page 23 for information about creating the initial
template).
E-Signatures
With E-Signatures, you can electronically sign
a PDF version of your completed page/reaction
page. This page/reaction page rendition is then
routed to co-authors (where applicable) and
witnesses. Once all required parties have
signed the page/reaction page rendition, it is
stored in a separate database for protection of
your intellectual property.E-Signature works
on the pages/reaction pages created.
Pages/Reaction Pages have several states
which define their lifecycles. You may perform
transitions on a page or reaction page to
move it from one state to another.
• Sign and Close
• Sign and Keep Open
• View Signed Versions
Sign and Close: The Closed state may be readonly.
It may be possible to edit the collection
while it is in this state. To perform this action:
1. Right click on any page/reaction page and
select sign and close.
A confirmation dialog appears. Click Yes.
A witness selection dialog box appears
where you have to select the user and then
click Add.
Page/reaction page is rendered and displayed
in PDF. Enter the password and click Sign and
Store. The Home Page displays the submitted
document.
Once the page/reaction page is signed and
closed, an icon is displayed (Lock Sign) in the
collection tree and History shows the status as
Sign and Close
Sign and Keep Open: The Open state may have
an optional annotation, it is write only, so that
you may provide a reason for a change you
wish. To perform this action:
1. Right click on any page/reaction page and
select sign and keep open.
2. A witness selection dialog box appears
where you have to select the user and then
click Add.
Page/reaction page is rendered and displayed
in PDF. Enter the password and click Sign and
Store. The Home Page displays the submitted
document. The History shows the status as
Sign and Keep Open.
You can see two panes on the Home Page:
• Waiting Document
• Document submitted by the user (person to
whom we have assigned the document).
View Signed Versions: The signed versions
rewardable, required annotation of changes,
changes visible on the screen and in the printed
Chem & Bio Office 2010 User Guide 11
E-Notebook

copy.To view the signed versions, right click
on the submitted document and select review.
Folders
You can use folders to organize and manage
other types of collections:
• Other Folders
• Searches – Collection Searches, Section
Searches, Text Searches, Chemical Structure
Searches, Unannotated Version
Searches
• References to any type of collection
Creating a Folder
To create a new, Folder collection:
3. Release the mouse.
The Reference appears in the Collection
Tree.
Alternatively, you may right-click the collection
you wish to reference, and select Copy
from the collection menu. Then, right-click the
folder collection and select Paste Reference.
The User Configuration Folder
Within your user collection, there is a User
Configuration Folder, which can contain Reactants,
AutoText, and Templates.
To expand your User Configuration folder and
view its contents, either double-click it in the
collection tree or click the plus sign next to it.
1. In the Collection Tree, right-click your user
collection.
A menu appears.
2. Click New>Folder.
A new Folder collection appears and you
are prompted to rename it.
Or, you may right-click an existing Folder collection
and select New, then Folder, to create a
Folder within a Folder.
Adding a Reference to the
Folder
You may add references to a folder if, for
example, you would like to keep the information
from several Pages/Reaction together, but
the Pages/Reaction exist in separate notebooks.
1. In the Collection Tree, click the Collection
to which you wish to create the reference.
2. While holding the CONTROL and SHIFT
keys, drag the collection until the folder
collection is highlighted.
• Reactants Folder – contains reactants whose
structures and properties you can add to
Reaction Sections. See Reactants Collections
for information.
• AutoText Definitions – contains predefined
text fragments that you can reuse to simplify
text entry in, for example procedure
text. See “Creating New Autotext Definitions”
on page 38 for information about
configuring AutoText.
12 Working with E-Notebook
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• Templates folder – contains templates of
various types that you can use to avoid
unnecessary reentry of data. See “Templates”
on page 23 for more information.
Reactants Collections
Reactants are named shortcuts for a commonly
used compounds. These could be either common
reagents, or named compounds that you
use frequently, and are kept in the Reactants
Folder in the Collection Tree.
You may populate reaction sections with the
properties of reactants.See “Working with
Reactions” on page 29 for more information.
Adding Reactant Section to
Collection
To add a new reactant section to an existing
collection:
1. Browse to the Reactants collection to which
you wish to add the Reactant, clicking the
collection in the collection tree to select it.
The Reactants collection appears, with the
existing reactants displayed in the right
frame.
In the right frame, click the New Acronym.
A New Acronym dialog appears. Enter the
name of the acronym and click Create.
A new reactant section appears with name
entered for the new acronym.
2. To rename the section, right-click the section
menu icon and select Rename Section
from the menu that appears. Then type in a
name.
3. Draw or import the structure using the
Chem & Bio Draw tools.
The formula and molecular weight properties
are updated automatically. The compound
name may be updated as well. The compound
name will be displayed in the table of contents
for the Reactants Folder that contains this reactant.
Click the Reactants Folder in the Collection
Tree to view its table of contents.
Adding a new Reactant
Collection
You can add a new Reactant Collection to your
User Configuration folder in E-Notebook. To
add a new Reactant Collection:
1. Right-click the Reactants Folder and select
New>Reactants.
A Reactants collection appears, and you are
prompted to rename it.
2. Enter a name for the Reactants collection.
3. Click the New Acronym tool in the right
frame.
A New Acronym dialog appears. Enter the
name of the acronym and click Create.
A new Reactant section appears.
You may populate reaction sections with the
properties of reactants.See “Working with
Reactions” on page 29 for more information.
Working with a Table of
Contents
E-Notebook collections often have Table of
Contents sections associated with them. The
Table of Contents lists all of the collections
that fall directly within the selected collection
in the Collection Tree. For example, if a Notebook
contains Reaction Page, all of the Reaction
Pages in the Notebook will be listed. Or, if
a Folder contains templates, all of the templates
in the Folder will be listed.
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Double-clicking the link by any of the contained
collections listed will allow you to navigate
to that collection. You may also print the
Table of Contents to create a hardcopy of it;
See “Printing Collections or Sections” on
page 26 for more information.
You can customize a Table of Contents to display
only columns of interest or sort columns
in ascending or a descending order.
Hiding Columns
To hide columns in the Table of Contents:
1. Right-click the column to hide.
A menu appears.
2. Select Show Columns.
The Show Columns dialog appears, listing
the columns you may select for display in
the Table of Contents. The columns that are
currently displayed are denoted with
checkmarks.
3. Select and deselect columns to customize
the Table of Contents display.
The columns you selected appear with
checkmarks next to them.
4. Click OK to close the dialog.
The dialog closes, and the screen refreshes
to display the additional columns.
Sorting Items in the TOC
You may sort items in the TOC in either an
ascending or descending order. To sort items in
an ascending order:
1. Right-click the column by which you wish
to sort the Table of Contents.
A menu appears.
2. Select Sort Ascending.
2. Select Hide followed by the name of the
column.
The screen refreshes, and the column is
hidden.
Showing Columns
To show additional columns that are hidden, or
are not currently displayed in the Table of
Contents:
1. Right-click A column in the Table of Contents.
A menu appears.
The items are sorted in ascending order
according to the column you selected.
To sort items in an descending order:
1. Right-click the column by which you wish
to sort the Table of Contents.
A menu appears.
2. Select Sort Descending.
The items are sorted in descending order by
the column you selected.
Browsing the Collection
Tree
Collections and their contents are organized in
the Collection Tree on the left side of the
14 Working with E-Notebook
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screen. E-Notebook offers several options for
browsing and viewing collections.
To begin browsing collections:
1. Click browse at the top of the screen.
The Collection Tree appears.
2. Select a collection from either the collection
tree or the dropdown list (between the
green arrows).
3. Click the green arrows to navigate the Collection
Tree view.
NOTE: Only one user can edit an collection at
a time. A message will inform you when a collection
is locked for editing by another user.
Showing and Hiding
Collections
The Collection Tree provides you with a
means of expanding and contracting collections
so that you only see the information you
need.
To show the contents of a collection:
• Click the plus sign next to the collection
whose contents you wish to see.
The collection is expanded, and you can
view its contents.
• Click the minus sign next to the collection.
The collection is minimized, so that you
cannot see its contents.
Hiding the Collection Tree
It is possible to hide the Collection Tree if you
would to increase the screen area you have for
entering data into a section.
To hide the Collection Tree:
1. Move your cursor to the right boundary of
the tree, so that the cursor becomes a double-headed
arrow.
2. Double-click.
The Collection Tree is hidden.
To view the Collection Tree again:
1. Move your cursor to the left boundary of
the section, until the double-headed arrow
appears again.
2. Double-click.(Or, you may click the touchbar
at the left boundary of the E-Notebook
window).
The Collection Tree reappears.
Limiting Collection Browsing
You can limit your browsing by selecting a
root collection for the collection tree. The root
collection becomes the highest browsing level
in the collection tree. Limiting the collection
tree view can make it easier to find specific
information.
To set a root for the collection tree:
1. Click the browse at the top of the screen.
The collection tree appears.
2. Right-click the collection you wish to be
the root collection for browsing.
A menu appears.
3. Select Browse Here.
The collection you selected appears at the
top of the collection tree.
Browsing from Home
You can browse from your home collection,
which contains all of the collections associated
with you as a user of E-Notebook. This is the
collection that appears when you first log in.
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E-Notebook

To browse to your home collection and bring
the home collection to the top of the collection
tree:
1. Click the browse.
The collection tree appears.
2. Do one of the following:
• Right-click a blank area of the collection
tree and click Go Home in the context
menu.
• Go to View>Go To>Home.
The home collection appears at the top of collection
tree.
Browsing at a Higher Level
You can browse at a higher level in the Collection
Tree, and see all the collections at that
level.
To browse at a higher level:
1. If the collection tree is not visible, click
Browse at the top of the screen. The Collection
Tree appears.
2. Do one of the following:
• Right-click a collection in the collection
tree and click Go Up To.
• Go to View>Go Up To.
The collections that either contain or reference
the item are listed.
3. Select the collection to bring to the top of
the Collection Tree.
The collection you selected appears at the
top of the tree. Its contained collections and
contained references are displayed.
Browsing the Entire Collection
Tree
Browsing the entire Collection Tree lets you
see all the E-Notebook collections at once.
To browse the entire tree:
1. If the collection tree is not visible, click
Browse at the top of the screen. The Collection
Tree appears.
2. Do one of the following:
• Right-click any blank area of the Collection
tree, and select Browse All from the context
menu that appears.
• Right-click any collection in the tree, and
select Browse All from the menu that
appears.
• In main menu, go to View>Go To>Browse
All.
NOTE: The Browse All command is available
only if you have the Read privilege for the collection
at the top of the collection hierarchy. If
not, you may need to conduct a collection
search to view some of the collections to which
you have access.
Behaviors of Collections
There are diverse behaviors associated with
Collections-such as the creating, hiding,
renaming, duplicating, and moving behaviors.
Your system configuration determines the
rules to define the traits reflected by a collection.
Therefore, depending on your system
configuration, there may be some additional
behaviors that these collections can show.
Auto-Numbered Collections
E-Notebook may be configured to automatically
number the collections contained within a
specific collection. Your system configuration
determines the parameters for auto-numbering
the collections.
16 Working with E-Notebook
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If E-Notebook is configured to auto-number
the collections then the newly created collections
will be automatically named by appending
a serial number to the name of the
collection that contains the newly created collection.
Collections that Cannot be Deleted
In E-Notebook, you may be prevented from
deleting the specific collections. Actually, your
system administrator may configure some specific
collections so as to prevent you from
deleting them once they have been created.
Therefore, the Delete command in the collection
menu of such collections will be grayed
out.
For example, if the Notebook collection has
been configured to avoid deleting then clicking
on it will show the menu with inactive Delete
option.
Your system configuration determines which
types of collections cannot be deleted. Also,
you cannot delete a collection if references to it
exist. E-Notebook, by default, is configured so
that you cannot delete specific collections such
as, User Collection, User Configuration
Folder, Notebook Collections and Offline
Folder.
Deleting Modified Collections
In some cases, you may delete collections only
if they have not been modified since they were
created. Once the collection is modified, the
Delete option in the collection menu is inactive
when collections of that type are selected.
Your system configuration determines which
types of collections cannot be deleted after
modification.
Renaming Collections
In E-Notebook, you may be prevented from
renaming specific collections, for example, a
collection whose name is generated by the
auto-numbering feature. If you attempt to
rename an auto-numbered collection, an error
message appears.
Your system configuration determines which
types of collections cannot be renamed.
Copying Collections that Contain
References
It is possible to copy collections that contain
references in the collection tree in the same
way as you would copy normal collections
without references. The copied collection contains
references to all of the collections that are
contained within the collection at the time the
copy is made.
In some cases, your system configuration may
prevent you from copying collections that contain
references to specific types of collections
that are in specific states. This pertains only to
references that exist in property lists and
tables. It does not pertain to references in the
collection tree. For example, an experiment/
page collection type may be configured to prevent
you from copying pages/reaction that contain
references to folders that are in a Closed
state.
Your system configuration determines which
types of collections you can copy, and into
which types of container collections you can
copy them.
For more information about copying collections,
See “Copying a Collection” on page 21
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18 Working with E-Notebook
Chapter 3

4
Managing Collections
All information in E-Notebook is organized
into collections. Collections may be notebooks,
folders, reaction/pages, templates, and
other content. Collections are listed in the collection
tree at the left of the screen. E-Notebook
lets you browse through collections and
to search them.
It is possible to manage collections in a number
of ways, as discussed in the following topics:
• Organizing Collections
• Templates
• Viewing Collection Properties
• Changing Collection Security Properties
• Performing a Collection Transition
• Importing and Exporting Collections
• Exporting to Word
• Printing Collections or Sections
Your system configuration determines the
types of collections that you can create within
E-Notebook and the rules that define their contents.
The permission to view, edit, and create
collections can be set up on a per-collection
basis. These rules are configurable in E-Notebook.
Organizing Collections
You can organize collections in the Collection
Tree to make their order meaningful to you and
other E-Notebook users. Collections can be
moved up and down within a container collection.
In some cases, collections can be moved
from one container collection to another. Your
system configuration determines which items
can be moved into which types of collections.
Moving a Collection
Within a Container Collection
You can organize collections within a container
collection by moving them up and down.
To move a collection within its container:
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E-Notebook

1. Click Browse at the top of the screen. The
Collection Tree appears.
Between Container Collections
You can move collections from one container
collection to another.
NOTE: Your system configuration defines the
rules that determine which collections can be
moved into which types of container collections.
Figure 4.1 A sample collection tree for a workgroup
that includes two users.
2. To expand a collection and view its contents,
either double-click the collection or
click the plus sign next to it.
3. Right-click the collection you want to
move.
In the context menu, select the appropriate
option:
• Move Up: moves the collection up one position
in the Collection Tree.
• Move Down: moves the collection down one
position in the Collection Tree.
TIP: You can also move collections using your
keyboard. Hold down the CTRL key and use the
up and down arrows.
To move a collection between container collections:
1. If the collection tree is not visible, click
Browse at the top of the screen. The Collection
Tree appears.
2. In the Collection Tree, click and drag the
collection you want to move to the new
container.
If your system configuration permits the move,
the collection appears in the new location.
Depending upon the rules that define your system
configuration, a copy or a reference may
appear instead. Also, it may not be possible to
move the collection into a particular type of
container. If the new container will not accept
the collection you are attempting to move, you
will be unable to highlight the container when
you attempt to drag the collection into it.
Creating a Reference
Within the collection tree, you can create a reference
to a collection that exists elsewhere in
the tree. The reference acts as a shortcut to the
original collection, and it reflects any changes
that are made to the original. Also, if you have
editing privileges to the original, any changes
made to the reference are reflected in the original.
To create a reference in the collection tree:
20 Managing Collections
Chapter 4

1. Click Browse.
The Collection Tree appears.
2. Click the collection that you wish to reference.
The collection is highlighted.
3. Holding down the CONTROL and SHIFT
keys, drag the item into the Collection
where you would like it to be referenced.
A Reference to the item appears in the Collection
Tree, within the collection you
selected. The icon contains a small arrow,
which indicates that it is a reference.
An alternate method for creating a reference in
the collection tree is the following:
1. Right-click the collection that you wish to
reference.
The collection menu appears.
2. Select Copy.
3. Right-click the collection into which you
wish to add the reference.
The collection menu appears.
4. Select Paste Reference.
The reference appears in the Collection
Tree, within the container collection you
selected.
NOTE: Your system configuration determines
which collections can be referenced within
which container collections.
It is also possible to create references to collections
from property lists and tables.
Duplicating a Collection
You can duplicate a collection within its container
collection in the Collection Tree. The
duplicate you create contains references to all
of the collections that are contained within the
collection at the time the copy is made.
To duplicate an item within the same container
collection:
1. Click Browse.
The Collection Tree appears.
2. Right-click the collection that you wish to
duplicate.
The collection menu appears.
3. Select Duplicate.
A copy of the collection appears within the
same container collection.
NOTE: Your system configuration determines
which collections can be duplicated, and where
the duplicates can reside in the Collection Tree.
Copying a Collection
You can copy a collection in the Collection
Tree.
To do this:
1. Click the browse.
The Collection Tree appears.
2. Right-click the collection you wish to copy
and select Copy from the menu that
appears.
3. Right-click the collection that is to be the
container collection for the copy.
4. Select Paste from the menu that appears.
A copy of the collection appears in the Collection
Tree, within the container you
selected.
Alternatively, you may click the collection you
are copying to select it. Then, while holding
Chem & Bio Office 2010 User Guide 21
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down the CONTROL key, drag it into a container
collection to create a copy.
NOTE: Your system configuration determines
which type of collections you can copy, and into
which type of container collections you can
copy them.
Renaming a Collection
You can rename a collection to avoid a duplicate
name, or simply to make the name more
meaningful to you and other E-Notebook
users.
To rename a collection:
1. Click the browse.
The Collection Tree appears.
2. Right-click the collection you wish to
rename in the Collection Tree.
The collection menu appears.
3. Select Rename.
You are prompted to enter another name.
4. Enter a name.
The collection is renamed.
Your system configuration determines naming
conventions for various types of collections. If
you enter a name that does not adhere to the
naming conventions, an error message appears
and you are prompted to enter another name. In
some cases, a name may be assigned to a collection
automatically, and it may not be possible
to rename the collection at all.
Deleting a Collection
You can delete a collection from the Collection
Tree so that you manage only the information
that is relevant to your current needs. Your system
configuration determines which types of
collections can be deleted.
To delete a collection from the Collection
Tree:
1. Click Browse.
The Collection Tree appears.
2. Right-click the collection you wish to
delete.
The collection menu appears.
3. Select Delete.
If your system configuration permits it, the
collection is deleted.
You may also delete a collection by clicking it
in the tree to select it, and then pressing the
DELETE key.
Note that you cannot delete a collection if references
to it exist. Also, in some cases, it may
only be possible to delete collections if they
have not been modified since they were created.
Viewing Collection
Properties
You can see specific information about a collection
by viewing the Collection Properties.
To view properties of a Collection:
1. If the collection tree is not visible, click
Browse at the top of the screen. The Collection
Tree appears.
2. Right-click the item whose properties you
wish to view.
A menu appears.
3. Select Collection Properties. The properties
dialog box appears.
The General tab lists the following:
Name - the name of the collection.
22 Managing Collections
Chapter 4

Owner - the user who created the collection.
Type - the type of the Collection or Page.
Contents - the number of collections contained
in the collection.
Created - the date on which the collection was
created.
Last Modified - the date on which the Collection
or Page was last changed.
Status - the status of the collection in its life
cycle. If no states are defined for the collection,
the status is Created.
Autosave Interval the time interval after which
the collection is saved automatically.
NOTE: To view the Collection Security or
Transition Security properties, click the appropriate
tab. If the collection is a user collection,
the Region tab also appears.
Importing and Exporting
Collections
E-Notebook provides the ability to export and
import collections as XML files. Each XML
file contains all of the data and formatting
associated with the collection.
Importing a Collection
To import a collection:
1. Click Browse.
The Collection Tree appears.
2. In the Collection Tree, right-click the collection
into which you would like the collection
to be imported. For example, if you
would like to import page/reaction page
into a Notebook, you would right-click the
Notebook.
The collection menu appears.
3. Select Import.
A dialog appears and you are prompted to
select the XML file you wish to import.
4. Select the file and click Open.
The collection is imported into E-
Notebook.
Exporting a Collection
To export a collection:
1. Click Browse.
The Collection Tree appears.
2. In the Collection Tree, right-click the collection
that you wish to export as an XML
file.
The collection menu appears.
3. Select Export.
A dialog appears, and you are prompted to
select a location for the exported file.
4. Select the location for the file and click the
save.
The collection is exported to the XML file.
NOTE: When a collection is exported, the
export file does not include any of the contained
collections. Each collection must be exported
separately. For example, if you export a Notebook
that contains Pages/Reactions, only the
Notebook is exported; each page/reaction must
be exported as a separate XML file.
Templates
E-Notebook gives you the ability to use templates
so that you can avoid re-entry of the
information. For example, you may create a
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template for a particular type of page/reaction
page. It may contain data and notes that you
often use, or typical values for various properties.
To create a new template:
1. In the Collection Tree, right-click the container
collection to which you wish to add
the template.
The collection menu appears.
2. Select New> Page Template
The template is created within the container
collection, and its sections appear in the
right frame.
3. Edit the template to your wish.
To use the template, click and drag it into
another collection to create a new Page, Reactant,
etc., and avoid creating a collection from
scratch each time. E-Notebook is often configured
so that you can drag a template of an
Experiment or Page into a Notebook, thereby
creating a new Experiment or Page based on
the template.
You may also right-click the template in the
Collection Tree and select Copy from the menu
that appears. Then, right-click the container
collection (for example, the Notebook) and
select Paste from the menu.
Your system configuration determines which
types of templates you can create as a user of
E-Notebook, and which types of collections
can contain them.
Form Tools
A form tool is used to perform a particular
function in an E-Notebook form/field. There
are several standard form tools in E-Notebook
that may be associated with the section or collection
types, for example, the New Section
Form Tool associated with Notebook collection
type or Import/Export Form Tool, which is
present in new section types you create.
NOTE: Your system configuration determines
the collections to which this form tool can be
added.
Changing Collection
Security Properties
You can change the access that other E-Notebook
users have to a specific collections. In
order to change the security properties of a collection,
you must have Full Control privileges
to the collection. Your system configuration
determines who has Full Control privileges for
each collection in E-Notebook.
The default security for any new collection is
Inherits Security, meaning that a collection has
the same security profile as its parent collection
in the Collection Tree.
To disable inherited security:
1. Right-click the collection for which you
wish to disable inherited security.
A menu appears.
2. If Inherits Security is checked, select it to
clear the checkmark.
Inherits Security is disabled.
Collection Security
To change the Security Properties of a collection:
1. Right-click the collection whose Security
Properties you want to change.
2. In the context menu, select Collection Properties.
The Collection Properties dialog box
appears.
24 Managing Collections
Chapter 4

3. Click the Collection Security tab.
The Groups and Users who have permission to
access this item appear in one of the two lists:
• Inherited Permissions
• Assigned Permissions
Inherited Permissions are permissions inherited
from the parent collection in the collection
tree. These permissions can not be changed
from this dialog. Only the Assigned Permissions
can be changed from this dialog.
Transition Security
Transition Security is the security applied to
the collection transitions. For example, some
users may be allowed to close a collection
while others can also reopen the collection.
To change the Transition Security Properties
of a collection:
1. Right-click the collection whose Security
Properties you wish to change.
A menu appears.
2. Select Collection Properties.
The Collection Properties dialog box
appears.
3. Click the Transition Security tab.
The Security tab appears. The Groups and
Users who have permission to apply a transition
to this item appear in one of the two lists:
• Inherited Permissions
• Assigned Permissions.
Inherited Permissions are permissions inherited
from the parent collection in the Collection
Tree. These permissions can not be
changed from this dialog. Only the Assigned
Permissions can be changed from this dialog.
Performing a Collection
Transition
Collections may be configured to have states
associated with them. These states define the
life cycle of the collections. For example, a
Notebook may have Open and Closed states;
the Open state may permit editing, and the
Closed state may be a read-only state that does
not allow edits. Transitions are the actions you
perform to move a collection from one state to
another, for example, from Open to Closed.
In order to perform a transition on a collection:
1. Click Browse.
The Collection Tree appears.
2. Right-click the collection in the Collection
Tree that is to undergo the transition.
The collection menu appears.
3. Select the name of the transition from the
menu, for example Sign and Close, Sign and
Keep Open, and View Signed Versions. See
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“E-Signatures” on page 11 for more information.
The transition occurs and the collection
enters the new state. You may always view
the state of the collection by right-clicking
it in the Collection Tree, and then selecting
Collection Properties.
Transitions may also perform certain functions,
such as printing a copy of the collection.
Your system configuration determines which
transitions may be performed, and by whom.
Exporting to Word
You can export collections and sections to
Microsoft Word. Afterward, they are just like
any Word documents.
To export to Word:
1. In the collection tree, right-click the item
containing the section(s) to export.
A menu appears.
2. Select Export to MS Word.
You are prompted to choose a destination
folder and file name.
3. Choose a folder and file name and click the
save.
You are prompted to choose an export
range.
4. Select an export range:
• All Sections – to export all of the Sections.
• Sections from X to Y – to export a range of
Sections, where X and Y are values you
specify.
• Current Section – to export only the current
Section.
5. Select the Open Document After Export if
you would like the file to be opened after
the export is complete.
6. Click export.
If you chose to open the document after export,
the MS Word document is opened, and it displays
the Sections you selected for export. If
you choose not to open the document, the document
is saved in the folder you specified.
Printing Collections or
Sections
You can print collections from E-Notebook to
maintain your hardcopy archives.
To print a collection:
26 Managing Collections
Chapter 4

1. From the Collection Tree, right-click the
collection.
The collection menu appears.
2. Select Print.
Your printer dialog box appears, and you
are prompted to enter the information you
normally do when printing, such as page
printer and number of copies, etc.
3. Select the printer options.
4. Select the Page Range:
• All – prints all of the sections in the collection.
• Selection – prints only the selected section.
• Pages – allows you to specify a range of
sections to print. For example 1-5 would
print the first five sections in the collection.
5. Make your selections and click OK.
The collection or the selected portion is
printed.
NOTE: Your system configuration contains
templates that determine exactly how the
printed page appears.
If Visual Display of Changes is enabled, the
print will include the following:
• The collection data as is exists in the current
version of the collection.
• The version history, including the date and
the author for each version after the baseline
version. (The baseline version is the
version that existed when visual display of
changes begin).
• A list of changes grouped by field.
In some configurations, there is a Final Print
transition that automatically creates a complete
printout of the collection.
Appendix Rendering
If you have administrator privileges, you can
apply headers and footers to printed collection
pages. The header and footer appears only on
the printed pages.
NOTE: Appendix rendering is available only
in E-Notebook Desktop.
Applying appendix rendering
You first need to import the header/footer
XML file into E-Notebook.
To import the file:
1. In the collection tree, right click a collection
type or user name and select Import in
the context menu.
2. In the Import dialog box, navigate to the
folder:
[drive]:\Program
Files\CambridgeSoft
\ChemOffice2010\Utilities\AppendixRenderer\
3. In the AppendixRenderer folder, select
to open the Import.xml file.
After you import the file, the default header
and footer is applied to all printed pages.
Customizing the header/footer
1. In the collection tree, right-click a collection
type and select Collection Type Configuration.
2. In the left pane of the Collection Type Configuration
dialog box, navigate to:
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[name of collection type]/Commands/Export
to PDF/Command
Listeners/.
3. In the left page, click Appendix Renderer
Config.
In the right pane, the name
AppendixRenderer9.ARConfig
appears in the Implementation dropdown
list.
4. Click Custom Properties.
5. In the Command Listener dialog box, edit
the Header and footer as desired.
NOTE: The three text boxes in the Header and
Footer tabs correspond to the left, center, and
right positions of the page.
6. When you are finished editing the header
and footer content, click OK.
28 Managing Collections
Chapter 4

5
Working with Reactions
This portion of the user guide provides instructions
for working with the various sections or
forms in E-Notebook data. Just as you would
use pages in a paper notebook for recording
various types of data, you can use sections in
E-Notebook for recording reactions, spectra,
and other types of information.
For general information about deleting, moving,
and copying sections, etc., see “Managing
Collections” on page 19.
You can also use templates to set up sections
automatically and uniformly. See “Templates”
on page 23. for more information.
Your system configuration determines the
types of sections that are available in E-Notebook.
• Table Sections
• MS Word Sections
• MS Excel Sections
Reaction Sections
A reaction section shows one step in a reaction.
It contains a stoichiometry grid that analyzes
the reaction drawing automatically. The Auto-
Text feature updates the preparation text when
you change the reaction drawing and/or information
in the stoichiometry grid.
Pre-configured Sections
E-Notebook comes preconfigured with a number
of useful Sections that you can add to your
pages. Your system administrator may have
modified these Sections, eliminated them, or
added new Sections that more closely match
your workflow.
The preconfigured Sections are:
• Reaction Sections
• Reactant Sections
• Spectrum and Spectra Sections
To create a Reaction Section:
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1. In the Collection Tree, click the collection
to which you would like to add the Reaction
Section.
2. Click the New Section menu icon on the
right side of the screen.
A menu appears, listing the sections you
may add.
3. Select Reaction.
A new blank Reaction Section appears in
the right frame.
Within a Reaction Section, you can record the
following:
• Chemical Structure – Draw and store chemical
structures and reactions using the Chem
& Bio Draw toolbar. You may import a
reaction drawing as well.
• Reaction Conditions – Record pressure,
temperature, and other conditions for the
reaction.
• Preparation for the Reaction — Enter the
procedure used to prepare for the reaction
in an AutoText field.
• Solvents - Records name, ratio and volume
for reaction.
Drawing and Analyzing
Reactions
You can draw a reaction using the Chem & Bio
Draw reaction field. When you draw a reaction,
the stoichiometry grid is automatically
populated with the properties of the reactants
and products. If you remove a reactant or product
from the stoichiometry grid, the corresponding
structure will be removed from the
reaction drawing.
The Chem & Bio Draw Toolbar allows you to
create a chemical structure by connecting frequently
used substructures together. For more
information about using the Chem & Bio Draw
Toolbar, please see the Chem & Bio Draw
User Guide.
Drawing a Structure or Reaction
To draw a reaction:
• Stoichiometry Table – The stoichiometry
table calculates and stores amount, formula
mass, molarity, density, volume, and many
other variables. This table is populated
automatically as you modify the reaction
drawing.
1. Click within a reaction field.
The Chem & Bio Draw toolbar appears.
2. Using the Chem & Bio Draw tools, draw a
reaction.
TIP: You can access a drawing menu by rightclicking
in the structure window. This menu
allows you to, among other things, copy and
paste structures.
Expanding the Drawing Window
To expand the drawing window:
30 Working with Reactions
Chapter 5

1. Double-click the title bar of the chemical
structure field.
The chemical structure field expands.
2. Using the Chem & Bio Draw tools, draw
the structure or reaction.
3. When you are finished editing, double-click
the frame of the chemical structure field to
return it to its original size in the form.
Analyzing a Reaction
After you draw a chemical reaction in the reaction
field of a reaction section, you can analyze
the reaction. When you analyze a reaction, the
Stoichiometry Grid of the reaction section is
automatically populated with information
about the reactants and products.
NOTE: You can automatically populate Stoichiometry
Grid only if information has not
already been added into it manually. For more
information about entering stoichiometric data
manually and adding reactant data automatically,
see “Adding Information” on page 35.
Based upon the chemical drawing in the reaction
field, new reactants and products are
added to the stoichiometry table. By default,
the names of the reactants and products are
determined from the molecular formulas in the
drawing.
When a value is calculated, the number of significant
digits is the minimum number of significant
digits for any cell in the table that has
been edited manually. If none of the table cells
have been edited, calculations are to four significant
digits.
The Reaction Toolbar
The reaction toolbar provides several features
for managing the reactants and products in
your reaction section.
The reaction toolbar normally appears just
below the reaction field.
See these topics for more information.
• Adding Structures with the Reaction Toolbar.
• Filtering Acronyms with the Reaction Toolbar.
• Defining a new Acronym with the Reaction
Toolbar.
• Deleting a Structure with the Reaction
Toolbar.
Name=Struct
The Name=Struct feature available in E-Notebook
Desktop 12.0 enables you to add the
names of compounds you draw in a reaction to
the stoichiometry grid automatically, using
ChemDraw’s Name=Struct feature.
NOTE: You need to have ChemDraw Ultra
installed on your computer to use this feature.
To convert a name to a structure:
1. Draw the structures in the reaction section.
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2. Save your changes. The structure names
appear in the stoichiometry grid.
If you make changes to the reaction drawing,
the names will be updated automatically.
4. At the top of the dialog box, click the Add
down arrow for a list of options for adding a
structure.
NOTE: If you manually change the name of
any structure in the grid, your change will NOT
be overwritten when you alter the corresponding
structure drawing.
Adding Structures with the Reaction
Toolbar
With the reaction toolbar, you can add reactants
and products from your Acronyms collections
in E-Notebook. There are two methods
for adding a structure with the reaction toolbar.
Adding a Structure
The Add on the reaction toolbar brings up a
dialog that allows you to select a structure and
add it to your reaction section.
To add a structure:
1. Click Add in the reaction toolbar.
The Select and Add Structure dialog
appears, displaying the acronyms in your
Reactants Folder.
2. In the Search In dropdown list, select the
structure list from which you want to
choose a structure.
3. In the right pane, select the name of a structure.
The structure itself appears in the left
pane.
The options are:
• Left of Arrow as Reactant – adds the structure
to the reaction drawing to the left of
the arrow, and adds it to the reactants table
in the grid.
• Above Arrow as Reagent – adds the structure
to the reaction drawing above the
arrow, and adds it to the reactants table in
the grid.
• Right of Arrow as Product – adds the
structure to the reaction drawing to the
right of the arrow, and adds it to the products
table in the grid.
• To Grid as Reagent – adds the structure to
the grid only, in the reactants table.
5. Select the desired option and click Add.
The structure is added to the reaction section in
the manner you selected.
There are several options for filtering the acronyms
displayed in the dialog. See Filtering
Acronyms with the Reaction Toolbar for more
information.
Quick Add
With the Quick Add, you can bypass the Add
Structure dialog and remove several steps from
the process of adding a structure to your reaction.
To add a structure with the Quick Add:
1. Select an acronym from the dropdown list
that appears in the reaction toolbar. This
32 Working with Reactions
Chapter 5

dropdown lists all of the acronyms in your
Reactants Folder.
2. Click the down arrow by the Quick Add in
the reaction toolbar.
The options for adding the structure are:
• Left of Arrow as Reactant – adds the structure
to the reaction drawing to the left of the
arrow, and adds it to the reactants table in
the grid.
• Above Arrow as Reagent – adds the structure
to the reaction drawing above the
arrow, and adds it to the reactants table in
the grid.
• Right of Arrow as Product – adds the structure
to the reaction drawing to the right of
the arrow, and adds it to the products table
in the grid.
• To Grid as Reagent – adds the structure to
the grid only, in the reactants table.
3. Select the option you desired.
4. Click Quick Add in the reaction toolbar.
The structure you selected is added to your
reaction.
Filtering Acronyms with the Reaction
Toolbar
The reaction toolbar offers several options for
filtering acronyms before selecting one to add
to your reaction section.
To jump to a particular structure:
1. Click the Add in the reaction toolbar.
The Select and Add Structure dialog
appears, displaying the acronyms in your
Reactants Folder.
2. Begin typing the name of the structure you
wish to select.
The selected structure changes to match the
text you have typed.
Applying a Filter
To filter the acronyms that are displayed in the
dialog
1. Click the Filter at the top of the dialog.
The Apply Filter window is displayed.
2. From the dropdown list, select either Names
Starting with or Names Containing.
3. Enter the text for the filter.
4. Click OK to close the Apply Filter window.
The filtered list of acronyms is displayed.
Removing a Filter
To remove a filter,
• Click the Remove Filter.
The filter is removed, and the entire list of
acronyms is displayed.
Defining a New Acronym
You can use the reaction toolbar to add new
acronyms to reactants collections in E-Notebook.
To do this:
1. In the reaction drawing, use the Chem &
Bio Draw tools to select the structure you
wish to define as an acronym.
2. Click the Define in the reaction toolbar.
A dialog appears, prompting you to select
the Acronyms collection where you wish to
add the new acronym.
3. Select the collection and click the Create
Here.
The structure you selected is added to the
collection.
4. Close the dialog.
Deleting a Structure
You can use the reaction toolbar to delete
structures from a reaction.
To do this:
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1. In the reaction drawing, use the Chem &
Bio Draw toolbar to select the structure you
wish to delete.
2. Click the down Delete in the reaction toolbar.
The structure is deleted.
The Stoichiometry Table
The stoichiometry table calculates and stores
stoichiometric data for a reaction. It is filled in
automatically as you modify a reaction drawing.
You may change values manually as well.
It is also possible to add reactants from the
Collection Tree to the stoichiometry table.
Depending upon your system configuration,
certain of these properties may not appear, or
additional properties may be present.
Reactant properties:
• Reactant – the text name of the reactant.
• MF (Molecular Formula) – the chemical formula
that shows the number and kinds of
atoms in a molecule of the reactant.
• Limit? – a yes or no value, indicating
whether the reactant is the limiting reactant
in the reaction.
• MW (Molecular Weight) – sum of the
atomic masses (atomic weights) of the
atoms in the molecular formula, as set forth
in the periodic table.
• Eq (Equivalents) – the proportion of the
reactant relative to the other components in
the reaction.
• Moles – the number of 6.023 * 10 23 molecules
of the reactant.
• Sample Mass- the total quantity of the reactant
sample.
• Vol (Volume) – the three-dimensional measurement
of the reactant, such as mL, L, etc.
• Molarity – the number of moles per volume
of the reactant.
• d (density) – the mass per unit volume of the
reactant.
• % Wt (% by Weight) – the percentage of
reactant in the sample.
• FM (Formula Mass) – sum of the atomic
masses (atomic weights) of the atoms in the
formula of the compound. This tends to be
a more general term than molecular weight,
and can be applied to compounds such as
ionic compounds.
• Reactant Mass – the total quantity of the
reactant.
• Loading - The number of reactant moles per
amount of the reactant sample.
Product Properties:
• Product – the text name of the product.
• MF (Molecular) Formula) – as above.
• Actual Mass – the actual mass of product
the reaction yields.
• Actual Mol – the actual number of moles of
the product that the reaction yields.
• Yield – the ratio of the actual amount to the
theoretical amount.
• Purity – the percentage of the actual amount
that is the product.
• MW (Molecular Weight) – as above.
• Eq (Equivalents) – the proportion of the
product relative to the other components in
the reaction.
• Theo Mol (Theoretical Moles) – the calculated
number of moles of the product that
the reaction yields.
• Theo Mass (Theoretical Mass) – the calculated
mass of product the reaction yields.
• FM (Formula Mass) – as above.
34 Working with Reactions
Chapter 5

• Loading - The number of product moles per
amount of the product.
See the following topics for more information:
• Adding Information
• Removing Reactants and Products
Adding Information
You can manually type stoichiometric information
into the stoichiometry table of a reaction
section, as well as add reactants from the
Collection Tree.
To manually add information to a Stoichiometry
Table:
1. In the reaction section, click a cell in the
stoichiometry table.
2. Type the information into the cell.
The information is saved, and the text is displayed
in blue. If you have entered a number
and there are default units associated with the
property, the units are displayed. (See “Numerical
Units” on page 79.
3. Repeat the process for other cells in the
table, if necessary.
To automatically enter reactant information
into the Stoichiometry Table:
1. Right-click a cell in the Reactants section
of the Stoichiometry Table.
A menu appears.
2. Select Add Reactant After to add a reactant
after the selected item, or Add Reactant
Before to add a reactant before the selected
item.
A new column (selected item) is added in
the stoichiometry table.
3. Type in the reactant information.
Removing Reactants and Products
You can remove all of the information pertaining
to a particular product or reactant from the
Stoichiometry Table automatically. If the reactant
you remove is the limiting reactant in the
reaction, the first remaining reactant becomes
the limiting reactant.
To remove a reactant or product from the stoichiometry
table:
1. Right-click the reactant or product you wish
to remove.
A menu appears.
2. Select Remove Product if it is a product, or
Remove Reactant if it is a reactant.
A message appears, asking you if you are
sure you want to delete the reactant or product.
3. Click Yes.
The reactant or product is removed from
the Stoichiometry Table as well as from the
reaction drawings, if already present.
Salts and Solvates
In a reaction section, it is easier to represent a
compound that is present in a salt or hydrated
form. You can enter a formula that accounts
for salts and hydrates.
To enter a formula:
1. In the stoichiometry grid, double-click the
molecular formula cell.
A dialog appears.
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Select a salt code or solvate from the dropdown
list. This list displays all of the salt codes
and solvates in your User Configuration folder.
2. Click OK to close the dialog.
The formula you entered appears in the stoichiometry
grid.
Adding New Solvates and Salts
To add a solvate or salt that does not appear in
the drop-down list:
1. Click the New Solvate. (Or, to add a new
salt code, click the New Salt Code).
A dialog appears and you can browse to
solvates or salts in your User Configuration
folder.
2. Click New Solvate (or New Salt Code) and
enter the structure and name.
Autotext
With the AutoText feature, you can add predefined
fragments of text to a field. This allows
you to create the contents of a text field
quickly. You may also add text that is pulled
from other fields, for example, reaction properties
or values in the stoichiometry grid of a
reaction section. As you update the reaction
drawing and the stoichiometry grid, your
changes are reflected in the AutoText.
The example below shows the Preparation
field of the reaction section.
See the following topics for more information:
• Inserting Reactants and Products with Auto-
Text- provides instructions for adding and
managing reactants and products in the text.
• Inserting Reactants and Products from the
Stoichiometry Grid– provides instructions
for adding and managing reactants and
products in the text.
• Adding items from the AutoText Pane - provides
instructions for adding AutoText
items (as shown in the left pane of the
image above) to the text.
36 Working with Reactions
Chapter 5

• Inserting Links with AutoText- offers instructions
for adding and managing hyperlinks
in the text.
• Inserting Custom AutoText – provides
instructions for using the Custom AutoText
dialog.
• Creating New AutoText Definitions – provides
instructions for setting up your own,
custom AutoText.
Inserting structure names with AutoText
When you modify reactants and products in the
reaction drawing or stoichiometry grid, the
AutoText is updated automatically.
Inserting structure names from the
Stoichiometry Grid
To insert a reactant or product from the stoichiometry
grid:
1. Right-click within the text field.
A menu appears.
2. Select Insert, followed by the name of the
reactant or product.
The name and properties of the reactant or
product you selected are inserted. The text
appears in purple, and is updated automatically
if you change the name or properties in the stoichiometry
grid.
You may also use the reactants/products to
populate the AutoText.
To do this:
1. With your cursor in the text field at the
point where you wish to insert the reactant
or product, click the reactants/products.
A menu appears.
2. Select one of the options:
• Insert Reactant... – allows you to browse to
a new reactant, and add it to the text and
stoichiometry grid.
• Insert Product... – allows you to browse to a
new product, and add it to the text and stoichiometry
grid.
• Insert “[Reactants]” AutoText – inserts the
text [Reactants], which you may then rightclick
to select a reactant from the stoichiometry
grid, or to browse to a new reactant.
• Insert “[Products]” AutoText – inserts the
text [Products], which you may then rightclick
to select a product from the stoichiometry
grid, or to browse to a new product.
The text is updated automatically if you
change the properties of the reactant or product.
Adding Items from the AutoText Pane
You can populate the text field by selecting
items from the AutoText pane. If you wish to
add your own custom AutoText to this pane,
set up your own AutoText definitions. See Creating
New Autotext Definitions.
To add AutoText items to the text field:
1. Click the drop down arrow next to the font
name [Arial] in the upper left corner of the
text field.
Chem & Bio Office 2010 User Guide 37
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The AutoText pane appears, listing the
available AutoText items.
2. Double-click any of the items in the list to
insert the corresponding AutoText.
Text that can have multiple values appears in
red.
A dialog appears, prompting you to enter
the text that will appear with the link.
3. Enter the text or accept the default text, and
click OK.
The link appears in the text field.
4. Double-click the link to browse to its target.
Alternatively, you may right-click within the
text field, and select Insert Link from the menu
that appears and follow the steps given above
(2-4).
Inserting Custom AutoText
You can insert custom AutoText in a text field.
To do this:
3. Right-click the text within brackets to view
a list of the options and select one of the
values.
In the example shown below, several possible
options are listed for the extraction solvent.
You may right-click the red text again to modify
your selection.
Certain items in the AutoText list may refer to
other data in the section. For example, doubleclicking
Conditions in the Autotext pane automatically
fills the Reaction Conditions into the
text field.
Inserting Links with AutoText
You can insert links in a text field to other sections
and collections
1. Click Link in the toolbar of the text field.
A dialog appears, prompting you to select a
collection or section you want to link to.
2. Select the collection or section and click
OK.
1. Right-click in the text field.
A menu appears.
2. Select Insert Custom AutoText.
The Insert Custom AutoText dialog
appears.
3. Select one of the AutoText items in the left
frame.
4. Click Insert.
The text appears in the text field.
5. Right-click the inserted text to see the
options associated with it.
Creating New Autotext Definitions
Depending upon your system configuration, it
may be possible for you to set up your own
AutoText definitions for use in E-Notebook
text fields. You can then use these predefined
fragments to add text to the styled text field
automatically.
1. In the collection tree, right-click the User
Configuration and select New>AutoText Definitions.
(Or, select an existing AutoText
collection to modify by clicking the collection
in the tree).
2. Enter a name for the new collection.
38 Working with Reactions
Chapter 5

3. In the new AutoText Definitions window,
click New Section.
4. Right-click the gray bar under Usage and
select New Row.
5. Right-click the new row and select Add
Property.
6. In the Add Property dialog box, select Field
and Section Type.
7. Enter the following information:
• Section Type – select a value from the dropdown
list if you would like the AutoText to
apply to a particular type of section exclusively.
For example, you may only want to
use the text in reaction sections. If you do
not select a section type, the AutoText will
be associated with all text fields, in all types
of sections.
• Field Type – if you select a Section Type,
you may select a particular field within it. If
you leave the Field blank, the AutoText will
apply to all text fields in the section type.
• Items – These are the AutoText items that
will appear in the AutoText list. Double
clicking the name of an item will fill in the
corresponding text. Click the New AutoText
Item to add a new item.
• Keywords – These are the keywords, or
choices, that you may define for a particular
item. Click the New Keywords to add new
AutoText keywords.
In the example below, AutoText has been set
up so that a user may automatically enter a sentence
for a machine type, and select from a list
of several machine types. Double-clicking
Machine Type in the AutoText list for any
styled text field would cause the corresponding
sentence to appear. Then, the user would rightclick
[MACHINE TYPES] to select from the
list of machine types.
NOTE: The title of the keywords tab must
match the field descriptor exactly. In this case,
MACHINE TYPES is the name of the keywords
tab, and [MACHINE TYPES] appears in the
AutoText item.
Autotext Based on Other Fields in the
Section
You may also set up AutoText that will fill in
the values from property lists and tables in a
section. To do this, you use a field name as a
keyword in an AutoText Item. The keywords
and the field names must match exactly in
order for the substitution to take effect.
Property Lists
For the AutoText Item to populate the styled
text field with all of the properties in a property
list, simply use the name of the property list as
the keyword in the AutoText Item. For example,
say there is a Conditions field, which is a
property list that contains reaction conditions.
The AutoText Item Conditions: [CONDI-
TIONS] (without quotes) will fill in all of the
properties in the Conditions property list - for
Chem & Bio Office 2010 User Guide 39
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example, Conditions: (Pressure: 200 atm,
Temperature: 100 °C).
The keyword CONDITIONS followed by a
property name, such as [CONDITIONS:Temperature],
will populate the styled text field
with that specific property, for example., Temperature:
100 °C.
Tables
As with Property Lists, the AutoText Item
referring to a Table should contain bracketed
UPPERCASE keywords. For example:
[REACTANTS1] is added dropwise to a 500
ml round-bottom flask charged with
[REACTANTS2] in [SOLVENT].
[REACTANTS1], [REACTANTS2], and
[SOLVENT] are replaced by the complete
description of a compound from one of these
tables. REACTANTS1 refers to a column in
the table REACTANTS (or, if the table is pivoted
with properties appearing as columns, it
refers to a row). REACTANTS is the name of
the table field.
In this case, the number — such as in
REACTANTS1 and REACTANTS2 — is
used to indicate that different compounds are
to be used in the AutoText. In order to determine
which reactant is to be used where more
than one is present in the reactants table, the
user right-clicks the keyword that appears
within brackets. This displays a popup menu
containing all of the possible values. Choosing
a value will substitute the data. If other keywords
refer to the same compound (for example,
REACTANTS1), they will be substituted
as well.
The description that populates the styled text
field consists of the name (or text of the form
Reactant 1 if the name is absent) followed by a
list of the properties of that compound.
To select individual properties, an AutoText
Item can contain a keyword followed by a
property name, for example, [REAC-
TANTS:Amount] is replaced by the value
from the Amount property for a reactant.
Section Names as Categories
If you add multiple sections to an AutoText
Collection, the section names will appear as
categories in the AutoText list. For example,
Reaction and Workup are two section names
that appear as categories below:
Solvents
You can populate the solvents in the reaction
section from the solvents folder in the User
Configuration Folder. These solvents are
named shortcuts for the commonly used solvents.
To enter a solvent into the Solvents Table:
1. Right-click a cell in the Solvents Table of
the reaction section.
A menu appears.
40 Working with Reactions
Chapter 5

2. Select Add Solvent After to add a solvent
after the selected item, or Add Solvent
Before to add a solvent before the selected
item.
A dialog box appears.
3. Select a solvent from the list. This list displays
all of the solvents in your User Configuration
folder.
4. Click Add to close the dialog.
The formula you entered appears in the solvents
table.
If a solvent which you wish to add in the solvents
table is not listed in the Solvents Folder
in your User Configuration Folder, then you
can manually add it in the table cell.
To do this:
1. Repeat the first two steps in the procedure
above.
The Add Solvent dialog appears.
2. Select the box Add Blank Solvent at the bottom
of the dialog box.
3. Click Add to close the dialog.
A blank row is added to the solvents table
in the reaction section where you can enter
the solvent of your choice manually.
4. Repeat the process for other cells in the
table, as necessary.
Adding a New Solvent Collection
To add a new solvent collection to your user
configuration folder:
1. Right-click your user configuration collection
in the collection tree and select
New>Solvents Folder.
A new Solvents Folder appears in the Collection
Tree and you are prompted to
rename it.
2. Enter a name for the folder.
3. Right-click the new solvents folder and
select New>Solvents.
A Solvents collection appears, and you are
prompted to rename it.
4. Enter a name for the solvents collection.
5. In the right pane, click New Solvent Table.
The solvents section containing the three
columns, Solvents, R Values, and Density
appears.
6. Right click the table header and select Add
Row.
7. Enter a value for the Solvent property, the R
values, and the Density property.
8. Click Save.
9. Repeat steps 6-8 to add more solvents.
Reactants
Reactants are named shortcuts for a commonly
used compounds. These could be either common
reagents, or named compounds that you
use frequently.
Adding a New Reactant to an Existing
Reactant Collection
To add a new reactant section to an existing
collection.
1. Browse to the Reactants collection to which
you wish to add the Reactant, clicking the
collection in the Collection Tree to select it.
The Reactants collection appears, with the
existing reactants displayed in the right
frame.
2. Click the New Acronym in the right frame.
A new acronym section appears.
3. To rename the section from the default
name (Acronym), right-click its section tab
and select Rename Section from the menu
that appears. Type a name in the text box
that appears.
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4. Draw or import the structure using the
Chem & Bio Draw tools.
The formula and molecular weight properties
are updated automatically.
5. Enter text for the compound name.
This text will be displayed in the table of
contents for the Reactants Folder that contains
this reactant. (Click the Reactants
Folder in the Collection Tree to view its
table of contents).
Adding a new Reactant Collection
You can add a new Reactant Collection to your
User Configuration folder in E-Notebook.
To add a new Reactant Collection:
1. Right-click your User Configuration collection
in the Collection Tree and select
New>Reactants Folder.
A new Reactants Folder appears in the Collection
Tree and you are prompted to
rename it.
2. Enter a name for the folder.
3. Right-click the Reactants Folder and select
New>Reactants.
A Reactants collection appears, and you are
prompted to rename it.
4. Enter a name for the Reactants collection.
5. Click the New Acronym in the right frame.
A new Reactant section appears.
You may populate reaction sections with the
properties of reactants. See “Adding Information”
on page 35 for more information.
Batch Explorer
Before performing the Batch Explorer, two
requirements are there:
• Creating a Task
• Creating a Template
To create a task:
1. Right click the User Configuration folder.
2. Select New>Tasks.
3. Right click on the Tasks folder and select
Batch Explorer.
For creating Template see “Templates” on
page 23. Add a reaction section to the templates
and draw reaction in this template.
There are different options in the Batch
Explorer to view the successor or predecessor
of the batch or compound created:
• View Batch Explorer
• View Synthetic Path
• Create Page As Next Step In same 'Untitled
Templates'
• Create Page As Next Step In Another 'Untitled
Templates'
• Create step Link To Existing 'Untitled Templates'
View Batch Explorer
View Batch Explorer option allows you to
view the reactants and products of the current
page template in the form of reaction tree.
To view the Batch Explorer in the current
Notebook:
1. Click the Batch Explorer tool icon in the
Reaction Section.
With the Batch Explorer, you can view a reaction
tree showing successors and predecessors
of a selected batch or compound.
42 Working with Reactions
Chapter 5

A menu appears.
2. Select View Batch Explorer. The Batch
Explorer section appears showing the reactants
and products of the current page template
in the form of reaction tree.
View Synthetic Path
View Synthetic Path option allows you to view
all the successors and predecessors of the current
page template.
To view synthetic path:
1. Click Batch Explorer tool icon in the reaction
section.
A menu appears.
2. Select View Synthetic Path option from
the Batch Explorer menu. The Batch
Explorer section appears showing the successors
and predecessors of the current
chemistry experiment.
Create Page/Reaction Page As
Next Step In same Notebook
This allows you to create a new page/reaction
page within the same notebook.
To do this:
1. Select the product of the reaction.
2. Click the Batch Explorer and select the
option from the menu “Create Page/Reaction
Page As Next Step In same Notebook”.
A dialog box appears.
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3. Select the template and click Select.
A dialog box for successful link setting
message and asking you to whether to navigation
from reaction section of the selected
notebook collection.
4. Click Yes for navigation.
Create Page/Reaction Page As
Next Step In Another Notebook
This allows you to create a new page/reaction
page in another notebook.
To do this:
1. Select the product of the reaction.
2. Click the Batch Explorer and select the
option from the menu “Create Page/Reaction
Page As Next Step In another Notebook”.
A dialog box appears.
3. Select the notebook in which you want to
create page/ reaction page.Click Select.
4. A dialog box appears.
5. Select the Template the reaction page.
A dialog box for successful link setting
message and asking you to whether to navigation
from reaction section of the selected
notebook collection.
6. Click Yes for navigation.
Create Step Link to Existing
Notebook
This allows you to create a between two existing
reactions same/existing notebook as a
result one product of a reaction is reactant in
the other.
To do this:
1. Select the product of the reaction.
2. Click the Batch Explorer and select the
option from the menu “Create Step Link to
Existing Notebook”.
A dialog box ‘Select a Section That Contains
a Reaction’ appears.
3. Select the page/reaction page that contains
a Reaction section with a molecule that will
be reactant in the other.
A dialog box for successful link setting
message and asking you to whether to navigation
from reaction section of the selected
notebook collection.
4. Click Yes for navigation.
44 Working with Reactions
Chapter 5

6
Spectra and Other Sections
This chapter continues the description of sections
begun in the previous chapter. For a list
of the preconfigured sections covered in this
chapter, see “Pre-configured Sections” on page
29.
Ancillary Data Sections
You can use an ancillary data section to associate
a file, such as a PDF or PowerPoint file,
with a page/reaction page. When you import
the file, the checksum, source path, and source
file name are populated automatically.
Although the file cannot be viewed from
within E-Notebook, it can be exported to a
selected location, and then opened and viewed
or edited from there.
1. In the Collection Tree, click the Page or
reaction page to which you would like to
add the Ancillary Data Section.
2. Click the New Section in the right frame.
A list of the section types that can be added
appears.
3. Select Ancillary Data.
A new Ancillary Data section appears in
the right frame.
4. To save the section, go to File>Save.
5. Click the Import to import a file.
A menu appears.
6. Select Import Ancillary Data.
A dialog box appears, and you are
prompted to select the file.
7. Select the file and click Open.
The type of file and its size are displayed in
E-Notebook.
To edit a stored document file, you must first
export it to another location.
1. Click the import tool.
A menu appears.
To create a new Ancillary Data section:
2. Select Export....
A dialog appears prompting you to select a
location for the exported file.
3. Enter a destination for the file and a file
name, and click the Save.
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4. Open the appropriate application, and open
the file you created.
5. Edit the file as you normally would.
6. Save the file.
7. From the section, click the import tool
again.
A menu appears.
3. Select Image.The new section appears
within the page.
4. To add an image or document, go to Import/
Export>Import Image and browse to the file
to import. The image appears in the image
pane.
8. Select Import....
A dialog appears and you are prompted to
select the file to import.
9. Select the file and click Open.
The edited document with your changes is
stored in E-Notebook.
To clear a stored document file from a section
in E-Notebook:
1. Click the import tool.
A menu appears.
2. Select Clear Ancillary Data.
You are prompted to confirm whether you
wish to clear the document file.
3. Click OK.
The file is cleared.
Captured Image Sections
Captured Image Sections let you import,
export, view, and annotate images and documents,
using the same tools as Adobe Reader
software. The section supports a wide variety
of file types, such as JPG, GIF, PNG, TIFF and
BMP.
To create a new Captured Image Section:
1. In the Collection Tree, click the page or
experiment to which you would like to add
the section.
2. Click New Section. A list of the section
types that can be added appears.
Managing Spectral data
You can manage your spectral data easily and
effectively using Spectrum and Spectra sections.
There are two types of sections for spectra.
Each type contains properties, and notes for
each spectrum.
• Spectrum Section – this section can contain
a single spectrum.
• Spectra Section – this section can contain
multiple spectra, organized in subsections.
To create a new Spectrum section:
1. In the Collection tree, click the page or
experiment to which you wish to add the
Spectrum section.
2. Click the New Section button.
A menu appears, listing the types of sections
that you may add.
3. Select Spectrum.
46 Spectra and Other Sections
Chapter 6

The new section appears in the page.
To create a new Spectra section for multiple
spectra:
1. In the Collection Tree, click the page/reaction
page to which you wish to add the
Spectra section.
2. Click the New Section button. A list of the
section types that can be added appears.
3. Select Spectra.
The new section appears within the page.
You may add as many spectrum subsections
as you wish by clicking the New Spectrum
button.
Adding a Spectrum
To add a spectrum:
1. From within a section with a spectrum
field, click the import/export button.
A menu appears.
2. Select Import Spectrum.
The Import Spectrum dialog box appears
and you are prompted to select a spectrum
image file.
spectrum section, you can replace the image.
To do this, you may import a new image, See
“Captured Image Sections” on page 46. The
new image will replace the old. Or, you may
copy an image from another section.
To replace a spectrum image:
1. From within the section containing the
image you wish to copy, click the import/
export button.
A menu is displayed.
2. Select Copy Spectrum.
3. Browse to the section containing the spectrum
image you wish to replace.
4. Click the import/export button.
5. Select Paste Spectrum. The new spectrum
image replaces the image in the section.
Zooming in on a Spectrum
Peak
To zoom in on a spectrum peak:
1. Click the spectrum image and drag your
mouse to draw a box around the area you
wish to zoom.
2. Click within the box. The zoomed view
appears.
3. To zoom out again, simply right-click in the
spectrum image.
Other Fields in a Spectra Data
After you add a spectrum, you can include
information about it.
Spectrum Properties – use this list to store Analyst,
Type, and Date.
Replacing a Spectrum
If you would like another spectrum image to
take the place of an image within a spectra or
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Notes – Record any notes that pertain to a
Spectrum in the text field.
See “Adding Properties” on page 63. for more
information.
Property After, to add a property after the
current property.
Table Sections
You can use table sections to organize the
chemical properties of compounds that interest
you. You can add properties to a table, pivot a
table, resize columns and rows, and organize
columns and rows. You can also insert links to
other sections or collections into a table.
4. In the Add Property dialog box, highlight
the properties to add and click Add.
The property appears as a column in the
table, immediately in front of the location
you selected.
To add a row to:
Adding Columns and Rows
You can add columns and rows to a table in E-
Notebook.
To add a column:
1. Browse to the section that contains the
table.
2. Right-click the table at the location where
you would like to add the column.
A menu appears.
3. Select Add Property Before, to add a property
before the current property, or Add
1. Right-click the table where you would like
to add the row.
A menu appears.
2. Select Add Row Before, to add a row before
the current row, or Add Row After, to add a
row after the current row.
NOTE: If the Table has been pivoted, you
would select Add Property to add a row, and
Add Row to add a column. (Pivoting transposes
the rows and columns in the table).
Removing Columns and Rows
You can remove columns and rows from a
table.
To remove a column:
48 Spectra and Other Sections
Chapter 6

1. Right-click the column or property you
wish to remove from the table.
A menu appears.
2. Select Remove Property.
A dialog box appears, asking you if you are
sure you want to delete the property from
the table.
3. Click Yes. The column is removed.
NOTE: If the table has been pivoted, rightclick
a row to remove a property.
To remove a row:
1. Right-click the row to remove from the
table.
A menu appears.
2. Select Remove Row.
A dialog box appears, asking you if you are
sure you want to delete the row from the
Table.
3. Click Yes. The row is removed.
Organizing Columns and Rows
You can easily rearrange rows and columns in
a table, organizing them so that the information
is displayed more effectively. You can move
columns left or right, move rows up or down,
and sort data in the table in ascending or
descending order.
To move a column left or right:
1. In the table, right-click the column you
wish to move.
A menu appears.
2. Select Move Property Left or Move Property
Right.
The column is moved either one place to
the left or one place to the right, depending
upon your selection.
To move a row up or down:
1. In the table, right-click the row to move. A
menu appears.
2. Select Move Row Up or Move Row Down.
The row is moved either up one place or
down one place in the table, depending
upon your selection.
Sort Data by a Property
To sort the table by a particular property:
1. Right-click the row or column corresponding
to the property by which you wish to
sort the table.
A menu appears.
2. Select either Sort Ascending or Sort
Descending.
The data is sorted according to the values of
the property you selected.
Resizing Columns and Rows
To resize a row or column:
1. Move the cursor to the border of the row or
column in a table.
A double-headed arrow appears.
2. Drag the border in the direction you desire
until the column or row is the correct size.
The resized column or row appears in the
table.
To autofit a column or row to the size of its
contents, move your cursor to the name of the
row or column and double-click. The column
or row resizes.
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Pivoting a Table
When you pivot a table, its rows become columns
and its columns become rows. Pivoting a
table does not alter the data.
To pivot a table:
1. Right-click the table.
A menu appears.
2. Select Pivot Table.
The rows and columns of the table are
transposed.
Figure 6.1 A table before and after pivoting.
Adding Information
There are a number of ways to add information
to a table cell. Data may be text, numbers,
dates, or structures. Your system configuration
determines what type of data it is possible to
add to any particular cell.
There are three ways to add information to a
cell:
• Choose a value from the drop-down menu
that appears in the cell. You will use this
option when the cell has a list of possible
values associated with it.
• Enter a value using the keyboard.
• Draw a Chemical Structure — See Structures
and Images for more information.
In some cases, your system administrator may
have configured E-Notebook such that a particular
property in the table has one or several
of the following qualities:
• Read-Only – certain properties in the table
may be for display only, and it may not be
possible to edit them.
• Required – it may not be possible to delete a
particular property from a table. If a property
is required, you will be presented with
an error message when you attempt to
delete it.
• Not Blank – it may be necessary to enter a
value for a particular property before you
can perform a transition on the collection.
For example, an experiment collection may
be set up such that it is necessary to enter an
equipment id before you can close the
experiment. If this is the case, you will be
prompted to add the values to the table
when you attempt to perform the transition.
See “Performing a Collection Transition”
on page 25. for more information about
transitions.
• Validated - Values you enter into a table
may be checked against an external database,
to ensure that they are valid values. In
50 Spectra and Other Sections
Chapter 6

this case, if you enter an invalid value, you
will receive an error message, and E-Notebook
will not accept the value.
• Enumerated from a database – values displayed
in a drop-down list for any particular
cell may be pulled from an external database.
Certain numerical properties in a table may
have units associated with them. See “Numerical
Units” on page 79. for more information.
The Edit Structure dialog box appears.
You can use the Chem & Bio Draw tools to
edit the structure or copy an image file into
the field.
Structures and Images
Tables may contain chemical structure fields,
which you can use to manage data about the
structures of compounds that interest you. You
can also add standard image files to the chemical
structure fields.
To add a structure or image to a table:
1. Double-click a table cell corresponding to a
structure or image.
The Edit Structure dialog box appears,
and you can use the Chem & Bio Draw
tools to draw the structure. Or, you may
copy a standard image file into the field.
2. Draw the structure or paste in the image and
click OK. Copy in an image by right-clicking
within the field and selecting Edit, then
Paste.
The structure or image appears in the table.
Editing a Structure or Image
To edit a structure or image in a table:
1. Double-click the table cell containing the
structure or image.
2. Edit the structure or change the image and
click OK.
The modified structure or image appears in
the table.
Delete a Structure
To delete a structure or image from a table:
1. Double-click the cell of the structure or
image you wish to delete.
The Edit Structure dialog box appears.
2. Using the Chem & Bio Draw tools, select
the entire structure or image and delete it.
3. Click OK.
The dialog box closes and the structure or
image is deleted from the table.
Changing Information in a
Table Cell
The data type of a cell determines what type of
information you add to a cell. For example,
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you can only draw a chemical structure in a
cell with a data type of structure.
Depending upon the data type, you can edit the
information in a cell one of the following
ways:
• Choose another value from the menu that
appears in the cell – use this option when
the cell has enumerated values associated
with it.
• Enter a value with the keyboard.
• Edit a Chemical Structure or change and
image – See Structures and Images for
more information.
Certain numerical properties in a table may
have units associated with them. See “Numerical
Units” on page 79. for more information.
Creating a Reference within a
Table Cell
Within a table cell, you can add a link to
another collection/section in E-Notebook or a
link to an external URL. This makes it easy to
browse back and forth between related data.
Adding a Link from a Table to a Collection
To add a link from a table cell to a collection in
E-Notebook:
1. In the Collection Tree, click the collection
containing the table, then select the section
containing the table.
2. Click the table cell to which you wish to
add the reference.
3. In the Collection Tree, click the collection
you would like to reference and, holding
the mouse down, drag the collection into
the upper-left corner of the table cell.
4. Release the mouse.
The reference is created, and the text in
table cell is converted into blue colored
hyperlink.
You can navigate to the collection you have
referenced by clicking the hyperlink text, and
click the Back arrow to return to the table.
Alternatively, you may right-click the collection
you wish to reference and select Copy.
Then, right-click within the table cell to which
you are adding the reference, and select Paste
Reference.
Adding a Link from a Table to a Section
To add a link from a table cell to a section in E-
Notebook:
1. In the Collection Tree, click the collection
containing section that you would like to
reference, then select the section.
The section to which you would like to
make a reference appears.
2. Right-click the Section menu icon, and
select Copy Section.
3. In the Collection Tree, click the collection
containing the table to which you are adding
the reference, and then click the section
that contains the table.
4. Right-click within a table cell and select
Paste Reference from the menu that
appears.
The reference is added to the table cell.
Clicking the hyperlink will display the section
you have referenced.
52 Spectra and Other Sections
Chapter 6

Adding a Link from a Property List to an
External URL
To add a link from a table cell to an external
URL or an intranet URL:
1. Right-click within the table cell to which
you wish to add the reference.
A menu appears.
2. Select Edit Reference.
The Edit Reference dialog appears.
3. Enter the URL and click OK.
The reference is added to the table cell. Clicking
the hyperlink will display the URL you
have referenced.
MS Word Sections
Use MS Word sections to manage information
that you record in Microsoft ® Word.
To create an MS Word Section:
1. In the Collection Tree, click the page or
experiment to which you would like to add
the MS Word Section.
2. Click New Section in the right frame and
select MS Word Document.
A new Word document appears in the right
frame.
Importing an existing Word Document:
1. Click the import/Export icon in the right
frame.
A menu appears.
2. Select Insert MS Word Document.
A file system dialog box appears.
3. Browse to the file and click Open.
The file appears in the MS Word field.
Exporting a Word Document:
1. Click the import/Export icon in the right
frame.
A menu appears.
2. Select Export MS Word Document.
A dialog box appears.
3. Enter a name for the file and click Save.
Editing Word document:
4. Open Microsoft Word, and open a file you
created.
5. Edit the file.
6. Save the file in MS Word.
7. From the E-Notebook section that contains
the MS Word field, click the import icon
again.
A menu appears.
8. Select Insert MS Word Document.
9. Select the file you edited.
The document with your changes appears
in E-Notebook.
Displaying MS Word Toolbars
The toolbars displayed with an MS Word field
in E-Notebook are the toolbars that appear
when you open MS Word. If you would like
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additional toolbars to appear with your MS
Word fields, close E-Notebook and open MS
Word. Then, change your settings for display
or hiding of tool bars in MS Word. When you
restart E-Notebook, it will use the settings
established by MS Word.
If you would like access to additional toolbars
within an MS Word field when you are editing,
right-click the toolbar at the top of the field to
select other toolbars to display. The toolbars
you add will persist until you navigate away
from the section.
Spelling Check
To conduct a spelling check on an MS Word
field, click within the field to select it, then hit
F7 on the keyboard.
MS Excel Sections
Use Microsoft Excel sections to manage Excel
spreadsheets in E-Notebook.
3. Select MS Excel Spreadsheet. A new MS
Excel Spreadsheet appears.
4. Edit the spreadsheet as desired.
To import an MS Excel document:
1. Click the import tool icon for the MS Excel
field.
A menu appears.
2. Select Import MS Excel Spreadsheet.
A dialog box appears, and you are
prompted to select the file.
3. Browse to the file, then click open.
The spreadsheet appears in E-Notebook.
The section of the spreadsheet that was
most recently active is displayed.
To export the file:
1. Click the import tool icon.
A menu appears.
2. Select Export MS Excel Spreadsheet.
A dialog appears prompting you to select a
location for the exported file.
3. Enter a destination for the file and a file
name, and click Save.
The file is exported to the location you
selected.
To clear an MS Excel file from a section in E-
Notebook:
To create a new, MS Excel Section:
1. In the Collection Tree, click the page or
experiment to which you would like to add
the section.
2. Click New Section.
A list of the section types that can be added
appears.
1. Click the import tool icon.
A menu appears.
2. Select Clear MS Excel Spreadsheet.
You are prompted to confirm whether you
wish to clear the document file.
3. Click OK.
The file is cleared.
54 Spectra and Other Sections
Chapter 6

7
Managing Sections
A section is a form for E-Notebook data. Just
as you would use pages in a paper notebook for
recording various types of data, you can use
sections in E-Notebook for recording reactions,
spectra, and other types of information.
You can also use templates to set up sections
automatically and uniformly. See “Templates”
on page 23. for more information.
Your system configuration determines the
types of sections that are available in E-Notebook.
A menu appears, listing the types of sections
that you may add.
Creating a Section
You can create a new section within a collection.
To create a section:
1. In the Collection Tree, click the collection
in which you wish to add the section.
If the collection already contains sections,
they appear in the right frame.
2. Click the New Section icon in the right
frame.
3. Select the type of section you wish to create.
A new section of that type appears.
Your system configuration determines which
types of sections can be added to which types
of collections. These rules are flexible, allowing
you to customize E-Notebook to your
workflow.
Modifying a Section
To modify a section within a collection:
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1. Go to the section you wish to change.
2. Edit the data in the section.
It is only possible for one E-Notebook user to
edit the sections in an individual collection at
any given time. If another user is editing a particular
collection and you attempt to edit it, you
will be presented with a message informing
you that the collection is locked for editing by
the other user.
In some cases, you will only have Read permission
for a collection, meaning that you may
view the collection but not edit it.
See Changes and Audit Trail in the E-Notebook
Administrator Guide for more information
about saving your changes.
Removing a Section
To remove a section from a collection:
1. Right-click the tab for the section to
remove.
2. In the context menu that appears, click
Delete Section.
A message appears, prompting you to confirm
that you wish to remove the section.
3. Click Yes.
NOTE: Your system configuration may prevent
you from deleting some sections. For example,
if you are working with a collection that has
Visual Display of Changes enabled, you cannot
delete a section.
In some cases, you may delete sections only if
no data has been added to them.
Moving a Section
You can organize sections within a collection.
To move a section:
1. Go to the section to move.
2. Right-click the section menu icon.
A menu appears.
3. Select Move Up to move the section the left
a single position, or select Move Down to
move the section to the right a single position.
The section is moved in the way you
selected.
4. Repeat the process until the section is in the
desired location.
Cutting and Pasting a
Section
To cut a section and paste it into another collection:
1. Go to the section you wish to cut.
2. Right-click the section menu icon.
The section menu appears.
56 Managing Sections
Chapter 7

3. Select Cut Section.
4. In the Collection Tree, click the collection
in which you would like the copied section
to appear.
5. Right-click the section menu icon.
The section menu appears.
6. Select Paste Section.
The section appears in the right frame.
NOTE: Your system configuration determines
where you may paste sections of various types.
Renaming a Section
To rename a section:
1. Go to the section you wish to rename.
2. Right-click the section menu icon.
The section menu appears.
3. Select Rename Section.
A dialog box appears, and you are
prompted to type in a new name for the section.
4. Type in a new name and click the Rename.
The dialog box closes and the new name of
the section appears.
NOTE: Your system configuration may prevent
you from renaming certain sections.
Duplicating a Section
1. Go to the section you wish to duplicate.
2. Right-click the section menu icon.
The section menu appears.
3. Select Duplicate Section.
A copy of the section appears.
In some cases, your system configuration may
prevent you from duplicating a particular section
within a collection.
To duplicate a section from one collection to
another:
1. Go to the section you wish to duplicate.
2. Right-click the section menu icon.
The section menu appears.
3. Select Copy Section.
4. In the Collection Tree, click the collection
in which you would like the copied section
to appear.
5. Right-click the section menu icon.
The section menu appears.
6. Select Paste Section.
A copy of the section appears in the right
frame.
NOTE: In some cases, your system configuration
may prevent you from copying the section
into a collection.
For Exporting Sections to MS Word and Printing
Section see chapter “Managing Collections”
on page 19.
To duplicate a section within a collection:
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58 Managing Sections
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8
Saving the Collection Changes
E-Notebook provides auditing and change control
features that you can use to save the
changes in a collection.
For every change made to E-Notebook data, an
audit trail records the logged in identity of the
user, the date, and the time. This is done automatically
when you add, delete, or update data.
The audit trail information is stored in the E-
Notebook database.
You can also view prior versions of collections
and, if Visual Display of Changes is enabled,
you can view and print the changes that were
made to the data in a collection.
Working With Save Icon
The Save icon appears in the main menu toolbar.
The appearance of the icon changes to
indicate various conditions:
• When you first select a collection in the collection
tree, the Save icon is disabled. This
indicates that you have not made unsaved
changes to the collection, and that you have
not opened the collection for editing.
• If you perform any modifications in any of
the section of a collection, the Save icon
gets enabled. This indicates that you have
locked the collection for editing and other
E-Notebook users may not edit it at this
time.
• The enabled Save icon also indicates that
you have made some unsaved changes to
the collection.
In addition, E-Notebook may be configured so
that you can annotate the changes you make to
collections by providing reasons for them.
Saving a Collection
There are several ways save changes to a collection:
• Click the Save icon.
• Select the collection in the collection tree
and go to File>Save or Save and Annotate.
• Browsing to another collection.
• Use the autosave function to periodically
save your work (see your system administrator
to set this up).
• Close E-Notebook.
Annotate and Save:
You can annotate a file with information that
you may not want appearing in the file. For
example, you can record changes you plan to
make or errors that you have fixed without
your comments appearing in the file itself.
To annotate a file:
1. Select the file in the collection tree.
2. Go to File>Save and Annotate.
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You are prompted to enter an annotation.
3. Click Save. The version is saved and is
listed in the History Pane.
NOTE: Your system configuration may require
you to enter an annotation every time you save.
See you system administrator for more information.
• The version is displayed in the section
frame, to the right.
• The Save icon is disables when you are
viewing older versions of a collection.
To view the properties of a version of a collection:
1. Right-click the version in the history pane.
2. Select Properties from the menu that
appears.
History Pane
The History Pane indicates whether prior versions
of a collection exist, and lets you view
them. A version of the collection is created
each time the collection is saved. For each version,
the history pane shows the date, time, and
the action name - which may be save,
autosave, or a transition name.
To view the History Pane of a collection:
1. Select Show History icon on the toolbar.
2. Select the collection in the Collection Tree.
The History Pane appears below the Collection
Tree. It displays all versions and
transitions for the collection, in reverse
chronological order. A save operation is
denoted with a paper and pencil icon. A
collection transition is denoted with a rubber
stamp icon.
3. To view a version, click the version in the
History Pane.
The Version Properties dialog appears.
• The dialog displays the following information
about the version you selected:
• Name – the action that created the version
(save, autosave, transition name).
• Operator – the person who performed the
action.
• Date – the date and time when the version
was created.
• If there is an annotation associated with
the change, the following information
appears as well:
a. Person who entered the annotation.
b. Date and time the annotation occurred.
c. Text of the annotation.
3. Click the Previous to view information
about the previous version of the collection,
or the Next to view information about the
next version of this collection.
4. Click OK to dismiss the Version Properties
dialog.
60 Saving the Collection Changes
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9
Working with Data
E-Notebook enables you to work with many,
diverse types of data, and then keep related
data together in collections such as reaction
and pages.
Your system configuration determines what
types of data you can add to the sections in E-
Notebook To model your workflow and ensure
that E-Notebook accommodates the data types
you frequently use, your system configuration
may include modified versions of these data
types. Also, certain data types may not appear
in your configuration, and additional, custom
data types may have been added.
Chemical Structure Data
Chemical structures can be drawn with the use
of the Chem & Bio Draw Toolbar. The Chem
& Bio Draw Toolbar allows users to create a
chemical structure by connecting frequently
used substructures together. For more information
about using the Chem & Bio Draw Toolbar,
please see the Chem & Bio Draw User
Guide.
It is also possible to paste standard image files
into chemical structure fields (see Images in
Chemical Structure Fields), and then use the
Chem & Bio Draw toolbar for annotation, such
as text and arrows. Text in the chemical structure
fields is searchable.
Drawing a Structure
To draw a chemical structure:
1. Click within a chemical structure field.
The Chem & Bio Draw toolbar appears.
2. Using the Chem & Bio Draw tools, draw a
structure or reaction.
TIP: Users can access a drawing menu by
right-clicking in the structure window. This
menu allows you to, among other things, copy
and paste structures.
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Expanding the Drawing
Window
The image appears in the chemical structure
field.
To expand the drawing window:
1. Double-click the frame of the chemical
structure field.
The chemical structure field expands.
2. Using the Chem & Bio Draw tools, draw
the structure or reaction.
3. When you are finished editing, double-click
the frame of the chemical structure field to
return it to its original size in the form.
Images in Chemical Structure
Fields
Chemical Structure Fields can also be used to
display and annotate standard image files.
You can paste standard image files into chemical
structure fields, and then use the Chem &
Bio Draw toolbar for annotation, such as text
and arrows. Text in the chemical structure
fields is searchable.
Inserting an Image in a Structure
To insert an image into a chemical structure
field:
1. Copy the image onto the clipboard. You
may do this by, for example, selecting the
Select All and Copy commands when the
image file is open in Microsoft Photo Editor.
2. Right-click within the structure field in E-
Notebook.
A menu appears.
3. Select Edit>Paste.
4. Use F7 to zoom in, and F8 to zoom out.
You can access the drawing menu by rightclicking
in the structure window. This
menu allows you to, among other things,
annotate the image.
Annotating the Image
To annotate the image:
1. Click the A in the Chem & Bio Draw toolbar.
2. Click in the chemical structure field, and
type any text you would like to enter.
The text appears in the field.
3. Click the arrow tool in the toolbar to select
it if you would like to draw arrows to annotate
the image.
Styled Text
You can use styled text boxes to record notes,
preparation information, and other content that
you may want to include with your experiment
data. Besides formatting text, you can also use
the autotext feature to quickly add long or
62 Working with Data
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complicated phrases (such as structure names)
without having to type them. See “Autotext”
on page 36. for more information.
To format the text:
• From within a section, click in the styled
text box.
• A cursor appears in the box, and you can
begin typing.
• Immediately above the box, there may be a
toolbar for formatting the text.
You can change these formats:
• Font type
• Font size
• Bolded Text
• Italicized Text
• Superscript
• Subscript
• Left-alignment
• Center-alignment
• Right-alignment
You can also type the text, highlight it, and
select the text options to apply. You can also
use the standard Windows editing keys such as
Control-C (for copy) and Control-V (for
paste).
NOTE: In your system configuration, the
styled text box may not include the formatting
toolbar or it may be read-only.
A styled text box may also be required. You
may need to enter text into the box before you
can perform a transition on a particular collection.
For example, you may need to enter text
into a text field before you can close a Page or
Experiment.
Subsections
In E-Notebook, certain sections may be set up
to contain other sections, known as subsections.
The subsections appear as tabs within a
section. For example, in a Spectra section each
spectrum is in a separate subsection.
Property Lists
Property Lists are used in forms to record various
types of data properties such as temperature
or pressure.
Adding Properties
To add a property to a property list:
1. Right-click the within the property list in a
section.
A menu appears.
2. Select Add Property....
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The Add Property dialog box appears, listing
the properties you may add.
The property is removed from the Property
List.
Setting and Editing Values
You can set and edit values for the properties
in a property list, such as the list shown below.
To set or edit the value of a property:
3. Click the property you wish to add. You
may use CTRL+click to select multiple
properties, or SHIFT+click to select a
range.
4. Click Add.
The property or properties appear in the
list.
You system configuration determines which
properties may be added to the list, and which
properties appear by default.
Removing Properties
To remove a property from a property list:
1. Right-click the property you wish to
remove from the Property List.
A menu appears.
2. Select Remove Property.
A message appears, asking you if you are
sure you want to remove the property.
3. Click Yes.
1. Click a cell in the property list. The values
you can enter will depend upon the data
type of the specific property.
2. Enter an appropriate value.
3. Click elsewhere in the section.
The value is displayed in the cell.
Depending upon your system configuration,
certain properties may have one or several of
the following attributes:
• Read-Only – certain properties may be for
display only, and it may not be possible to
edit them.
• Required – it may not be possible to delete a
particular property from a property list. If a
property is required, you will be presented
with an error message when you attempt to
delete it.
• Not Blank – it may be necessary to enter a
value for a particular property before you
can perform a transition on the collection.
For example, an experiment collection may
be set up such that it is necessary to enter an
equipment id before you can close the
64 Working with Data
Chapter 9

experiment. If this is the case, you will be
prompted to add the values to the table
when you attempt to perform the transition.
See “Performing a Collection Transition”
on page 25. for more information about
transitions.
• Validated – Values you enter into a property
list may be checked against an external
database, to ensure that they are valid values.
In this case, if you enter an invalid
value, you will receive an error message,
and E-Notebook will not accept the value.
• Enumerated from a database – values displayed
in a drop-down list for any particular
property may be pulled from an external
database.
When searching with the Property Query Field,
numeric values for properties are interpreted
by evaluating the longest possible set of characters
that are converted into a number, starting
with the first character. For example, a
search for 37.5 will find 37.5g. A search for 2
will find 2 ATM/50. Also, conversion is performed
to find equivalent values. For example,
when searching over a volume property for
which mL are the default units, a search for 50
mL (without quotes) will return both 0.05 L
and 50 mL.
Creating a Reference
Within a property list, you can add a link to
another collection/section in E-Notebook or a
link to an external URL. This makes it easy to
browse back and forth between related data.
Adding a Link from a Property List to a
Collection
To add a link from a property list cell to a collection
in E-Notebook:
1. In the Collection Tree, click the collection
containing the property list, then select the
section containing the property list.
The section containing the property list
appears.
2. Click the cell of the property list to which
you wish to add the reference.
3. In the Collection Tree, click the collection
you would like to reference and, holding
the mouse down, drag the collection into
the upper-left corner of the property list
cell.
4. Release the mouse.
The reference is created.
Alternatively, you may right-click the collection
you wish to reference and select Copy.
Then, right-click within the property list to
which you are adding the reference, and select
Paste Reference.
Adding a Link from a Property List to
Section
To add a link from a property list cell to a section
in E-Notebook:
1. In the Collection Tree, click the collection
containing section that you would like to
reference, and then select the section.
The section to which you would like to
make a reference appears.
2. Right-click the Section menu icon, and
select Copy Section.
3. In the Collection Tree, click the collection
containing the property list to which you
are adding the reference, and then click the
section that contains the property list.
The reference is added to the property list
cell. Clicking the hyperlink will display the
section you have referenced.
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4. Right-click within a property list cell and
select Paste Reference from the menu that
appears.
Adding a Link from a Property List to an
External URL
To add a link from a Property List cell to an
external URL or an intranet URL:
1. Right-click within the property list cell to
which you wish to add the reference.
A menu appears.
2. Select Edit Reference.
The Edit Reference dialog appears.
3. Enter the URL and click OK.
The reference is added to the property list
cell. Clicking the hyperlink will display the
URL you have referenced.
Rendering
Rendering is the computer term for converting
objects such as graphics into visual form. Here,
we are using it to describe the export of the
contents of a collection to a PDF or MS Word
file, or to a printer.
E-Notebook provides several options for rendering
the contents of your pages/reaction and
other types of collections. See “Exporting to
Word” on page 26 and “Printing Collections or
Sections” on page 26.
66 Working with Data
Chapter 9

10
Searching
Searching allows you to find information in E-
notebook that meets the criteria you specify. E-
Notebook makes it possible to search for:
• Chemical Structures
• Text
• Collections - Notebooks, Folders, etc.- that
meet specific criteria, such as creation date,
owner’s name, or state.
The Query tab appears.
2. From the More Options list, select the type
of search you want.
3. Select the type of query you would like to
run.
An empty query form is displayed. An
example is shown below:
See the following topics for more information:
• Conducting a Search
• Working with Query Results
• Saving a Query
• Refining a Query
• Search Query Types:
• Simple Text Query
• Advanced Text Query
• Reaction Query
Searching
You can search for information in E-Notebook
that meets the criteria you specify. You can
then save your queries and the results.
To conduct a search:
1. Select Search at the top of the E-Notebook
screen.
4. Specify the parameters that will determine
the search results.
The parameters you can specify are determined
by the type of query you are conducting.
5. Do one of the following:
• Click Search Now to execute the query.
A results list appears.
• Click Save Search to save the query.
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The Collection Tree appears with a new
search, and you are prompted to give the
search a name.
See the following topics for information about
entering the search criteria for the various
types of searches:
• Simple Text Query
• Advanced Text Query
• Reaction Query
Working with Query
Results
shown below.The Collection Tree appears,
with the item displayed.
When you conduct a Search in E-Notebook,
the results are displayed in a list. You can save
the results list, and/or view any item on the list.
Viewing Items in a Results List
To view an item on the results list, click the
name of the item that you want to open, as
Saving a Results List
To save the results list:
1. Click Save Search.
A dialog appears, prompting you to browse
to the location in the Collection Tree where
you would like the results to be saved.
2. Click a collection to select it in the tree and
click Save.
3. The Collection Tree appears, showing the
search results as a new collection. The links
are maintained so that you may browse to
any of the items.
Related Topics
• Conducting a Search
• Saving a Query
• Refining a Search
• Defining different Types of Search Queries
68 Searching
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Saving a Query
When you create a query, you can save it in the
Collection Tree.
To save a query:
1. Click Save Search to the left of the query
form.
A dialog appears, and you are prompted to
select the location where you wish to save
the search.
2. Click a collection to select it as the location,
and click the Save.
The Collection Tree appears, and the query
appears in the tree.
3. You can also rename the query.
NOTE: The last query you created will appear
by default when you enter Search mode again.
Running a Saved Query
To run a query that is saved in the collection
tree:
1. Click Browse at the top of the screen.
The Collection Tree appears.
2. Click the query in the collection tree.
The query form appears in the right frame.
3. Right-click the query form tab and select
Copy Section.
4. Click Search at the top of the screen.
Search mode appears.
5. From the More Options list, select the type
of query that corresponds to the query form
you are copying.
6. Right-click the query form tab menu and
select Paste Section.
Refining a Search
Once you have conducted a search, you can
further refine it - performing a search that is:
• An intersection of two searches.
• A union of two searches.
• The exclusion of one set of search results
from another.
It is possible to refine your search based on
your requirements.
To do this:
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1. From the dropdown list at the top of the
query form, choose any of the following
options:
• Create a New Set of Search Results -
deletes the previous search results and
replaces them with the search results generated
by the new query.
• Refine the Previous Search - uses the previous
search results to limit the collections
in which a search is done. The stored hit
list will contain the intersection of the previous
search results and the results specified
by the new query.
• Refine the Previous Search By Section -
uses the previous search results to limit
the sections in which the search is done.
The stored hit list will contain the intersection
of the previous search results and
the results specified by the new query. If
the current search engine is a collection
search engine, then this option is not
present.
• Exclude Collections from the Previous
Search - excludes collections from the
stored hit list that are part of the previous
search results. The stored hit list is completely
replaced.
• Add to the Previous Search - adds the
results specified in the search query to the
previous search results. Duplicate collections
and/or sections will not be added.
• Remove from the Previous Search -
removes the results specified in the search
query from the previous search results.
2. Fill in the new search criteria.
3. Click the Search Now.
The hitlist appears, modified according to
the option you chose in step 1.
4. If you wish, you may refine your search
further, by selecting another option from
the dropdown list.
You can create these types of search queries:
• Simple Text Query
• Advanced Text Query
• Reaction Query
By Default, the Simple Text Query form is displayed.
To change the type of search, click
More Options and select the desired type of
query form.
Simple Text Query
Using a simple text query, you can search for a
section or collection by specifying the text
associated with it. To create a simple text
query:
1. Click Search in the main menu toolbar.
2. Click the More Options icon and select Simple
Text Query.
3. In the Simple Text Query tab, enter the text
string for which you want to search.
4. Do one of the following:
• Click Search Now to execute the query.
The Result tab displaying a list of pages/reaction
which contain the specified text appears.
• Click Save Search to save the query.
A dialog appears, and you are prompted to
select a location for the saved query. Then, you
are prompted to give the search a name.
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Advanced Text Query
Advanced Text Query allows you to obtain
more precise search results. In addition to
specify the text associated with the experiment,
you can also specify Search Location. You can
also specify the metadata about the experiment
that you want to search. For example, Collection
Name, Owner Name, Creation Date, and
Status.
To create an Advanced Text Query:
1. Click the Search in the main menu toolbar.
2. Click the More Options icon and select
Advanced Text Query.
3. Enter the text and metadata for which you
want to search.
• Click Save Search to save the query.
A dialog appears, and you are prompted to
select a location for the saved query. Then,
you are prompted to give the search a name.
Reaction Query
Using a reaction query, you can search for
structures. You can also specify other criteria
such as reactant name, product name, solvents
and reaction conditions associated with a reaction.
To create a reaction query:
1. Click Search in the main menu toolbar.
2. Click the More Options icon and select
Reaction Query.
4. Do one of the following:
• Click Search Now to execute the query.
The Results tab displaying a list of pages/
reaction, which match the specified criteria,
appears.
3. Enter the structure associated with the
experiment that you want to search.
4. Specify the values for the fields, such as
Reactant Name and field of the reactant
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associated with the experiment that you
want to search.
The Results tab displaying a list of pages/reaction,
which match the specified criteria,
appears
5. Do one of the following:
Click Search Now to save the query.
• Click Save Search to save the query.
A dialog appears, and you are prompted to
select a location for the saved query. Then, you
are prompted to give the search a name.
Related Topics
• Conducting a Search
• Working with Query Results
• Saving a Query
• Refining a Search
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11
Working Offline
You can work in offline mode in E-Notebook
12.0 when server or network connection is not
available. The changes or the data you have
added during the offline mode will get synchronized
as soon as the network or server is
available.
Creating an offline folder
You can create a offline folder:
1. Right-click on the user collection in the
Collection tree.
A menu appears.
2. Select New>Offline.
3. A new Offline folder is created and the
Work Offline appears in the upper corner
of the screen.
except for the first notebook, its reference
needs to be created manually (Copy/Paste
Reference).
Working in the Offline
mode
You can log into offline mode in two ways:
• Click the Work Offline on the upper right
corner of the screen
• While logging to E-Notebook, click Work
Offline.
NOTE: You should have only one offline folder
in the user collection.
NOTE: Once the offline folder has been
created, all notebooks and reaction created
will have a reference in the Offline folder,
You can work in the offline mode after clicking
it. You can see that User Collection contains
only two collections:
• Offline
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• User Configuration
A dialog Box appears showing you the list of
changes at the top of the dialog box, the original
contents and the updated contents, contents
of the new page/reaction page.
You can make changes and additions as you
did in online mode.
To reconnect:
1. Click Connect on the upper right corner of
the screen.
A dialog appears prompting you to enter
the password.
2. As soon as you come online a Synchronization
Change dialog appears:
The changes in a reaction page/page can be
described as:
• Content Changed: The contents in a page/
reaction page is added or changed.
• New reaction page/page: If the reaction is a
new reaction page then the word “Reaction”
is replaced by the type of the newly
created reaction “New Reaction”.
3. You can review the changes done. Click
Show Details.
When the Show Details is clicked for a reaction
that has contents changed or new page/
reaction page. Dialog box appears in which
you can see a list of the changes, the original
contents and the updated contents, contents of
the new page/reaction page. At the top of the
dialog box is a list of the changes.
4. Click Synchronize to update all the changes
that were done when you were offline in the
online content.
When the Synchronize is clicked, the synchronization
process occurs as follows:
5. Click Cancel button to cancel the login.
Limitations to Offline
Working
There are certain limitations to working offline
in E-Notebook.
1. You will not be able to create new notebooks
or any new collection in offline
mode.
2. You will not be able to make any transition
changes.
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12
E-Notebook Batch Import Facility
The batch import facility in E-Notebook lets
you import a partial or complete configuration
in a single menu command. This process is
controlled by an import script called the Batch
File, which is an XML file adhering to the
schema described in this document. The batch
file typically refers to additional files, either E-
Notebook content files created with the Export
command (called Content Files) or subsidiary
batch files. This process is initiated by selecting
a collection in the E-Notebook collection
tree (which will be referred to as the Parent
Collection) and choosing the Import command.
The root element must be a . There are
no attributes defined for the batch element. A
batch may contain zero or more of any of the
following elements, interspersed in any order,
except as dictated by the dependencies
between the imported collection and section
types.
•
•
•
•
The import element causes a single file to be
imported. This file may contain any content,
including section types, collection types, collections,
or sections. There are no attributes
defined for the import element. Each import
element may contain a element, if
none is specified, the target is the parent collection.
Each import element must contain a
element.
The target element describes where in the E-
Notebook collection hierarchy the imported
content is to be placed. This element must contain
one of the following elements, depending
on what sort of content is being imported:
•
•
A collectionType element indicates that the
relationships for a previously imported collection
type are to be imported. The name
attribute specifies the name of the collection
type for which relationships are to be imported,
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and the collectionType element must include a
collection element which specifies by position
the first (and only) collection which defines
that collection type. For example:
Collection Types/
Binder.xml
A indicates a reference to a
collection contained within the Parent Collection.
This element must contain a name or
position attribute, but is invariably used with a
name. For example, this may be used to create
a grandchild of the Parent Collection, as follows:
Section Types.xml
General Information.xml
Assuming Section Types.xml describes a collection
named Section Types and that General
Information.xml describes a section type, this
will create a Section Types collection,
and within that, a General Information
section type.
The E-Notebook collection hierarchy distinguishes
between the nodes, called collections,
and the links between the nodes, called references.
Every reference has one container collection
and one target collection, and a
collection may be referred to as the target of
any number of references. Thus, the
describes a reference, but if a
specifies a reference, it is assumed
that the target is the reference’s target collection.
A may contain a
element explicitly to indicate
that the target is the collection, not the reference,
but this is optional unless one wishes to
further specify a collection contained within
this collection. For example, to specify deeper
levels in the collection hierarchy, one might
use:
Deeper Folder.xml
The source element contains text which specifies
the path of the file to be imported. This is
interpreted relative to the batch file.
The log element contains text which is written
to the client log file, if logging is enabled. If
76 E-Notebook Batch Import Facility
Chapter 12

logging is not enabled, this element is ignored.
Example:
General Information section
type created
The alert element causes a message to be displayed.
This element must contain the text to
be displayed, and may have a title attribute
which specifies the title of the message box,
and may have a buttons attribute which may be
0 or 1. If the buttons attribute is 0 or not specified,
the message box will have an OK only. If
the buttons attribute is 1, the message box will
have OK and Cancel, and if Cancel is pressed,
the import process will stop.
The refresh element causes the client to refresh
the display of section and collection type information
to show the effect of any imported
objects. One commonly uses a refresh element
at the end of the import script.
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78 E-Notebook Batch Import Facility
Chapter 12

A
System Features
This chapter contains general information
about E-Notebook Workgroup.
Viewing User Information
As an E-Notebook Workgroup administrator,
you can see specific information about the user
who is currently logged in.
1. Click Browse.
2. Right-click any blank area in the Collections
Tree.
A menu appears.
3. Select User Info....
The User Properties dialog box appears. It
contains the following information:
• Login ID – the Login ID of the user who is
currently logged into E-Notebook.
• Password – Depending upon the type of
login authentication your system uses, this
field may be used to change the password
for the logged-in user.
• Administrator – a checkbox that indicates
whether the user has administrative privileges.
This checkbox is visible only if the
logged-in user is an administrator.
Refreshing E-Notebook
If other users add information to E-Notebook
Workgroup, you may need to refresh your
view of E-Notebook workgroup so that you
can see their changes. To refresh E-Notebook
Workgroup:
1. Click the Browse.
The Collection Tree appears.
2. Right-click any blank area in the Collections
Tree.
A menu appears.
3. Select Refresh.
E-Notebook Workgroup information is
updated.
Numerical Units
Tables and property list may contain numerical
properties, which may have default units associated
with them. Your system configuration
determines the default units for any given
property in a table. The following types of
measurements may be specified or displayed in
the permitted units shown below.
For example, there may be a property of mass
and its default units may be grams (g). If you
Chem & Bio Office 2010 User Guide 79
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.
enter a numerical value into the property without
specifying units, the units will be displayed
and stored as grams. You may also enter any of
the permitted mass units shown below, such as
mg or kg.
NOTE: In all cases, the standard units are the
SI units for the given type, which may not be the
units commonly entered or displayed
Type of
Measurement
Standard
Units
Permitted
Units
density kg/m3 g/ml µg/ml
mg/ml µg/l
mg/l g/l kg/l
kg/m3
length m m Å nm µm
mm cm
mass kg g µg mg kg
molality
(quantity per
mass of
solvent or
substrate)
mol/kg
mol/kg mol/g
mmol/kg
mmol/g
µmol/kg
µmol/g
molar mass kg/mol g/mol kg/mol
dalton D kD
molarity
(quantity per
volume of
solution)
mol/m3
mol/l µmolar
mmolar
molar
Type of
Measurement
moles (quantity
of
substance)
normality
(ion equivalents
per
volume of
solution)
Standard
Units
mol
Permitted
Units
mmol µmol
mol
mol/m3 N mN µN
pressure Pa atm Pa kPa
torr bar mbar
temperature K °C °K °F
time s s ms µs min
hr
velocity m/s m/s km/hr
mi/hr
volume m3 ml µl l m3
When you are in Search mode, the table or
property query field allows you to find all
equivalent values entered in various units that
share the same unit type. For example, a search
for a volume of 500 mL will return both 500
mL and 0.5L. The search will assume the
default units for the property if you do not
enter units. Using the same example, if mL
were the default unit for a volume property,
and a search were conducted for a property
value of 0.5, no hits would be returned. A
search for 0.5 L would return both 500 mL and
0.5 L.
80 System Features
Appendix A

Using the Session Manager
In certain situations an E-Notebook session
may be left open. With the Session Manager,
you can end your old session, and release any
collection that may be locked by it.
To access the Session Manager:
1. Right-click any blank area in the Collections
Tree.
A menu appears.
2. Click Session Manager....
The Session Manager appears.
This dialog shows the Users, Session numbers,
and Start Times for each current session.
Ending a Session
If you wish to end a session displayed in the
Session Manager:
1. Click the session in the list.
The session is highlighted.
2. Click the End Session.
A message appears, asking you to confirm
that you wish to end the session.
3. Click Yes.
The session is ended. Any record that was
locked by the session is released.
NOTE: You must have Full Control permission
over your home collection (your user collection)
to end your sessions.
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82 System Features
Appendix A

B
Glossary
Terminology
The following terminology is used in the
E-Notebook application and throughout this
guide:
Collection– A set of related items in E-Notebook
Collections are the items that appear in
the E-Notebook Collection Tree.
Collection Listener– Collection Listeners is a
behavior that modifies the behavior of collections,
such as creating, hiding, renaming,
duplicating and moving behaviors. Administrators
assign them to collections.
Collection Type – A collection type defines the
properties of a collection. Each collection type
has a name, an icon for displaying collections
of that type in the collection hierarchy and a set
of business rules that describe what kinds of
operations can be performed on collections of
that type.
Field– Fields are the basis for the forms in
E-Notebook. Each field is based on an add-in
field type. Each field has a type, which
describes the type of data stored in the field,
and a name. Examples of different types of
fields include a property list, a table, a chemical
structure, a spectrum, a Microsoft Word
document. Depending on the type of data
stored in the field, the field may also contain
additional configuration information. For
example, a property list field contains a list of
the properties that can be included in the property
list.
Form– It is a layout which contains Fields,
Boxes, and possible Form Tools. The term
Form is associated with a Section. When you
click on a Section type you can see the layout
of a Form.
Form Tool– a Form Tool is used to perform particular
function in an E-Notebook section, such
as data analysis or data import/export.
Full Control privilege– The privilege required to
manage the security settings of a collection.
The Full Control privilege includes all of the
features associated with the Read & Write
privilege
History– A list of the versions and transitions
that have been made to a collection.
Home– The collection that appears when you
first log in to E-Notebook. It is the collection
associated with you as a user.
Meta-data– Data that describes other data. For
example, you can use meta-data such as creation
date or owner’s name as parameters
when searching for data and information in
E-Notebook.
Owner, of a Collection– the E-Notebook user
who created the collection.
Property List– A list of data properties corresponding
to a particular section. For example,
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the property list in a reaction section may contain
pressure, temperature, etc.
Read privilege– The privilege required to view
a collection in the collection tree, along with its
contents.
Read & Write privilege– The privilege required
to modify the contents of a collection. The
Read & Write privilege subsumes all of the
features associated with the Read privilege.
Region - A geographic area where each user is
associated with his home collection in E-Notebook.
The regional setting determines which
collection type print templates will be used
when the user exports to MS Word or prints.
Table– A section (or part of a section) in which
you can record data in a tabular format.
Template– A collection containing data or
information that you wish to reuse multiple
times. You can use the template as the basis for
new collections.
Section– A set of data. Each piece of datum is
described by a field. For example, a reaction
section might contain a chemical structure
drawing, a table of reactants, a table of solvents,
a table of products and a description of
the procedure used to create the drawing.
Section Listener– Section Listeners is a behavior
that modify the behavior of sections, such
as renaming and moving behaviors. Administrators
assign Section Listeners to various
types of sections.
Section Type– A configuration that contains a
set of fields, form tools and a form. You can
associate section listeners with a section type
to implement business rules associated with
sections of this type.
Transition– Are the actions performed to move
a collection from one state to another.
Transition Listener– Transition Listeners modify
the effect of a transition, usually by performing
an operation that is associated with the
transition. System administrators configure
Transition Listeners.
Version– The contents of a collection saved at a
particular time.
84 Glossary
Appendix B

BioAssay
Desktop & Workgroup

BioAssay Desktop & Workgroup
BioAssay enables research biologists to store,
analyze, and create reports on biological assay
data. This application is optimized for handling
data related to high-throughput screening.
However, it can also be effectively used to
manage data related to low-throughput and in
vivo studies.
Protocols are the basic data entities in BioAssay
application. Protocols contain tables representing
various physical storage entities, such
as plates and wells. Data is actually stored in
these tables. BioAssay lets you define protocols
for storing raw data, summary data, and
aggregate data. In addition to storing data, Bio-
Assay also facilitates curve fitting and data
manipulation.
This figure shows the start page of the BioAssay
application:
What’s New
Excel Analysis. This feature lets you integrate
BioAssay with Excel. For more information,
see “Integrating with Excel” on page 120.
About this Guide
Welcome to the BioAssay Desktop and Workgroup
User Guide. Inside this guide, you will
find a full description of BioAssay, its features,
and complete instructions on how to use them.
This guide is available in print (this file) and
CHM formats.
Logging in to BioAssay
To start the BioAssay client application:
1. Click Start>All Programs>ChemBioOffice
2010>BioAssay 12.0>BioAssay Desktop
12.0. to display the Login dialog box.
2. Enter relevant information in the Username,
Password, Data Source, and Initial Catalog
text boxes. For more information about
these fields, contact your system administrator.
Terminology
• High Throughput Screening (HTS): Testing
thousands of compounds in a short period
of time.
• Low Throughput Screening (LTS): In-depth
screening of fewer compounds.
• Protocol: A collection of database tables
and calculations that hold data about a
given biological experiment.
• Plate: A means of holding multiple samples
in an easily transportable unit.
• Plate Format: The layout of the wells on a
plate.
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• Well Format: The type of contents in a well,
such as Compound, Control, and Empty.
• Aggregate: A calculation that summarizes
multiple results in one number, such as
Average, Maximum, Minimum, Standard
Deviation, and Curve Fits.
• Grouping: A method used in conjunction
with aggregate calculations to summarize
data.
• Primary Protocol Tables: The collection of
tables that are automatically filled and calculated.
• Summary Tables: Tables that provide alternate
ways of summarizing primary data.
• File Import Template: A map that tells how
to take data from a file and place it into an
HTS assay.
• Graph Template: A template that specifies
how to place data in a 2-D graph.
• Browse Table: A table that lets you interact
with data and perform Quality Control
tasks.
• Search Table: A table that lets you search
all protocol data.
• % Inhibition: An experiment to identify
potential drug candidates.
• IC50, EC50, LD50: Measures of compound
potency, which refers to the concentration
in a protocol at which a compound is effective
at the 50% level.
• Valid, Invalid, Not Validated: Measures of
confidence in data. Generally, data that has
less confidence assigned is less visible.
• Curve Fitting: The process of using an algorithm
to determine the line that best fits a
set of points. The parameters of this equation
can then be used in further calculations.
• Picklist: A defined list of items in an assay
from which you may select the desired
item.
Navigation
The user interface of the BioAssay application
is split into two major frames: Navigator and
Content. The following figure displays the user
interface of the BioAssay application:
In the preceding figure, the left-hand side
frame is referred to as the Navigator frame. In
the Navigator frame, projects, and protocols
are organized in a tree structure in the same
way as folders are organized in Microsoft
Explorer. You can navigate through the tree
structure to access the desired protocol.
The right-hand side frame in the preceding figure
is referred to as the Content frame. This
frame displays the content of the following
items, which can be selected in the Navigator
frame:
• Protocols
• Lists
• Plate Formats
• Well Formats
• Picklists
• Field Dictionary
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In addition to viewing, you can also manage
the content of the above mentioned items
through the Content frame. The Content frame
lets you define and import data into protocols.
The Content frame can also be used to manage
the content of the plates, wells, and picklists in
the following three modes:
• Browse
• Filter
• Edit
There are some common operations, which
you can perform through the Content frame
irrespective of the data being displayed. These
operations are as follows:
• Resizing and Moving Columns
• Sorting Data
• Filtering Data
• Refreshing the Data View
• Printing
• Exporting data to Excel
• Getting Help
Resizing and Moving Columns
You can resize the columns of tables displayed
in the Content frame using the click and drag
method, in the same way as you resize columns
in table/spreadsheet interfaces.
To resize columns in a table in the Content
frame:
1. Move the mouse over the border between
two columns in the table header row, until
the mouse pointer turns into a double sided
arrow, as shown in the following figure:
2. Click the mouse and drag it, while holding
down the mouse button. The column will
resize as you drag the mouse.
3. Release the mouse when the size of the
selected column becomes appropriate, as
shown in the following figure:
In some tables, such as assay data tables, the
columns can also be moved within the table.
To move a column within a table in the Content
frame:
1. Move the mouse over the column header,
which you need to be move.
2. Hold down the mouse button and drag the
column to its new location, as shown in the
following figure:
NOTE: A column line appears when you have
dragged the column to a new column location.
3. Release the mouse button when you have
dragged the column to the proper location,
as shown in the following figure:
This new column arrangement will be saved and displayed when the table is opened in future.
Sorting Data
You can sort the data in any table based on the
content of any of the columns in the table.
After you sort the data based on a particular
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column, the data will appear in the same sorted
manner when you open the table in future.
To sort the data on the basis of a particular column,
click on the column header. To invert the
sort, click the corresponding column header
again.
Filtering Data
You can use the Filter mode of the Content
frame to filter data contained in tables. To use
the Filter mode, click the Filter button in the
toolbar of the Content frame. In the Filter
mode, you are able to filter the table data based
on any criterion. When data of a table is filtered,
only the data matching the entered criteria
is displayed.
To filter the data in a table:
1. Click Filter. A row with a green background
appears at the top of the table.
2. Enter a criterion into the new row, as shown
in the following figure:
The criterion can be entered using drop
down lists, ranges for numerical columns,
or the appropriate characters for text columns.
NOTE: To search for an empty field, type
“NULL” as the value of the field to be searched.
To search for a field starting with one or more
empty spaces, type the appropriate number of
spaces in the search criterion.
3. Click Apply. The filtered and sorted data
appears:
4. Click Clear to remove the filter.
Refreshing the Data View
You need to refresh the Content frame in order
to view the updated data contained in the
tables. This is because, unless you close the
windows in the Content frame and reopen
them, the data contained in the tables is not
updated. To refresh the Content frame, click
the Refresh button.
Printing
The Content frame lets you print any table contained
in BioAssay. To print a table:
1. Click the Print icon. The Print dialog box
appears.
2. Select the appropriate printing options and
click the OK button to print the selected
table.
Exporting Data to Excel
The Content frame lets you export any BioAssay
table to MS Excel. To export a table to MS
Excel, open the table in the Content frame and
click the icon in the menu bar. The Excel
sheet corresponding to the selected table
appears.
Table and Form View
You can view any data table in BioAssay in
either Table or Form view. You can switch
90 BioAssay Desktop & Workgroup
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etween these views by clicking the appropriate
icon. The Table view can be seen by clicking
the Table icon, while the Form view can be
seen by clicking the Form icon. By default, all
data is displayed in Table view. The following
figures display the Table and Form views of a
table:
Table View
Form View
numerical data, a calculation, or an attachment,
such as a picture or document. After defining
the type of fields contained in a table, you can
import data into the table from files through
the use of a user defined file import template.
Protocol Navigation
The Protocols folder in the Navigator frame
contains any number of protocols that can be
accessed through a folder within the Protocols
folder. You can navigate to the desired protocol
in the Navigator frame through the Protocols
folder. The following figure displays the
Navigator frame along with the Protocols
folder:
Getting Help
The BioAssay User's Guide, provided as Windows
Help files (a compiled HTML format),
can be accessed from the Content frame by
clicking the Help icon available in the menu
bar.
Protocols
Protocols are the basic data entities in BioAssay.
The BioAssay application enables you to
store and analyze assay data through the use of
protocols. The interface provided by BioAssay
for managing assay data is similar to that of
Microsoft Access.
Protocols contain tables in which data is actually
stored. The fields contained in these tables
can be defined as simple text, a piece of
In the preceding figure, The Protocols folder
contains folders, projects, and protocols.
Right-clicking on the projects and/or folders in
the Navigator frame exposes a menu, which
lets you create projects/folders/protocols,
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ename the project/folder, or remove a project/
folder.
Right-clicking on a protocol in the Navigator
frame exposes a menu which lets you perform
the following tasks:
• Create new protocol
• Remove a protocol
• Move a protocol
• Duplicate a protocol
• View protocol properties
The Unclassified folder appears by default and
it cannot be deleted because of the following
reasons:
• When a project is deleted, the protocols
contained in that project are moved to the
Unclassified folder
• When a duplicate protocol is created, that
duplicated protocol is placed, by default, in
the Unclassified folder.
Moving a Protocol or Project
To move a protocol or a project:
1. Right-click on the project or protocol,
which is to be moved. A menu is displayed.
2. Select the Move Protocol or Move Project
menu item from the menu. The Move a Protocol
dialog box appears.
3. Select the destination project in the list of
projects within the Protocols folder. The
Destination Project text box will be filled
automatically.
4. Click OK to move the selected protocol to
the destination project.
Duplicating a Protocol
To duplicate a protocol:
1. Navigate to the protocol, which you need to
duplicate.
2. Right-click on the protocol. A pop-up menu
is displayed.
3. Select the Duplicate Protocol menu item
from the menu. A copy of the selected protocol
is added to the Unclassified project in
the Navigator frame. You can rename and/
or move the protocol as per your requirements.
Viewing Protocol Properties
To view the properties of a protocol:
1. Navigate to the protocol whose properties
you need to view.
2. Right-click on the protocol in the Navigator
frame to display a menu.
3. Select the Properties menu item in the
menu. The Protocol Properties dialog box
appears.
4. Click OK to close the Protocol Properties
dialog box.
NOTE: You can also rename the protocol in the
Protocol Properties dialog box.
Protocol Data and Definitions
Protocol data and definitions are accessed by
selecting or clicking the appropriate protocol
in the Navigator frame of the BioAssay interface.
The content of the protocol is displayed
in the Content frame, which shows the following
three tabs:
• Tasks
• Data
• Definition
92 BioAssay Desktop & Workgroup
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The following figure shows the above mentioned
tabs in the Content frame of the BioAssay
interface:
The Primary Data tables of a protocol are represented
throughout the application using the
blue data table icon. The Summary tables are
denoted by a green data table icon. These
tables are defined under the Definition tab in
the Content frame when the protocol is
accessed. To view the data stored in these
tables, perform a search or click the Retrieve
All button.
Searching Protocol Data
BioAssay lets you perform search operations
over protocol data according to your specified
criteria. To perform search operations over
protocol data:
Protocol Tasks
The BioAssay application enables you to perform
various tasks through the Tasks tab, after
you select a protocol in the Navigator frame.
These tasks are as follows:
• View and manage experimental data
• Manage tables, fields, and file import templates
• Get help using the associated help files
Protocol Data
The data stored in a protocol is accessed by
clicking the Data tab of the protocol in the
Content frame. When you click the Data tab,
the Open Datasource dialog box appears.
NOTE: The term 'datasource' refers to an
internal table that is used to select data. It differs
from the term 'external datasource'
because an external datasource refers to a
view/table that is not a part of the protocol. The
table may belong to a different schema.
1. Select the protocol in the Navigator frame.
2. Click the Data tab in the Content frame. If
the Data tab was already open, click the
Datasource button. The Open Datasource
dialog box appears:
3. Select the table over which you want to perform
the search operation in the Select Datasource
list.
4. Enter your search criteria in the cells corresponding
to the fields displayed. The search
fields vary depending on the data table
selected.
5. Click Search to get the search results.
NOTE: BioAssay performs a like search from
all search dialogs.
Browsing Protocol Data
The data is arranged in hierarchical tables, as
defined in the protocol Definition tab. Doubleclicking
a row in a table exposes the data
related to that row in the next table in the hierarchy.
For example, your protocol may contain
2 tables, a Plates and a Wells table. Doubleclicking
on a row in the Plates table exposes
the data in the Wells table associated with the
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selected plate. The following figure shows the
data in the Wells table associated with the plate
having plate ID, P1002:
be loaded into the Wells table, as shown in the
following figure:
Tables are arranged in the Data tab according
to the hierarchy defined in the protocol definition.
In other words, tables that are higher in
the hierarchy are found at the top of the data
browser and nested tables are displayed lower.
If the number of tables displayed exceeds 4, a
button lets you bring the hidden tables back
into view.
Changing the selection to a table higher in the
hierarchy cascades the change through the
child tables. Thus, to see data for plate 2
instead of plate 1, click plate 2’s row in the
Plates table. Information related to plate 2 will
NOTE: Data in the tables can be edited
through the edit mode by clicking the Edit icon
in the menu bar.
By default, the table view of data is shown. If a
plate view or a graph is available, the menu bar
that appears above the bottommost table will
show additional icons.
Related Plate Data
In some BioAssay protocols, the table located
at the lowest level in the hierarchical table
structure contains the Plate and MultiPlate tab.
For example, in an IC50 protocol, the Wells
table contains the Plate and MultiPlate tab as
shown in the following figure:
94 BioAssay Desktop & Workgroup
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The Plate tab lets you view data for a single
plate, as shown in the following figure:
table, the table displays the Graph: Study
Graph tab, as shown in the following figure:
NOTE: The Graph: Study Graph tab is visible
only when you view the protocol tables in the
Data tab of the protocol.
The MultiPlate tab lets you view data for multiple
plates, as shown in the following figure:
Clicking the Graph: Study Graph tab enables
you to view the graph related to the table data
as shown in the following figure:
Related Graphical Data
BioAssay also lets you view table data in
graphical format. To view data in graphical
format, you first need to create a graph template
within the appropriate table. You can create
graph templates by using the Definition tab.
When a graph template is created within a
In order to view data for more than one row at
a time, hold down the Ctrl or Shift keys when
selecting rows. By doing this, you can select
multiple rows and display the results for the
data on one plot, as shown in the following figure:
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Plate Template Manager
BioAssay lets you create or add plates to the
Plates table of a protocol by using the Plate
Template Manager tool. When creating a new
plate, you need to select an existing plate format.
The newly created plate will inherit well
format and concentration related information
from the selected plate format. When creating
a plate, you can pin or double-click enable the
fields related to that plate.
Pinned Fields
Pinning is a feature using which you can manage
the visibility of data for a field in the Plate
Template Manager window. When a field is
pinned, the well values for that field will
always be visible at the bottom of the well. For
example, if the Well Format field is pinned, its
values appear in the wells of other fields also,
as shown in the following figure:
Double-click Enabled Fields
The double-click enabling feature lets you
select wells containing same values for a field.
When this feature is enabled for a field, double-clicking
on a well selects all other wells
containing the same value for the double-click
enabled field.
If no field is double-click enabled, the doubleclick
behavior applies only to the currently
selected field. Fields that are pinned and double-click
enabled, are represented by the following
icon:
Creating a New Plate
To create a new plate:
1. Create a plate based (IC50) protocol.
2. Import data into the protocol using a file
import template.
3. Right click a row in the Plates table when
the Data tab of the protocol is open. A popup
menu is displayed.
4. Select the Create Plates menu item. The
Add Plate dialog box appears.
NOTE: Although you can select different
values in the drop down lists corresponding to
Rows and Cols, the selections will be ignored.
Letters and numbers designation must be made
in the plate format definition.
In the preceding figure, the values of Well Format
are displayed in lower section of each well
corresponding to the Concentration field.
Fields that are pinned are represented by the
following icon:
5. Type a name for the plate in the Name text
box.
6. Select a plate format in the Plate Format
drop down list. The number of rows and
columns will be automatically populated
based on the plate format selected.
7. Click OK. The Plate Template Manager window
appears.
NOTE: In the Plate Template Manager
window, the Well Format tab is selected by
default. In addition, the Well Format field will
be pinned and double-click enabled by default.
96 BioAssay Desktop & Workgroup
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You can edit the well values and toggle the
pinning or double-click enabling settings as per
your requirements.
8. Click OK to add the plate to the Plates table.
Editing the Plate Fields
To edit the plate fields:
1. Click a field's tab in the Plate Template Manager
window. For example, click the Concentration
tab.
2. Click Edit. The Concentration dialog box
appears.
3. Type a concentration value in the text box
corresponding to the Add button.
4. Click Add to add the value to the New list
box.
5. Click OK. The new concentration value will
appear within the Concentration list in the
Plate Template Manager window.
6. Select a well and click the new concentration
value in the Concentration list. The
value of the selected well changes to the
new concentration value.
7. Click OK.
NOTE: Plate values in a Wells table can be
edited under the Plate tab. To edit a plate value,
double-click on a cell and click the Edit button
in the Details dialog box. After editing, click the
Save button to save the changes.
• Select Toggle Pin or Toggle Double Click
from the Edit -> Layer menu in the menu
bar.
• Click the Pin/ Double Click Layer toolbar
button to display the Pin/ Double Click Layers
window and select the fields to be
pinned or double-click enabled. Thereafter,
click the OK button.
Protocol Definitions
BioAssay lets you define protocols for storing
data. You can access the interface for defining
protocols by clicking the Definition tab in the
Content frame. The Definition tab appears in
the Content frame only when you select a protocol
in the Navigator frame. The Definition
tab lets you define the protocol's structure and
the calculations that can be performed over the
protocol's data. The protocol tables must be
defined before importing data.
For more information about defining tables for
an assay, see “Defining Tables and Fields” on
page 100.
When the Definition tab of a protocol is
opened, the protocol structure is displayed in
the Content frame, as shown in the following
figure:
Pinning and Double-click Enabling Fields
To pin or double-click enable a field, you can
perform one of the following tasks:
• Right click on the field's tab in the Plate
Template Manager window and select Toggle
Pin or Toggle Double Click, as per your
requirements.
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The hierarchical tree in the Content frame of
the protocol groups information in six ways,
which are as follows:
• Primary Tables
• Calculation Tables
• Summary Tables
• Additional Tables
• File Import Templates
• Graph Templates
Primary Tables
In BioAssay, the primary tables contained
within protocols are arranged in a hierarchical
tree structure. A primary table situated lower in
the tree contains rows which hold aggregate
data of a row in a higher table. For example, a
plate based protocol has at least two tables:
Plates and Wells. The Plates table is higher on
the tree than the Wells table. This makes sense
because each plate contains several wells. The
Plates table defines plate attributes, such as
barcode, while the Wells table holds data associated
with a particular well, such as the well
ID.
Each field falls under the appropriate table in
the tree. Clicking on a table name or field name
prompts the application to display details about
the table or field under the appropriate tab in
the right-hand section.
Parent Tables
Every primary table in a protocol, except the
table at the top of the hierarchy, has a parent.
The parent table is the table found in the next
highest level in the protocol tree. For example,
in the above figure, the Plates table is a parent
of the Compounds table. Since, the Plates table
is located at the top of the hierarchy, it does not
have a parent.
Every parent table holds information summarizing
the data contained in tables below itself.
For example, the Plates table contains a Plate
ID field because all the data in the Compounds
table have a common Plate ID.
Child Tables
Every primary table in a protocol, except the
table at the bottom of the hierarchy, has a
child. Child tables contain data that is related
in some way to the data in the corresponding
parent table. For example, the Compounds
table in the above figure is a child of the Plates
table. When you click on a row of the Plates
table, the details of the compounds in that particular
plate appear in the Compounds table.
Calculation Tables
Calculation tables in BioAssay are used to calculate
data for a protocol, in ways that may not
fit into the standard protocol hierarchy. For
example, the standard protocol hierarchy may
be Plates->Wells, but you would like to run
some calculations over the same compound
that is placed on multiple plates. In such cases,
you need calculation tables.
NOTE: The basic difference between calculation
tables and summary tables is that calculation
tables are used for performing calculations
on specific data derived from various tables
whereas summary tables are used for obtaining
the overall picture of a protocol. For example,
calculation tables may use data from only two
tables, but summary tables must use data from
all the tables in a protocol to provide the overall
picture.
Calculation tables contain one or more grouping
fields in addition to calculation fields. The
grouping fields indicate which data should be
used in a calculation. For example, if the
Experiment ID is used as the grouping field,
calculations are made for each Experiment ID.
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Without the grouping field, calculations would
be based on all valid data recorded for the protocol.
Summary Tables
Summary tables in BioAssay are used to
summarize data for a single protocol. Calculations
in the primary tables of a protocol are
usually based on grouped data, such as data for
an individual plate. Therefore, you can not
obtain the overall picture of the protocol using
primary tables.
Summary tables allow you to select fields from
different primary tables and perform calculations
over the selected fields. For example, by
taking averages and standard deviations of data
in more than one plate, you can visualize the
overall picture of the protocol.
Additional Tables
Additional tables are tables that contain data
related to the rest of the data in a BioAssay
protocol. However, unlike summary tables, the
data contained in additional tables are not
linked to the data contained in other tables.
Additional tables can contain any number of
fields. These tables allow you to enter additional
data, which is mapped to the protocol
but is not associated with fields of other tables.
File Import Templates
BioAssay includes a wizard, which enables
you to design templates called File Import
Templates. These templates define how data
should be imported into protocol tables. The
advantage of creating a template is that you
need to specify the format of a data file only
once and reuse the template in future for
importing data into protocol tables.
The format of a data file includes parameters,
such as the type of delimiter used and the number
of header lines in the file being imported.
You must define at least one File Import Template
for any file being imported.
For more information about using the File
Import Template wizard, see “File Import
Templates” on page 111. For more information
about importing data, using a defined File
Import Template, see “Importing Data” on
page 115.
Graph Templates
Graph templates are used to plot data. After
creating a graph template within a protocol
table, you can plot data by clicking on the
Graph: Study Graph tab in Data view of the
protocol table. For more information, see
Related Graphical Data under the section
“Browsing Protocol Data” on page 93.
Graph templates include information related to
both data and the way of displaying that data.
For more information about creating graph
templates, see “Creating a Graph Template” on
page 122.
Protocol Security
Protocol security in BioAssay is mostly related
to the permissions for viewing and modifying
information related to protocols. The user who
creates a protocol is automatically given
appropriate permissions for the protocol. However,
all other users must be explicitly added to
the Protocol Security list, which defines the
permissions granted to each user.
There are three levels of protocol security for
users. The following table describes those
three levels:
Security
Change
Data
Description
Edit, add, and delete protocol
data.
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Security
Validate
Data
Change
Protocol
Definition
Description
Validate data already present
in protocol data tables.
Edit, add, and delete table
definitions, file import
templates, and graph
templates.
6. Click OK. The new protocol is inserted in
the Navigator frame under the selected
project.
NOTE: The protocol definition must be complete
and at least one file import template must
be added to the protocol before you can import
data.
For information about granting permissions to
users for accessing a particular protocol, see
“Defining Security” on page 110.
Designing a New Protocol
BioAssay lets you design your own customized
protocol using pre-defined protocol templates.
In order to design a new protocol, you
must know the type of protocol template to be
used and the kind of data to be imported into
the protocol. The table included below
describes the various types of protocol templates
available in BioAssay.
You need to select the desired template when
creating a new protocol. To create a new protocol:
1. Navigate to the project within which you
need to create a new protocol.
2. Right-click the project in the Navigator
frame to display a pop-up menu.
3. Select the New Protocol menu item. The
New Protocol dialog box appears.
4. Type a name for the new protocol in the
Protocol Name text box.
5. Select the protocol template to be used in
the Choose a template for the protocol list
box.
Defining Tables and Fields
In BioAssay, you need to define protocol
tables and the corresponding fields before you
can import data into the protocol. You can
define any number of tables in a BioAssay protocol.
When defining tables, you need to specify
how the tables are arranged in a
hierarchical tree structure.
The arrangement of tables depends on the data
and the desired result. If the data of a table
depends on the data in another table, the
dependent table must be higher in the structure
than the other table. Typically, raw data values
are found in a table at the lowest level. The
table structure can be defined most efficiently
by defining the lowest level table first, and
working up to the highest level table.
NOTE: It might be helpful to make a sketch of
the table structure before you start defining the
tables and fields.
There are in-built protocol templates in BioAssay
that will help you to get started with creat-
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ing protocols. See “Designing a New Protocol”
on page 100 for more information.
NOTE: After importing data, you will be limited
to adding new fields and adjusting calculation
definitions.
3. Perform the appropriate action:
If you would like
to...
Rename the table or
edit the table
comments
Then...
Click on the table and
edit the fields in the far
right frame.
Defining a Primary Protocol Table
To define tables:
1. Locate the protocol in the Navigator frame
within which you need to define a primary
table.
2. Click the protocol and click the Definition
tab in the Content frame. The protocol definition
appears:
Add a parent table
Add a child table
Remove a table
Right-click on the
table name and select
Create parent table
Right-click on the
table name and select
Create child table
Right-click on the
table name and select
Remove table
4. Click Save Changes after you have finished
performing the table related tasks.
Defining Fields in a Table
After defining a table, you need to define the
fields of that table. However, if you have used
a template or a duplicate protocol, some fields
may already exist.
NOTE: When defining tables and fields, if you
use a pre-defined template or a duplicate
protocol, the table that you need to define may
already exist. Depending upon the template
chosen, the contents of the frame will differ.
NOTE: Templates do not define calculations,
they only insert a field with type calculation.
After tables are created, the table fields must
be defined before data can populate them.
To define fields:
1. Locate the table within which you need to
define fields.
2. Right-click the table to display a pop up
menu.
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3. Select the New Field menu option as shown
in the following figure:
If you would like
to...
Then...
Move a field from a
lower table to a higher
table
Right-click on the
appropriate field
name and select Move
Up To...
NOTE: You can also define a field by editing an
existing field.
To edit an existing field:
a. Click on the appropriate field in the tree.
In the right frame, field definition
appears.
b. Edit the appropriate data as required.
After creating or editing a field, you can
perform various tasks, such as moving the
field or removing the field. The following
table lists the various field related tasks that
you can perform:
If you would like
to...
Remove a field
Move a field from a
higher table to a lower
table
Then...
Right-click on the
appropriate field
name and select
Remove Field
Right-click on the
appropriate field
name and select Move
Down To...
Move a field up
within a table
Move a field down
within a table
4. Click Save Changes.
Right-click on the
appropriate field
name and select Move
Up
Right-click on the
appropriate field
name and select Move
Down
Field Types
In BioAssay, the protocol tables contain fields,
which can be of various types, such as text and
date. When creating fields within protocol
tables, you need to choose the appropriate field
type from the available field types. The field
options that can be defined for a field vary
according to the field type chosen. The following
table lists the various field types and the
corresponding field options available in Bio-
Assay:
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Field Type
Number (Real)
Number
(Integer)
Text
Date
Elapsed Time
(hh:mm:ss
format)
Yes/No
Picklist Value
Calculation
(Numeric
Output)
Calculation
(Text Output)
Compound ID
Well Index
Plate Identifier
Plate Format
Well Format
Concentration
Attachment
(Data Storage)
Field Options
• Use Scientific Notation
• Decimal Places
• Use Scientific Notation
• Decimal Places
None
None
• Use Scientific Notation
• Units of Time
None
Picklist
• Use Scientific Notation
• Defined calculation
Defined calculation
None
None
None
None
None
Use Scientific Notation
None
Field Type
Attachment
(External
Storage)
None
Field Options
NOTE: The Elapsed Time field is a numeric
field. It is meant to simply store an integer, but
it differs from a simple numeric field in the way
of processing data values that are imported into
it from a file.
NOTE: When you enter a value into the data
grid for an Elapsed Time field, the value is
stored as it is. However, when time values are
imported from a file, the Elapsed Time field
attempts to parse the values into integer number
of time intervals for which the field has
been configured through the Field screen on the
Definition tab. For example, suppose the
Elapsed Time field has been configured for seconds,
and the file contains the following values:
00:00
00:30
00:60
01: 30
On import, the Elapsed Time field will take the
following values:
0
30
60
90
The parsing is done because BioAssay does not
support data and time arithmetic. Once the time
values are represented as numbers, calculations
can easily be carried out on them.
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Indexed Fields
Indexed fields are the fields, which are used to
search data in protocol tables. Indexed fields
help to improve searching speed. However, the
time to taken to import data into indexed fields
is slightly more than the time taken to import
data into a non-indexed field. Examples of
indexed fields are Compound ID and protocol
data fields, which are often searched over.
To index a field of a protocol table:
1. Locate the field in the protocol tables tree in
the Definition tab of the protocol.
2. Click the field to display its details in the
Content frame on the right side.
3. Select the Indexed check box.
4. Click Save Changes.
Key Fields
In BioAssay, key fields are used to perform the
following functions:
• Optimize the data returned such that the
returned data is related only to the row
selected in the previous table.
• Group data for calculations such that only
data with the same value in the key field are
used to determine calculations.
NOTE: If you do not use any key fields in a
plate based protocol, the positive and negative
control averages for every plate will be same.
This is because, in the absence of key fields, all
well data will be used for calculating positive
and negative control averages instead of well
data for a particular plate.
To mark a field as a key field:
1. Locate the field in the protocol tables tree in
the Definition tab of the protocol.
2. Click the field to display its details in the
Content frame on the right side.
3. Select the Key Field check box.
4. Click Save Changes.
Required Fields
Required fields are fields, which can not be
empty. If a field is a required field, you must
give a value to that field before a data import is
complete.
To mark a field as required field:
1. Locate the field in the protocol tables tree in
the Definition tab of the protocol.
2. Click the field to display its details in the
Content frame on the right side.
3. Select the Require Value check box.
4. Click Save Changes.
Allow Editing
BioAssay lets you specify whether users can
edit the data of a particular field in a protocol
table. This feature is enabled when the Allow
Editing check box in the field definition is
selected. If this checkbox is unchecked for a
field, users will not be able to manually edit the
value of the field in the data table.
To allow users to edit the data of a field:
1. Locate the field in the protocol tables tree in
the Definition tab of the protocol.
2. Click the field to display its details in the
Content frame on the right side.
3. Select the Allow Editing check box.
4. Click Save Changes.
Show Field
BioAssay provides you with the option of hiding
some fields of a protocol table when the
table is displayed in data view. This feature
may be useful for fields that are necessary for
certain calculations, but not relevant to the user
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owsing the data. By default, all fields are visible.
To hide a field:
compute the calculation. The following figure
shows the Calculation Wizard dialog box:
1. Locate the field in the protocol tables tree in
the Definition tab of the protocol.
2. Click the field to display its details in the
Content frame on the right side.
3. Uncheck the Show Field check box.
4. Click Save Changes.
Assigning a Calculation to a Field
In BioAssay, four different types of calculations
are available for being assigned to fields.
These four types of calculations are as follows:
• Aggregate: Calculations made on a row's
aggregate data found in a lower table.
• Mathematical: Calculations dependent upon
a user defined equation.
• Curve Fit: Calculations made to fit a set of
data to a particular curve.
• Conditional: Calculations that fill a field
based on a set of user-defined conditions.
• External: Calculations that are run externally
on BioAssay data through customized
calculation engines. You can import the
results back into BioAssay.
For more information about defining calculations
and assigning values, click on the type of
calculation in the above list.
The above mentioned calculations can be
assigned to fields by using the Calculation wizard.
The Calculation wizard helps you to
define the calculation and the data used to
To define a calculation for a field:
1. Click the field for which you need to define
calculation. The field type must be either
Calculation (Numeric output) or Calculation
(Text output).
2. Click the Edit Calculation button in the Content
frame to display the Calculation Wizard
dialog box.
3. Select the tab for the appropriate calculation
in the Calculation Wizard dialog box.
4. Select the appropriate type of calculation.
5. Click Next.
6. Select the tables and fields that you want to
use for variables in the calculation. The
fields listed depend on the type of calculation
you are creating and the field type of
field.
• Except for Conditional calculations, only
fields with a field type of Number (Real),
Number (Integer), or Calculation are displayed.
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• For Aggregate calculations, only fields in
tables below the current table are displayed.
• For Mathematical, Conditional and Curve
Fit calculations, only fields in the current
table or tables higher than the current table
are displayed.
7. Click Next.
8. Specify the value for limiting the results.
9. Click Finish.
Aggregate Calculations
Aggregate calculations are calculations that are
performed on a data set resulting in one figure
that is representative of the whole data set.
Therefore, aggregate calculations must be
included in a table higher than the location of
the data set.
The default aggregate calculations are as follows:
• Mean: Takes an average of all aggregate
data.
• Standard Deviation: Finds the standard
deviation of all aggregate data.
• Sum: Computes the sum of all aggregate
data.
• Maximum: Returns the maximum value in
the aggregate data.
• Minimum: Returns the minimum value in
the aggregate data.
The aggregate calculations can be accessed
using the Aggregate tab in the Calculation
Wizard dialog box. When you click the Edit
Calculation button in the field definition, the
Calculation Wizard dialog box appears.
To insert an aggregate calculation to a field:
1. Select the appropriate calculation in the
Aggregate tab of the Calculation Wizard dialog
box.
2. Click Next. The Input Values page appears.
3. Select the table where the data to be used
for the calculation is located, in the Table
drop down list.
4. Select the field where the data to be used
for the calculation is located, in the Values
drop down list.
5. Click Next. The Define Conditions page
appears.
6. Add a condition if you would like to use
only those data points that meet the condition.
To add a condition:
a. Click Add.
b. Select a field where the data must fulfill
the condition.
c. Select a mathematical equality symbol.
d. Finish the condition by entering the
value that the data must fulfill.
7. Click Next button. The Finished screen
appears.
8. Select the number of decimal places that the
result should be limited to, in the Limit
result to drop down list.
9. Click Finish.
Mathematical Calculations
Mathematical calculations are calculations that
are performed using a defined equation containing
variables that are related to table data.
Therefore, mathematical calculations must be
made on data in the same table in which the
calculation is inserted or any table higher than
that table. BioAssay contains some pre-defined
mathematical calculations, which are as follows:
• % Inhibition: Returns the % inhibition calculated
using the following formula: (100 *
((Value - LowControlAverage) / (HighControlAverage
- LowControlAverage))).
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• Log(x): Returns the log of a value.
• 10^x: Returns the inverse log of a value
(base 10).
• Addition: Returns the sum of two values
derived from a data table.
• Subtraction: Returns the difference between
two values derived from a data table.
• Multiplication: Returns the product of two
values derived from a data table.
• Division: Returns the quotient when one
value derived from a data table is divided
by another one.
• Percentage: Returns the percentage result
using the following formula: ((first value/
second value)/100)
• Half Life: Returns the result of the following
formula: (Time * ln(2)) / (ln(100 /
PctRemaining)).
• Z' Factor: Returns the result of the following
formula: 1 - ((3*SDPosCtl +
3*SDNegCtl) / abs(AvgPosCtl -
AvgNegCtl))
• Normalization: Returns the result of the following
formula: (100 * (Value - LowCtl) /
(HighCtl - LowCtl))
When you click the Edit Calculation button in
a field definition, the Calculation wizard
appears. Clicking the Mathematical tab provides
access to the mathematical calculations.
When performing a mathematical calculation,
you can use two options, which are as follows:
• Use a default equation
• Define a new equation
Use a Default Mathematical Calculation
To use a default mathematical calculation:
1. Click the Mathematical tab in the Calculation
Wizard dialog box. The Select Calculation
page of the Calculation Wizard appears.
2. Select the calculation that you would like to
use.
3. Click Next. The Calculation Parameters
page appears.
4. Select the values that should be used for the
variables in the equation. This involves first
selecting a table and then a field in that
table from the drop down list boxes.
5. Repeat step 4 for all the variables listed in
the Equation Parameters table.
6. Click Next. The Finished page appears.
7. Select the number of decimal places to
which the result should be limited, in the
Limit result to drop down list.
8. Click Finish.
Define a New Mathematical Calculation
To define a new calculation:
1. Click the Mathematical tab in the Calculation
Wizard dialog box. The Select Calculation
page appears.
2. Click New. The Edit Custom Function dialog
box appears.
3. Enter a name for the calculation in the
Function text box.
4. Enter an equation for the calculation in the
Equation text area. General information
about defining an equation is provided in
the help section of this dialog box. Supported
operators are found under the Operators
tab and predefined functions are listed
under the Functions tab.
5. Click OK. The Select Calculation page of the
Calculation Wizard dialog box appears.
6. Select the calculation, which you defined in
the third step.
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7. Click Next. The Calculation Parameters
page appears.
8. Select the values that should be used for the
variables in the equation. This involves first
selecting a table and then a field in that
table from the drop down list boxes.
9. Repeat step 8 for all the variables listed in
the Equation Parameters table.
10.Click Next. The Finished page appears.
11.Select the number of decimal places to
which the result should be limited, in the
Limit result to drop down list.
12.Click Finish.
Curve Fit Calculations
Curve Fit calculations are calculations that are
used to fit data to an equation so that a curve is
generated in a graph plot. Therefore, calculations
must be made on data in the same table in
which the calculation is defined or any table
higher than that table.
When you click the Edit Calculation button in
a field definition, the Calculation Wizard dialog
box appears. Clicking on the Curve Fit tab
provides access to the Curve Fit calculations.
The list will contain the curve fits that are
applicable for the given table, based on the
graph templates that have been set up and the
curve equations that have been defined for
those graphs. If the list does not contain any
values, go back to the Graph Templates section
and set up the graphs and curve fits that you
wish to perform. For more information, see
“Creating a Graph Template” on page 122.
To define a Curve Fit calculation for a field:
1. Select the curve parameter to be used for
the calculation in the Insert Value section
within the Curve Fit tab. The options displayed
will be limited to curve parameters,
which are related to the selected Curve Fit
calculation.
NOTE: If no predicted values were defined in
the Curve Fit calculation definition, there will
be no options in the corresponding drop down
list when the Predicted option is selected.
2. Click Next. The Finished dialog box
appears.
3. Select the number of decimal places to
which the result should be limited, in the
Limit result to drop down list.
4. Click Finish.
Define a New Curve Fit Calculation
To define a new Curve Fit calculation:
1. Create a graph template.
2. Click the Curve Fits tab in the definition of
the graph template to display the Add or
Remove Curve dialog box.
3. Click New. The CurveFit Template dialog
box appears.
NOTE: For more information about creating
new models, see the topic, “Defining a New
Model” under “Curve Fit Calculations” on
page 108.
4. Enter a name for the calculation in the
Name text box.
5. Select the model to be used in the Defined
Models list.
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6. Enter parameter information under the
Parameters Tab, as shown in the following
figure:
To enter parameter information:
a. Select Variable or Constant in the Type
column, for each parameter.
b. Enter a numerical value or select a value
from the drop-down menu in the Value
column.
7. Enter additional calculation options under
the Advanced tab.
8. Enter the desired predicted values for variables
under the Predicted tab
To enter predicted values:
a. Click Add. The New Predicted Value dialog
box appears.
b. Enter a name for the predicted value.
c. Select which value is given (X or Y).
The value not provided is the value
which is predicted.
d. Enter a value for the variable.
e. Click OK to close the New Predicted
Value dialog box.
9. Click OK in the Curve Fit Template dialog
box. The Add or Remove Curve dialog box
appears.
10.Select the curve you have just defined and
click the Add to List button.
11.Click OK.
Defining a New Model
To define a new model:
1. Click New under the Model tab in the Curve
Fit Template dialog box. The User-Defined
Model dialog box appears.
2. Enter a name for your model in the Name
text box.
3. Enter an equation in the Equation text box.
Equation definition tips and conventions
can be found in the lower half of the window.
4. Click Validate Equation to ensure that the
equation entered is written in the correct
syntax.
5. Click OK. The new model is listed under the
Model tab.
Editing a Curve Fit Calculation
To edit a Curve Fit calculation:
1. Select the Curve Fit calculation that you
need to edit within the Available Curves list
in the Add or Remove Curve dialog box.
2. Click Edit. The CurveFit Template dialog
box appears.
3. Edit the name for the calculation in the
Name text box, if necessary.
4. Select a different model, if required.
5. Edit the parameter information under the
Parameters tab, as shown in the following
figure:
To edit parameter information:
a. Select Variable or Constant in the Type
column, for each parameter.
b. Enter a numerical value or select a value
from the drop-down menu in the Value
column.
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6. Edit the calculation options under the
Advanced tab.
7. Click OK in the Curve Fit Template dialog
box. The Add or Remove Curve dialog box
appears.
8. Select the curve you have just edited and
click the Add to List button.
9. Click OK.
Conditional Calculations
Conditional calculations allow you to fill a
field based on the contents of other fields in a
protocol. Conditional calculations are the only
calculations that may output either a text value
or a numeric value. In order for a conditional
calculation to hold a text value, the filed type
of the corresponding field must be defined as a
Calculation (Text Output) in the Field Type
section of the field definition.
To define a conditional calculation:
1. Click Edit Calculation in a field definition to
display the Calculation Wizard dialog box.
2. Click the Conditional tab. The Conditional
tab page appears.
3. Click Next. The Define Output Values page
appears.
4. Choose a value that will be placed in the
field when none of the conditions are met
(the default value).
5. Add as many conditions and output values
as you need by clicking the Add button and
filling in the table. In the above example,
the Then Output column will contain the
value, In Range if the value of the Successful
Curves field is between 1 and 5, and will
contain the appropriate out of range message
if it is high or low.
6. Click Next to display the Finished page.
7. Click Finish.
External Calculations
The calculation engine of BioAssay lets you
perform calculations externally and include it
in a protocol definition as if it were native to
the calculation engine.
To define an External calculation:
1. Click Edit Calculation in a field definition to
display the Calculation Wizard dialog box.
2. Click the External tab. The External tab
screen appears.
3. Click Configure Calculation. The following
dialog box appears:
4. Select the field whose average you need to
calculate.
5. Click OK.
6. Click Next. The Finished page appears.
7. Select the number of decimal places to limit
the result.
8. Click Finish.
Defining Security
Users, other then the creator, must be given the
appropriate permissions to access and edit protocols.
To give a user permissions to a protocol:
1. Open the appropriate protocol definition.
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2. Click on the Security tab in the Content
frame.
NOTE: The Security tab is accessible only to
an administrator user.
3. Enable the Lock valid data check box.
4. Click Edit Protocol Security. The Protocol
Security dialog box appears.
You can add or delete a user or group from
the security list.
To add a user or group to the protocol security
list:
a. Select the user or group in the Available
list.
b. Click Add.
c. Select the check boxes corresponding to
the permissions you would like to give
the user or group. For more information
about your options, see “Protocol Security”
on page 99.
To remove a user or group from the protocol
security list:
a. Select the user or group in the table (on
the right).
b. Click Remove.
5. Click OK.
Importing and Viewing Data
In order to import data into a BioAssay protocol,
you must define the protocol tables first.
The only way to import data into a BioAssay
protocol is to use the File Import wizard and
file import templates. Therefore, a file import
template compatible with the data being
imported must also be defined before importing
data.
File Import Templates
File import templates are used to import data
from a file and populate user-defined tables
with that data.
To define a file import template:
1. Open the protocol definition.
2. Right-click the File Import Templates folder
in the tree to display a pop-up menu.
3. Select the New Template menu item. The
File Import Template Wizard dialog box
appears.
4. Enter a name and description for your file
import template.
NOTE: File import templates contain a default
name. If you do not rename your file import
template, you may lose it later.
5. Click Next. The File Format Information
page appears.
6. Select a file delimiter. The following
options are available:
• Commas
• Tabs
• Spaces
• Tecan
• Other
7. Select the type of file you are importing.
The following table describes the available
file types:
File Type
Columnar
(Excel-
Type)
Description
A series of columns; each
column contains the values for
one variable.
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File Type
Plate Block Raw data is arranged in a
block or blocks, sometimes
separated by header lines; the
block may be arranged to
coincide with plate arrangement,
or it may be in a
columnar format.
Custom
File Type
Description
Enables you to select a custom
file importer.
8. Complete the details related to your file
type.
• Columnar:
• Specify if your data file has header lines
(lines not containing actual data). If there
are header lines, enter the number of
header lines in the text box.
• Specify how you want to treat empty values
in your data. You can either leave
those fields blank, or fill them with the
last non-blank value encountered in the
file. For example, your data file may contain
the following data:
• Even though all the above data apply to
compound AB-00001, the compound name
is not repeated for clarity.
Compound ID
AB-00001 34.5
AB-00001 56.4
AB-00001 67.8
Result
• All results are properly associated with the
correct compound id.
• Plate Block:
• Check the available boxes to indicate
which sections are present in your plate
block file. Enter the number of rows in
each category.
• Custom File Type:
• Select the customized file importer. You
can also configure it by clicking the Configure
button.
NOTE: When you click the Configure button, a
DOS window flashes and disappears.
Compound ID
AB-00001 34.5
56.4
67.8
Result
9. Click Next.
• If you have selected a Columnar type file,
the Other Options page is displayed. In
this page, you can specify whether you
want to truncate the resultant data. You
can also specify the action that should be
taken when the input data is in incorrect
format.
• If you have selected a Plate Block file, the
Other Options page is displayed. In this
page, you can select how many values
appear for each well in your file. The fol-
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lowing table describes the available
options:
Option
A single
value for
each well.
Multiple
values for
each well -
separate
data blocks,
separate
fields.
Description
A standard protocol which
measures a single value for
each well. There may be data
for multiple plates in a single
file, but each well has just one
number associated with it.
A protocol where multiple
values are measured for each
well. In the most common
case, a reader reads at 2
different wavelengths and
outputs a data block for each
wavelength.
NOTE: If you have selected a Custom File
type, the Map Fields page is displayed.
Continue from step 11.
10.Click Next. The Map Fields page appears.
11.Assign values to the fields in the selected
table by selecting the type of value to populate
the field. Choices depend on the type of
file you have chosen and the type of file
being imported. For a description of
options, see “File Import Data Source
Options” on page 114.
12.Click Finish.
Multiple
values for
each well -
separate
data blocks,
same field.
A kinetic protocol where
multiple values are measured
for each well at different time
points. All the values will go
in the same field, but there are
many values for each well.
Multiple
values for
each well -
columnar
format,
separate
fields.
Multiple
values for
each well -
columnar
format,
same field.
A protocol where multiple
values are measured for each
well, and the data is arranged
in a columnar format similar
to an Excel file.
A kinetic protocol where
multiple values are measured
for each well at different time
points, and the data goes into
the same field.
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Plate Block Data Format
• A: 1 line at the top of cf file
• B: 2 lines before plate block data
• C: 2 columns before plate block data
• D: 4 lines after plate block data
• E: 3 lines of plate block data
File Import Data Source Options
The file import data source options are as follows:
• Leave Blank
• Field Type: Columnar (Excel) or Plate
Block
• Description: No data is imported into
this field.
• System Assigned
• Field Type: Columnar (Excel) or Plate
Block
• Description: The application automatically
assigns a value for this field (e.g.
Well Format for a plate linked protocol).
• Data in File Column Number
• Field Type: Columnar (Excel)
• Description: Data is found in a column in
a data file - enter the column number to
the right.
• Use Filename Data
• Field Type: Columnar (Excel) or Plate
Block
• Description: Data is part of the filename.
• Use Default
• Field Type: Columnar (Excel) or Plate
Block
• Description: A default value should be
entered for this field - enter the default
value to the right.
• Prompt Me
• Field Type: Columnar (Excel) or Plate
Block
• Description: During import, you will be
prompted for the value of this field.
• Upload File
• Field Type: Columnar (Excel) or Plate
Block
• Description: For attachment fields only.
The file itself will be uploaded to the
database, into the field.
• Plate Block Data
• Field Type: Plate Block
• Description: Data is the data found in the
plate block.
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• File Header Cell
• Field Type: Plate Block
• Description: Data is in a particular cell in
the File Header Block - enter the cell to
the right.
• Block Header Cell
• Field Type: Plate Block
• Description: Data is in a particular cell in
the Block Header Cell - enter the cell to
the right.
• Block Footer Cell
• Field Type: Plate Block
• Description: Data is in a particular feel in
the File Block Footer Cell - enter the
cell to the right.
• Block Column Cell
• Field Type: Plate Block
• Description: Data is in a particular feel in
the Block Column Cell - enter the cell to
the right.
• Use Import Time
• Field Type: Columnar (Excel) or Plate
Block
• Description: Uses time on your machine
when file is imported.
• Use Current User
• Field Type: Columnar (Excel) or Plate
Block
• Description: Uses username of user who
imports file.
Importing Data
You can import data into a protocol using
Import File Wizard after defining the protocol
primary tables and a File Import Template
compatible with the data file being imported.
To import data into a protocol:
1. Open the protocol by selecting it in the
Navigator frame.
2. Click the Import a data file link in the Tasks
tab. The Import File Wizard dialog box
appears.
3. Select an import template in the Import Template
list.
4. Click Next. The Select Data File (s) page
appears.
5. Click Browse to select the data files, which
you would like to import.
6. Click Next.
7. Enter the appropriate information, if the
wizard asks. This page may differ depending
on the File Import Template being used.
If the wizard does not ask for additional
information, continue from step 9.
8. Click Next. The Import File page appears.
9. Select the appropriate import option as per
your requirements.
10.Click Finish. The appropriate table is populated
with data. If some fields in the protocol
tables are calculations, those
calculations are performed by the application
and the results are displayed. You can
view the table data in the Data tab of the
protocol.
Searching for and Viewing Data in Tables
To search for and view your data:
1. Click the Data tab. The Open Datasource
dialog box appears.
The left hand side shows the data tables that
are available for opening. By default, the
topmost table in the Primary Data tables
hierarchy is selected. From here, you can
browse your primary assay data, make
changes, and validate data. Other tables that
may be available are calculation tables,
summary tables, additional tables, and a
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flattened view of your primary called data
called "All Primary Data - Read Only".
When you select these tables, the fields on
the right hand side change.
2. Enter search criteria and click the Search
button or click the Retrieve All button to
retrieve all data. The Search By List button
lets you search for a list that you have saved
earlier. For more information, see “Compound
Lists” on page 145.
Viewing and Browsing Data
After data has been retrieved, data is browsed
in a hierarchy. To view data in a child table,
click the plus sign (+) in the left most column
of the data table. If there is no plus sign, there
is no child data associated with the data you
are viewing.
Validating Protocol Data
When protocol data is first imported, the letter
N appears in the left most column in the data
table. This indicates that data has not been validated
yet.
To validate protocol data:
1. Open the protocol data tables that contain
the data to be validated. The data tables can
be accessed using the Data tab in the Content
frame when the protocol is opened.
2. Select the data to be validated.
3. Select Actions --> Change Validity menu
option from the menu bar. The Change
Validity dialog box appears.
4. Select the validity you would like to assign
to the selected data. The following table
describes the available validity options:
Validity
Option
Not Validated
Icon Description
N
No validation
decision
has
been made.
Valid V Data is
found to be
valid.
Invalid I Data is
found to be
invalid.
Invalid data
is not used in
calculations
or curve fits.
Request
Review
R
Data must be
reviewed
before
making a
validation
decision.
Used in
Calculations?
Yes
Yes
No
Yes
5. Select the appropriate cascading options.
The available options are as follows:
• Cascade validity change to detail
records: Apply the same validity decision
to records summarized by the selected
record
• Override current invalid records:
Change invalid records summarized by
the selected data to the new validation.
6. Click OK.
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Importing Data from External Data Source
Data can be imported from an external data
source into BioAssay by using the feature,
Structured Data Manager (SDM). Apart from
facilitating data import from external sources,
SDM also lets you validate the data contained
in external sources and populate the protocol
data table based with the result of validation.
In order to ensure that data is imported efficiently,
SDM classifies BioAssay users into
three groups and clearly distinguishes the roles
that can be performed by these users. The three
groups of users recognized by SDM, are as follows:
• Administrator
• Protocol Administrator
• End User
Administrator
Only users of the Administrator group are
allowed to define external data sources, which
can be used for importing data into BioAssay.
When defining an external data source, an user
of the Administrator group needs to provide
information related to the external data source.
This information includes various entities,
which are as follows:
• Map data source return values to protocol
fields
• Run external data source manually
• Specify whether the changes made to the
external data source parameters would take
effect after updation or after next data
import.
End User
The SDM feature of BioAssay allows users of
the End Users group to perform various functions,
which are as follows:
• Run external data source manually
• Specify whether the changes made to the
external data source parameters would take
effect after updation or after next data
import.
Defining a New External Data Source
To define a new external data source:
1. Right-click on the External Datasources
folder in the Navigator frame and select the
New Datasource menu option. The New
External Datasource window appears:
• Data Source Name
• Connection String
• SQL Query
• SQL Parameters
• SQL Return Values
Protocol Administrator
The SDM feature of BioAssay allows users of
the Protocol Administrator group to perform
various functions, which are as follows:
• Add an external data source to a protocol
• Set data source parameter values
2. Enter appropriate information in the Name
and Description fields.
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3. Select a database type in the Data Source
Type drop down list.
4. Click the icon corresponding to the Connection
String field.
• For data source type, Oracle, the following
Configure Connection String window
appears:
• For data source type, SQL Server, the following
Configure Connection String
window appears:
5. Enter relevant information in the Data
Source, Initial catalog, User ID, and Password
fields.
6. Click OK.
7. Enter a relevant SQL query in the SQL field
to fetch data from an external application or
database.
The SQL query should be in one of the following
forms:
• SELECT value FROM table
• SELECT value1, value2……. FROM
table
NOTE: Use appropriate parameter marker
with parameters in where clause.
8. Click OK.
9. Click the + icon within the Parameters section
to add a new row to the table displayed
within the Parameters section.
10.Enter relevant information about the parameters
supplied through the SQL query.
11.Click the + icon in the Return Values section
to add a new row to the table displayed
within the Return Values section.
12.Enter relevant information about the return
values supplied through the SQL query.
13.Click OK. The newly defined external data
source appears within the External Datasources
folder in the Navigator frame.
Adding and Mapping an External Data
Source to a Protocol
To add and map an external data source to a
protocol:
1. Create a plate-based protocol.
2. Add relevant fields to the Plates table so
that these fields can hold the values
returned by the mapped external data
source.
3. Right-click on the Plates table within the
Primary Data Tables folder to display a popup
menu.
4. Select the New Datasource menu option.
The Select External DataSource window
appears.
5. Select an external data source in the Data
Source list box and click the OK button. The
New External DataSource window appears.
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6. Modify the data in the first row of the
Parameters table corresponding to the
Query Value column.
NOTE: The Query Value field is the only field
through which you can pass different values to
the external database through the SQL query
and observe the result of the query.
7. Select the appropriate fields in the drop
down list corresponding to the Protocol
Field column in the various rows of the
Return Values table. These fields will hold
the data returned by the SQL query, which
is defined in the external data source.
NOTE: The external data source within the
Navigator frame is called the parent data
source, while the mapped data source within the
protocol is called the child data source. After
mapping an external data source to a protocol,
when you make changes to the parent data
source, the changes get propagated to the child
data source. However, if you make changes in
the return values of the parent data source, the
changes get propagated but are not reflected
until the protocol administrator edits the child
data source and assigns the return values to a
field within the protocol.
8. Click OK.
Running the External Data Source Manually
To run the external data source manually:
1. Click the Data tab to display the Open Datasource
dialog box.
2. Click Retrieve All to display the data view
of the protocol.
3. Select Actions > Get Data: [External data
source name] menu item. The Run External
Data Source window appears.
4. Change any data in the Query Value column
of the Input Parameters table.
5. Click Preview to view the changes in return
values due to the change in input parameters.
6. Click OK. The changed data appears in the
data view of the protocol.
NOTE: An end user can also specify that the
data table will be automatically populated during
updation or data import, by selecting the
appropriate check box in the Configure Data-
Source window. For example, by enabling the
Run when data is imported check box, a user
can ensure that data table will automatically
updated by external data during data import.
NOTE: When the Run when data is imported
check box is enabled, the data fetched by external
data source will take precedence over data
imported from a file.
For example, suppose you have two fields in a
protocol: Animal Response and Animal Diet.
You have connected the protocol to an external
datasource and enabled the Run when data is
imported check box. You have also created a
file import template for importing data into the
protocol.
Now, if you perform a file import operation to
populate the protocol fields, the Data Preview
window will display the data fetched by the
file import template. However, the protocol
fields will be actually populated with data from
the external data source when the import operation
is completed.
Validating Data
To validate data using SDM:
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1. Define the external data source so that it
contains a SQL query, which validates data
based on some condition.
2. Run the external data source with different
input values to check validity.
Integrating with Excel
1. The Excel Integration feature is available
only in BioAssay Desktop 12.0.
BioAssay provides Excel Integration 1 feature.
You can select rows of data from the primary
data tables, export the data to an Excel spreadsheet,
and perform operations on the exported
data.
A configuration interface lets you specify how
the data is organized when it is exported to
Excel. For example, you can specify the columns
that are to be exported, sorting order of
the columns, and macro to run once the data is
imported into Excel.
After manipulating the exported data in Excel,
you can import it into BioAssay using the Bio-
Assay File Importer. The BioAssay File
Importer allows you to load data directly from
Excel or choose how existing data is dealt with
when data is imported. The choices for dealing
with existing data are as follows:
• Overwrite: Overwrite existing data with
new data.
• Don’t Overwrite: Do not overwrite any
existing data. This is equivalent to the current
file import data merge algorithm
employed by the BioAssay File Importer.
• Warn: The user is warned if data is about to
be overwritten. At this time the user has the
option to cancel the action, if desired.
To integrate BioAssay with Excel:
1. Create a plate based IC50 protocol.
2. Create a file import template and import
data into the protocol.
3. Create a file import template for Excel analysis.
a. Right-click the File Import Template
folder in the protocol definition tree and
select New Template. The Template Name
page of File Import Wizard appears.
b. Enter template name and description.
c. Click the Next button. The File Format
Information page appears.
d. Specify the number of header lines in
the Columnar (Excel-Type) tab.
e. Click the radio button, Fill field with last
non-empty value encountered.
f. Click the Next button. The Other Options
page appears.
g. Click the Next button. The Map Fields
page appears.
h. Select the fields and enter values for the
selected fields.
i. Click the Finish button.
4. Right-click on the Plates table in the protocol
definition tree and select New Excel
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Analysis. The Excel Analysis Configuration
dialog box appears:
12.Click the Data tab.
13.Click Datasource -> Retrieve All.
14.Select a row in the Plates table.
15.Select Action -> Run Excel Analysis. The
Select Excel Analysis dialog box appears.
16.Click the OK button. The exported data
appears in the selected Excel file.
NOTE: The BA_Analysis_Results worksheet
appears only if you are using a macro. You can
make changes to the data in this worksheet and
import the updated data into BioAssay.
5. Enter name and description for the Excel
analysis.
6. Locate an Excel file using the Browse button
and select it so that file path appears in
the Excel WorkBook text box.
7. Specify the macro name in the Excel Macro
text box.
8. Select the file import template that you created
for Excel analysis.
9. Select the fields to be exported; all the protocol
tables and their fields are listed in the
Fields section. In the right section the
selected fields appear:
10.Click the OK button.
11.Create a database attachment field in the
Plates table. The field name should the
name of the Excel analysis that you created,
followed by ‘_Rslt’. For example, if the
name of the Excel analysis is Exe1 then the
database attachment field should be
Exe1_Rslt.
17.Click the BA_Prompt_Me worksheet.
18.Enter values corresponding to the fields displayed.
19.Click Continue to BioAssay in the dialog
box that appears on the Excel worksheet.
The Excel Analysis dialog box appears.
20.Click the Yes button. The Data Preview window
appears.
21.Click the Load All button. A success message
appears.
22.Click the OK button. The changes made to
the data in the Excel file will be reflected in
the Plates table.
Data Manipulation and Curve
Fitting
In BioAssay, any set of data can be plotted and
fit to a curve if desired. The only constraint is
that both fields being plotted are found in the
same table.
In order to plot your data, you must first design
a graph template for your protocol. Graph templates
define the data being plotted, the location
from where the graph template is
accessed, and the physical properties of the
graph.
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Creating a Graph Template
Graph templates are used to plot data in a protocol.
These templates define the following
properties of the resultant graph:
• The data that is to be plotted
• Physical properties of the graph, such as
error bars, gridlines, graph type, and data
point markers
• The location from where the graph template
can be accessed
• The curve equations that will be fit to the
data by default
To create a new graph template:
1. Browse to the definition of your protocol
and right-click a primary table to display a
pop-up menu.
2. Select the New Graph Template menu item.
The graph template details open in the right
frame.
3. Enter the name and other details as follows:
• Template Name: A name for the template.
• Comment: Additional comments for the
template.
• Summary Table: The table in the protocol
where the graph images will be stored.
For instance, if you are preparing a graph
of activity versus concentration for each
compound, you would select the Compounds
table as the Summary Table, and
the data table would contain the activity at
each concentration.
• Data Table: The table from where the
plotted data is taken. This will typically be
the direct child table of the Summary
Table.
• X-Axis: The field from which the application
should populate the X-axis.
• Y-Axis: The field from which the application
should populate the Y-axis.
When you enter the above details, the following
screen appears:
4. Click Conditions to limit the points that are
included in your graph. For instance, you
may wish to include only points where the
Y-axis value is above 0.
5. Click Graph Storage to define how to store
images of the graphs in your data table. You
can store the full image, or strip the titles
and legends from the stored image. These
stored images are recreated when the data is
recalculated.
6. Click Curve Fits to change the list of curve
equations that are fit to the data by default
when calculations are done. The set of
curves that you define here will be available
for use when you set up Curve Fit calculations.
You can either use the default equations
or create your own.
NOTE: To define a new calculation, see
“Mathematical Calculations” on page 106.
7. Click Display Options and define the graph
display options.
8. Click Save Changes.
Plotting Data using a Graph Template
In BioAssay, you can plot data using a graph
template after defining the graph template in
the Definition tab. There are two ways to dis-
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play the graphs that have been defined using
the graph templates:
• Graph images
• Interactive graphs
Graph Images
Graph images are image fields, which store
graphs. When defining a graph template for a
graph image, you must indicate which table is
the summary table for the graph. Image fields
for storing the graph are then added to the summary
table. When calculations are performed,
a small and a large image of the graph are
stored in the image fields. By default, the
graphs are shown as hyperlinks with the text
"Graph", as shown in the following figure:
NOTE: The graphs can be displayed by double
clicking the hyperlink or right-clicking and
choosing Show Pictures from a pop-up menu.
Interactive Graphs
When defining a graph template for an interactive
graph, you must indicate the location from
where the data for the graph template should
come. If the data for the graph template is
defined to be available from a table, a button
for that graph will appear in the display bar, as
shown in the following figure:
Using Annotation in Graphs
An annotation refers to a collection of text that
is added to a graph in order to provide some
extra information about the graph. For example,
when plotting a bar graph, you can insert
text into the bars in order to identify the compounds
to which the respective bars are related.
The Graph Annotation feature in BioAssay lets
you insert and delete annotations within the
graph plots.
NOTE: You cannot add annotations to graphs
within the calculation tables.
Inserting Annotation
To insert an annotation:
1. Plot a graph in the Data tab of a protocol by
using graph templates.
2. Right-click on an empty area of the graph
and click Insert Text. The Enter text dialog
box appears.
NOTE: Empty area refers to a place within the
graph plot that does not include data points or
axes. However, you can insert text within a bar.
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3. Enter text in the available text box and click
the OK button. The entered text will be displayed
at the location where you rightclicked
to insert text. The entered text is
persistent. Therefore, you can navigate
away from the graph and view the annotation
again.
the equation as close as possible to the data
points. The following figure shows the
graph after fitting the curve:
Deleting Annotation
To delete an annotation:
1. Click on the annotation present in the
graph. The BioAssay Modules dialog box
appears:
2. Click Yes to delete the text.
Fitting Data to a Curve
The graphing interface of the BioAssay application
will fit any data to any curve as long as
the curve is defined in the application. By
default, two curves are defined in BioAssay:
• Sigmoidal-dose response
• One phase exponential decay
For more information about how to define a
new curve fit equation, see “Curve Fit Templates”
on page 124.
If the correct curve is already defined, you can
fit data to the curve. To fit data to a curve:
1. Click Curve after plotting the data in the
Data tab to display the Add or Remove Curve
dialog box.
2. Highlight the name of the curve in the Available
Curves list box.
3. Click Add to List. The name of the curve
appears in the Curves to Display list box.
4. Repeat step 2 and step 3 until all the curves
that you want to plot are listed in the Curves
to Display list box.
5. Click OK. All curves listed in the Curves to
Display list box are added to the plot, fitting
NOTE: The graph characteristics, such as
scaling type and distance between the fitted
curve and data, are defined in the Graph
Options dialog box.
NOTE: After fitting the data to a curve, the
Data tab will display equation parameter values
and curve fit statistics.
Curve Fit Templates
Curve fit templates are listed in the Available
Curves list box within the Add or Remove
Curve dialog box. To access the Add or
Remove Curve dialog box, click the Curve button
in the menu bar of any plot. For more
information about using a template that is
already listed, see “Fitting Data to a Curve” on
page 124.
Creating a New Template
To create a new curve fit template:
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1. Click New in the Add or Remove Curve dialog
box. The CurveFit Template dialog box
appears.
2. Enter a name for the template in the Name
text box.
3. Highlight the model to be used. For more
information about creating new models, see
“Defining a New Model” under “Curve Fit
Calculations” on page 108.
4. Enter Parameter information under the
Parameters Tab.
a. Select Variable or Constant, in the Type
column, for each parameter.
b. Enter a numerical value, or select a
value from the drop-down menu in the
Value column.
5. Enter additional information under the
Advanced tab.
6. Click OK. The name of the new template
will be listed in the Available Curves list
box.
Editing a Template
The edit template interface is similar to the
interface for creating new template. To edit a
template, click the Edit button in the Add or
Remove Curve dialog box. The CurveFit Template
dialog box opens with the fields populated
according to the current template settings.
Viewing the Plotted Data
When you plot data in BioAssay, the Data tab
available in the menu bar of the plot, displays
the plotted data along with information about
any curves fitted to the data. The Data tab itself
contains three tabs, which are as follows:
• Equation
• Data Statistics
• Fit Statistics
Equation
The Equation tab displays the equation in
which the data is fit. The x and y variables
define the x and y coordinates for the fitted
curve. The values for other parameters in the
equation are assigned to fit the data in the best
possible way. The final values are recorded in
the Parameter Values table.
Data Statistics
The Data Statistics tab defines various statistics
for both the X and Y values.
Fit Statistics
The Fit Statistics tab records statistics, which
define how well the equation, found under the
Equation tab, fits the table data. The information
found under this tab will help you to determine
if the data is meaningfully fit to the
curve.
Manipulating Data Points
BioAssay lets you manipulate Data points of a
plot in several ways when viewing the plot
(For more information on how to view plots,
see “Plotting Data using a Graph Template” on
page 122). This feature may be useful in
removing outliers in order to produce a better
curve fit.
You can include or exclude data points from
the plot, specify points as invalid, or specify
points as not validated. By marking the points
beforehand, you can perform an operation on
more than one points at a time. The operations
can be performed using the Point Status Button
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Panel or through the context menu, which
appears on right-clicking on the graph.
NOTE: By default, active data points appear in
blue whereas inactive data points appear in
red. All data points are active by default.
To manipulate Data points in a plot:
1. Click the points, which you need to manipulate.
The size of the clicked points
increase, indicating that they have been
marked.
NOTE: You can select all the data points by
clicking the Mark All button. To unmark all the
data points, click the Unmark All button. These
functionalities of marking/unmarking all data
points are also available in the context menu of
the graph.
2. Click on the appropriate button to manipulate
the marked points as per your requirements.
The buttons available are as follows:
• Marked -> Exclude
• Marked -> Include
NOTE: The above buttons temporarily exclude
or include data points from the graphing interface
irrespective of the validity status and do
not affect the recalculation. To include/exclude
selected data points, you may also right-click on the
graph and select the appropriate option from the
context menu.
• Marked -> Invalid
• Marked -> Not Validated
NOTE: The above buttons permanently invalidate
data points or mark them Not Validated.
These buttons also affect the recalculation. To
validate/invalidate selected data points, you may
also right-click on the graph and select the appropriate
option from the context menu.
NOTE: Points invalidated from the graphing
interface are also marked as invalid in the data
tables and are excluded from calculations.
However, you can include the invalidated
points to the graphing interface by marking
them and then clicking the Marked -> Include
button.
NOTE: You can display the plots for more than
one row by selecting multiple rows in the corresponding
table. The items of selected rows are
displayed in the Active Data Series list box.
Manipulating Detail Points
At times, you may need to plot the aggregate
value of one field against all values of another
field. In the same graph, if you plot the individual
values of the former field then the points
corresponding to these values will be called
Detail points.
For example, you may plot data values of Concentration
field in X axis and aggregate value
of Raw Value field in Y axis. In the same
graph, you may also plot the points wherein the
individual values of the Raw Value field map
with the values of the Concentration field.
These points will be called Detail points.
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By default, the Detail points are white in color
whereas the Data points are filled with a solid
color. Unlike Data points, the Detail points are
inactive by default.
To manipulate Detail points in a plot:
1. Create a graph using aggregate value of a
field in Y axis.
2. Open the Graph Options dialog box.
3. Click the Protocol Data tab.
4. Select the Show detail data points check
box.
5. Click OK. The BioAssay Modules dialog
box appears.
6. Click Yes.
7. Right-click on the graph plot and click
Select Detail Point in the context menu. The
Detail points are activated and you can
manipulate the Detail points in the same
way as you manipulate Data points. For
more information, see “Manipulating Data
Points” on page 125.
• Protocol Data: Defines display characteristics,
such as plot color, plot type, and data
point style.
• Additional Content: Defines information
related to error bars and curve extensions.
To access the Graph Options dialog box, click
the Options button in the menu bar of a graph
plot or click the Display Options button in the
definition of a graph template.
Graph Options General Tab
The graph options under the General tab allow
you to specify whether a plot is a line graph or
a bar graph. These options also allow you to
remove and add specific parts of a plot, such as
the legend, title, and axes labels. The following
figure shows the General tab of the Graph
Options dialog box:
NOTE: By default, the Select Detail Point
menu item is unchecked and you need to check
it before manipulating Detail points. After you
click the Recalculate button, the Select Detail
Point menu item returns to its default state.
Graphing Options
The various graphing options available in Bio-
Assay can be accessed through the three tabs in
the Graph Options dialog box. These tabs are
as follows:
• General: Defines general plotting characteristics,
such as graph type, title, legend, X
axis, and Y axis.
Graph Type
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You can plot table data in the form of a line
graph or a bar graph by selecting the appropriate
option in the Graph Type section. When
you select the Bar option, the scaling options in
the X Axis section disappear, which indicates
that you can not set these options for a bar
graph.
Title and Legend
This section lets you display title and legend
on a plot. Selecting the check box next to a
Show option, such as Show Title, will display
the corresponding item in the plot. Un-checking
the check box will hide the item. You can
enter a name for the title in the Graph Title text
box and set its font using the Font drop down
list.
In addition, you can specify the location of the
legend on the plot. The options available are as
follows:
• Left
• Top
• Bottom
• Right
Scaling
By default, the graph window will fit itself to
the data being plotted. Therefore, the maximum
and minimum numbers shown on the
scales may vary in each graph. To prevent this,
you can manually lock either or both axes to a
maximum and minimum value in the X Axis
and Y Axis sections.
The Use Field check boxes in the Scaling section
allow you to specify the maximum and
minimum values of axes using table fields
instead of specifying the values directly. The
Max and Min text boxes convert to combo
boxes when you select the corresponding Use
Field check box. You can select table fields
from these combo boxes.
GRAPH OPTIONS PROTOCOL DATA TAB
The graph options in the Protocol Data tab
allow you to select the color and type of the
plot. You can also specify the types of data
points that will be displayed. In addition, you
can specify the color and style of the different
types of points. The following figure shows the
Protocol Data tab of the Graph Options dialog
box:
In the preceding figure, the Data Set Identification
button lets you select the fields that are to
be used to identify datasets. By default, the
datasets are identified based on key fields.
To select a field for identifying datasets:
1. Click the Data Set Identification button. The
Select Fields dialog box appears.
2. Select the field based on which you need to
identify the datasets.
3. Click OK.
4. Click OK in the Graph Options dialog box.
The BioAssay Modules dialog box appears.
5. Click Yes to save the current settings as the
default settings.
6. Select a row in the table containing the
graph and click the Recalculate tab to
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efresh the table data. The following graph
appears:
Additional Content tab of the Graph Options
dialog box:
NOTE: The legend in the graph displays the
current row value of the field, which you chose
to identify the datasets.
Graph Options Additional Content Tab
The graph options in the Additional Content
tab allow you to define error bars and curve
extension. The following figure shows the
Error Bars
Error bars are lines in a plot that specify the
margin of error in a data point. In other words,
error bars specify the range within which a
point lies. BioAssay lets you add error bars to
any plot based on aggregate data or individual
data. However, only one error bar option can
be chosen at one time.
Curve Extension
The Curve Extension drop down list determines
how much the fitted curve should extend
from the data points. The default is 10%,
which means that the fitted curve will extend
10% more from the data points at the two ends
of the curve. Making this value larger will
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extend the curve further, as shown in the following
figures:
for external analysis, you need to create an
external analysis template.
Sample External Analysis
To perform an external analysis using the Sample
External Analysis add-in:
1. Right-click on a protocol table and select
New Analysis Template. The Analysis Template
folder and new analysis template
appears:
NOTE: By clicking the Save As Default button,
you can ensure that the values for error bars
and curve extension are stored as default values.
External Analysis
Bioassay lets you create an add-in to perform
calculations or connect to third party products
to perform analysis. Thereafter, you can store
the analysis results in BioAssay data tables.
BioAssay lets you create the add-in, Sample
External Analysis. Before creating the add-in
2. Right-click on the new analysis template
and select Edit Analysis. The Edit External
Analysis window appears.
3. Specify a name for the external analysis in
the Analysis Name text box.
4. Select Sample External Analysis in the
Select Analysis Add-In list box.
5. Click Configure Add-In to configure the
selected add-in. The ExtAnalysisMain - Customer
Application window appears.
6. Select the fields you need to export to the
external analysis.
7. Click OK. The Edit External Analysis window
appears.
8. Specify the field names in the Return Values
section.
9. Click OK. The external analysis appears
within the Analysis Template folder.
10.Click the Data tab and retrieve all data.
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11.Right-click on a row in the Summary data
table and run the external analysis.
12.Select a control group and click the OK button.
The analysis result appears in the data
table.
A Sample Protocol - IC50
Overview
The IC50 protocol in BioAssay enables scientists
to manage IC50 assay data. An IC50 assay
is a kind of experiment wherein scientists measure
the effectiveness of a drug candidate in
inhibiting a given enzyme’s function.
In the IC50 assay experiment, known concentrations
of an enzyme are combined with various
known concentrations of a drug.
Thereafter, the results are compared to identify
the extent to which the enzyme’s function is
inhibited by the presence of the drug.
In order to allow you to manage IC50 assay
data, this IC50 protocol in BioAssay makes use
of four components, which are as follows:
• Test Instances: Contains information common
to the entire IC50 assay experiment
run.
• IC50s: Refers to the IC50 and log(IC50)
values for each compound.
• Averages: Contains averages of the raw
data resulting in one data point for each distinct
compound ID.
• Raw Data: Refers to the data file, which
describes the conditions in which data was
collected.
In this section, you will learn to manage IC50
assay experiments using the preceding components
of the IC50 protocol. This section covers
the following topics:
• Creating an IC50 protocol
• Setting up plate format
• Setting up the Wells table
• Setting up a File Import template
• Importing the data file
• Setting calculation options
• Positive control average
• Negative control average
• Verifying results
• Normalizing values
• Creating graphs
• Calculating IC50 values
• Adding graph attachment fields
• Viewing data of attachment fields
• Adding a Notes attachment field
• Modifying the File Import template
Creating an IC50 Protocol
To create an IC50 protocol:
1. Open the BioAssay application to display
the BioAssay window:
2. Right-click the (Unclassified) folder to display
a pop-up menu.
3. Select the New Project menu item. The New
Project dialog box appears.
4. Type Demo Project 1 in the text box.
5. Click OK. The new project, Demo Project 1
is displayed under the Unclassified folder in
the Navigator frame of the BioAssay window.
In case the Demo Project 1 project is
not displayed, expand the ((Unclassified)
folder.
6. Right-click the Demo Project 1 project to
display a pop-up menu.
7. Select the New Protocol menu item. The
New Protocol dialog box appears.
8. Type Demo IC50 Protocol in the Protocol
Name text box.
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9. Select the IC50 protocol template.
10.Click OK. The following window appears:
3. Click the Plate Formats folder. In the Content
frame, the existing plate formats
appear.
NOTE: You can click any plate format in the
Name column to view the details of that folder.
You can also right click on the table containing
the detailed data and select Concentration to
view the concentration of the compounds in the
wells.
NOTE: You need to add a new plate format to
the preceding list.
11.Click the Definition tab. The following window
appears:
Setting up Plate Format
To set up a plate format:
1. Expand the Settings folder in the Navigator
frame to display the Plate Setup folder.
2. Expand the Plate Setup folder in the Navigator
frame to display the Plate Formats
folder.
4. Click Edit. The plate formats appear in edit
mode.
5. Click Add in the menu bar to add a new
row.
6. Type FP Cpd IC50 in the Name column and
select 96 Well Plate in the drop down list of
the Physical Plate Type column.
7. Click Save to save the changes.
8. Double-click the FP4 Cpd IC50 plate format
in the Name column. The contents of the
FP4 Cpd IC50 plate format appear.
9. Click Edit to switch to edit mode. You can
click any cell and select the desired compound
placeholder from the drop down list
of that cell.
10.Click Save to save the changes.
11.Select Actions -> View -> Concentration
from the menu bar and edit the concentration
values of the compounds through the
edit mode.
12.Click Save to save the changes.
Setting up the Wells Table
To set up the format of the Wells table:
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1. Click Demo IC50 Protocol in the Navigator
frame. The following window appears:
6. Select the New Field menu item. The following
window appears:
2. Click Raw Value in the Wells table. The following
window appears:
3. Type Parallel Reading in the Field Name text
box.
4. Click Save Changes to save the changes.
5. Right-click the Wells table to display a popup
menu.
7. Type Perp Reading in the Field Name text
box.
8. Select Number (Real) in the Field Type drop
down list.
9. Click Save and Add Another to add another
field.
10.Type Ratio in the Field Name text box.
11.Select Number (Real) in the Field Type drop
down list.
12.Click Save Changes to save the changes.
Setting up a File Import Template
To set up a file import template:
1. Right-click the File Import Templates folder
in the protocol tree to display a pop-up
menu.
2. Select New Template. The File Import Wizard
window appears.
3. Type Plate Reader File in the Template Name
text box.
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4. Click Next. The following window appears:
8. Click Next. The following window appears:
5. Select Tabs in the This file is delimited by
drop down list.
6. Ensure that the Plate Block tab is selected.
You need to set the Plate Block attributes.
To set the Plate Block attributes:
• Select the Plate Header check box.
• Type 2 in the lines before each plate text
box.
• Type 3 in the data block(s) for each plate
text box.
• Select the Data Block Header check box.
• Type 4 in the lines before each data
block text box.
• Ensure that the Data Block check box is
selected.
• Ensure that the value 8 exists in the lines
in each data block text box.
NOTE: The values of the Plate Block attributes
are based on the content of the IC50Data.txt
file.
7. Click Next. The Other Options page
appears.
You need to select the fields to be
imported. To select the fields:
• Select Plate Header Cell; in the Plate ID
drop down list.
• Type 1,2 in the next cell of the Plate ID
row.
• Select Use Default; in the Plate Format
drop down list.
• Select FP Cpd IC50 in the next cell of the
Plate Format row.
• Select Prompt Me in the Scientist drop
down list.
• Select Prompt Me in the Notebook drop
down list.
• Select Data Block Number; in the Parallel
Reading drop down list.
• Type 1 in the next cell of the Parallel
Reading row.
• Select Data Block Number; in the Perp
Reading drop down list.
• Type 2 in the next cell of the Perp Reading
row.
• Select Data Block Number; in the Ratio
drop down list.
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• Type 3 in the next cell of the Ratio row.
9. Click Finish to display the protocol definition.
Importing the Data File
To import the data file:
1. Click the Data tab. The Open Datasource
dialog box appears.
2. Click Retrieve All to display a blank screen
under the Data tab, as shown in the following
figure:
7. Type your name in the Scientist field and
Notebook 1 in the Notebook field.
8. Click Next. The Import File page appears.
9. Click Finish. The Data Preview window
appears.
10.Click Load File to display the Plates table
data, as shown in the following figure:
3. Click the Import File tab. The Select Template
page of the Import File Wizard dialog
box appears.
4. Click Next. The Select Data File(s) page
appears.
5. Click Browse to locate and select the
IC50Data.txt file. After you had selected the
file, the Select Data File(s) page appears
again.
6. Click Next. The Additional Data page
appears.
11.Click the + icon in the first row of the Plates
table to display the Compounds table data,
as shown in the following figure:
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12.Click the + icon in any row of the Compounds
table to display the Concentrations
table data, as shown in the following figure:
4. Click Next. The Input Values page appears.
5. Select Wells in the Table drop down list.
6. Select Ratio in the Field drop down list.
7. Click Next. The Define Conditions page
appears.
8. Click Add. The following dialog box
appears:
13.Click the + icon in any row of the Concentrations
table to display the Wells table data,
as shown in the following figure:
14.Click the icon in the Plates table to close
all the tables.
Setting Calculation Options
To set calculations for the Positive Control
average:
1. Click the Definitions tab.
2. Click the Pos Ctl Average field in the Plates
table. The definition of the Pos Ctl Average
field appears.
3. Click Edit Calculation. The Select Calculation
page of the Calculation Wizard dialog
box appears.
9. Select Compounds in the Tables drop down
list.
10.Select Well Format in the Field drop down
list.
11.Select is in the Is drop down list.
12.Click the... button in the Value column. The
Condition Value dialog box appears.
13.Select Positive Control in the Constant Value
drop down list.
14.Click OK to close the Condition Value dialog
box.
15.Click Next. The Finished page appears.
16.Select 4 in the Limit result to drop down list
17.Click Finish.
To set calculations for the Negative Control
average:
1. Click the Neg Ctl Average icon in the Plates
table.
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2. Click Edit Calculation. The Select Calculation
page of the Calculation Wizard dialog
box appears.
3. Click Next.
4. Select Wells in the Table drop down list.
5. Select Ratio in the Field drop down list.
6. Click Next.
7. Click Add.
8. Select Compounds in the Tables drop down
list.
9. Select Well Format in the Field drop down
list.
10.Select is in the Is drop down list.
11.Click the... button in the Value column to
display the Condition Value dialog box.
12.Select Negative Control in the Constant
Value drop down list.
13.Click OK to close the Condition Value dialog
box.
14.Click Next. The Finished page of the Calculation
Wizard dialog box appears.
15.Click Finish to close the Calculation Wizard
dialog box.
Verifying Results
To verify the results of setting calculation
options:
1. Click the Data tab. The contents of the
Plates table is displayed, as shown in the
following figure:
2. Select the values in the Scientist column in
the Plates table.
3. Click Recalculate. Data in two new columns
appear in the Plates table, as shown in
the following figure:
Data in the two new columns indicate the
negative and positive control average values.
Normalizing Values
To normalize the values:
1. Click the Definitions tab.
2. Right-click the Wells table in the protocol
tree to display a pop-up menu.
3. Select the New Field menu item to display
its definition, as shown in the following figure:
4. Type Normalized in the Field Name text box.
5. Select Calculation (Numeric output) in the
Field Type drop down list.
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6. Click Edit Calculation. The Select Calculation
page of the Calculation Wizard dialog
box appears.
7. Ensure that the Mathematical tab is selected.
NOTE: If the Normalization calculation is not
present, you need to create it using the New
button. The equation for the Normalization
calculation is as follows:
Y = 100 * ((Value - LowCtl)/(HighCtl -
LowCtl))
8. Select Normalization and click the Next button.
The Calculation Parameters page
appears:
• Select Plates in the Table column of the
Highctl row.
• Select Pos Ctl Average in the Field column
of the Highctl row.
• Select Plates in the Table column of the
Lowctl row.
• Select Neg Ctl Average in the Field column
of the Lowctl row.
• Select Ratio in the Field column of the
Value row.
10.Click Finish to display the protocol definition.
11.Click the Average Raw Value field in the
Concentrations table to display its definition.
12.Type Average Normalized in the Field Name
text box.
13.Click Edit Calculation. The Select Calculation
page of the Calculation Wizard dialog
box appears.
14.Click Next. The Input Values page appears.
15.Select Normalized in the Field drop down
list.
16.Click Next. The Define Conditions page
appears.
17.Click Next. The Finished page appears.
18.Click Finish to close the Calculation Wizard
dialog box.
Creating Graphs
To create graphs:
1. Right-click the Compounds table in the protocol
definition tree to display a pop-up
menu.
2. Select the New Graph Template menu item
to display its definition, as shown in the following
figure:
NOTE: The drop down lists in each cell enable
you to select the specified values.
9. Click Next. The Finished page appears.
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3. Type 4 Parameter Fit in the Template Name
text box.
4. Select Average Normalized in the Y-Axis
drop down list.
5. Click Display Options. The Graph Options
dialog box appears.
6. Ensure that the Standard radio button in the
X Axis section is selected.
7. Click OK to close the Graph Options dialog
box.
8. Click Curve Fits. The Add or Remove Curve
dialog box appears.
9. Select Linear Model in the Available Curves
list.
10.Click Add to List. The Linear Model appears
in the Curves to Display list.
11.Click OK to close the Add or Remove Curve
dialog box.
12.Click Save Changes.
13.Click the Data tab to display its contents, as
shown in the following figure:
16.Click Recalculate. The values of the Average
Normalized field appears:
17.Click the Graph: 4 Parameter Fit tab in the
Concentrations table. The resultant graph
appears:
NOTE: Although you have created the graph
template at the Compounds level, the graph
actually appears at the Concentrations level
because the data required for the graph is
contained in the Concentrations table
14.Click the + icon in any row of the Plates
table to display the Compounds table.
15.Click the + icon any row of the Compounds
table.
Calculating IC50 Values
To calculate IC50 values:
1. Click the Definitions tab to display the protocol
definition.
2. Click the IC50 field in the Compounds table
display the field definition.
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3. Click Edit Calculation. The Select Calculation
page of the Calculation Wizard dialog
box appears.
4. Click the Curve Fit tab. The following dialog
box appears:
13.Click Edit Calculation to display the Select
Calculation page of the Calculation Wizard
dialog box.
14.Click the Curve Fit tab. The following dialog
box appears:
5. Select Slope in the drop down list within the
Insert Value section.
6. Click Next. The Finished page appears.
7. Ensure that the value 4 is selected in the
Limit result to drop down list.
8. Click Finish to close the Calculation Wizard
dialog box.
9. Right-click the Compounds table to display
a pop-up menu.
10.Select the New Field menu item to display
the field definition.
11.Type Adjusted R^2 in the Field Name text
box.
12.Select Calculation (Numeric output) in the
Field Type drop down list.
15.Click the Fit Statistic radio button in the
Insert Value section.
16.Select Adjusted R^2 Value in the drop down
list within the Insert Value section.
17.Click Next to display the Finished page of
the Calculation Wizard dialog box.
18.Click Finish to close the Calculation Wizard
dialog box.
19.Click the Data tab.
20.Click the icon in the Plates table to close
all the other open tables.
21.Select the Plate Format column of the Plates
table and click the Recalculate button.
22.Click the + icon corresponding to any row
of the Plates table to display the Com-
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pounds table, as shown in the following figure:
24.Click the Graph: 4 Parameter Fit tab in the
Concentrations table to display the graph,
as shown in the following figure:
You can view the value of IC50 and
Adjusted R^2 in the Compounds table.
23.Click the + icon corresponding to any row
of the Compounds table to display the Concentrations
table, as shown in the following
figure:
Adding Graph Attachment Fields
To add an attachment field:
1. Click the Definitions tab to display the protocol
definition.
2. Click the 4 Parameter Fit graph template in
the Compounds table to display the graph
template definition, as shown in the following
figure:
3. Click Graph Storage. The Graph Storage
dialog box appears.
4. Select the check box, Store a full-size image
of each graph, with legend and titles.
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5. Select the check box, Store a smaller image
each graph, without legend and titles.
6. Type 100 in both the pixels text boxes
below the check box, Store a smaller image
each graph, without legend and titles.
7. Click OK to close the Graph Storage dialog
box. The graph template definition appears:
3. Select the Plate Format column of the Plates
table and click the Recalculate button to
recalculate data of the Plates table.
4. Click the + icon corresponding to any row
of the Plates table to display the Compounds
table, as shown in the following figure:
You can observe that two new attachment
fields have been automatically added to the
Compounds table.
Viewing Data of Attachment Fields
To view the data contained in the attachment
fields:
1. Click the Data tab to display the protocol
tables.
2. Click the icon in the Plates table to close
all the open tables.
You can view the newly added columns in
the Compounds table.
5. Click Recalculate. Hyperlinks are displayed
in the Graph 4 Parameter Fit and Thumbnail
columns, as shown in the following figure:
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6. Double-click any hyperlink in the Graph: 4
Parameter Fit column. The graph for the
corresponding compound appears:
7. Select any cell in the Thumbnail: 4 Parameter
Fit column and right-click to display a
pop-up menu.
8. Select the Show Pictures menu item to display
the thumbnail graph, as shown in the
following figure:
You can view the graphs stored in the
Thumbnail: 4 Parameter Fit attachment
field.
Adding a Notes Attachment Field
To add a notes field:
1. Click the Definitions tab to display the protocol
definition.
2. Right-click the Plates table to display a
pop-up menu.
3. Select the New Field menu item to display
the definition of the new field.
4. Type Extended Notes in the Field Name text
box.
5. Select Attachment (Database Storage) in the
Field Type drop down list.
6. Click Save Changes to save the changes.
7. Right-click the Plates table to display a
pop-up menu.
8. Select the New Field menu item.
9. Type Raw Data File in the Field Name text
box.
10.Select Attachment (Database Storage) in the
Field Type drop down list.
11.Click Save Changes to save the changes.
Modifying the File Import Template
To modify the file import template:
1. Click the Plate Reader File template in the
File Import Templates folder.
2. Click Edit Template to display the Template
Name page of the File Import Wizard window.
3. Click Next. The File Format Information
page appears.
4. Click Next. The Other Options page appears.
5. Click Next. The Map Fields page appears.
6. Select Upload File in the Raw Data File drop
down list.
7. Click Finish to close the File Import Wizard
window.
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8. Click the Data tab to display the data tables,
as shown in the following figure:
22.Click Load All to display the imported data,
as shown in the following figure:
9. Click the icon in the Plates table.
10.Delete all the rows of the Plates table using
the edit mode.
11.Click Save to save the changes.
12.Click the Actions button in the Plates table
menu bar to display a pop-up menu.
13.Select the Import Data File menu item to display
the Select Template page of the Import
File Wizard dialog box.
14.Click Next. The Select Data File(s) page
appears.
15.Click Browse. The Select File(s) to Import
dialog box appears.
16.Locate the IC50Data.txt file and click OK to
close the Select File(s) to Import dialog box.
17.Click Next to display the Additional Data
page.
18.Type your name in the Scientist field.
19.Type Notebook 1 in the Notebook field.
20.Click Next to display the Import File page.
21.Click Finish. The Data Preview window
appears.
23.Double-click any cell in the Raw Data File
column of the Plates table to display the
raw data file in a new window.
24.Click the + icon in the first row of the Plates
table to display the Compounds table, as
shown in the following figure:
25.Click the + icon in any row of the Compounds
table to display the Concentrations
table, as shown in the following figure:
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26.Click the Graph: 4 Parameter Fit tab in the
Concentrations table to display the graph,
as shown in the following figure:
5. Select the desired field and click the OK
button. The compound list appears in the
Navigator section under the Lists folder.
NOTE: If the list contains the same compound
ID more than once, that compound ID will be
saved only once.
Compound Lists
Compound lists are lists of compounds that can
be used in plate templates.
To create a new compound list:
1. Select the rows in a data table containing
the compound IDs of the compounds that
need to be included in the compound list.
NOTE: A Compound list can be created using
the values of any table field, not necessarily,
Compound ID. Also, it can be created by
passing values from a file.
2. Right-click to display a pop-up menu and
select the Save List menu item.
3. Enter name for the list created.
4. Click OK. The Select Field dialog box
appears.
Manipulating Compound Lists
Manipulating compound lists includes various
actions, such as merging two compound lists,
intersecting a list, and subtracting a list.
To manipulate a compound list:
1. Open a compound list by clicking on it in
the Navigator section.
2. Click on the Actions button and select the
appropriate operation. The following
options are available:
• Merge: Produce a new list by combining
two lists.
• Intersect: Produce a list with only those
compound IDs, which are included in both
the original list and the selected list.
• Subtract: Produce a list with only those
compound IDs, which appear in either the
selected list or the original list, but not in
both.
3. Select a list on which you need to perform
the operation.
4. Click OK. The new list appears.
Reporting
The Reporting feature in BioAssay lets you
create reports by using the data stored in the
protocol data tables. In addition, you can create
custom reports using the data returned by SQL
queries.
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In order to create reports, you need to use
report templates. You can either use the existing
report templates or create a new report
template. After creating a report you can preview
and print it. By previewing your report,
you can ensure that the resultant report is in
accordance with your requirements.
The Reporting feature also lets you select the
printers for printing your report. For example,
you can either select the same printer for printing
all the pages of your report or select different
printers for printing different pages.
Creating Reports
To create reports using the data of a BioAssay
protocol:
1. Open the data view of the protocol.
2. Right-click on any cell to display a pop-up
menu.
3. Select the Create Report menu item. The
Report Templates dialog box appears.
4. Select a report template in the Choose a
report template list box.
NOTE: The Choose a report template list box
displays only those report templates that have
been created earlier. To create a report
template, see “Creating Report Templates” on
page 146.
5. Click Print. The Print Options dialog box
appears.
6. Select the Preview item in the Direct to drop
down list.
7. Click Start. The Preview window appears.
8. Close the window to display the Report
Templates dialog box. Follow steps 9 and
10 if the preview report suits your requirements.
Else, select a different report template
or create a new one.
9. Click Print. The Print Options dialog box
appears.
10.Click Start to print the report.
Creating Report Templates
To create a report template:
1. Click New in the Report Templates dialog
box. The New Template dialog box appears.
2. Enter the name and description of the template
in the Template Name and Description
text boxes.
3. Click Design Template. The Choose report
file dialog box appears.
4. Type a file name in the File name drop
down list and click the Open button. The
Welcome page of the Project Wizard dialog
box appears.
5. Click Next. The next page of the Project
Wizard dialog box appears.
6. Accept the default settings and click Next to
display the next page of the Project Wizard
dialog box.
7. Click Choice if you need to change the
printer settings. After setting the printer
options, click OK.
8. Click Next to display the next page of the
Project Wizard dialog box.
9. Chose whether you need to include page
numbers in your report.
10.Select the options for the title as per your
requirements.
11.Click Done. The Choose Object Type dialog
box appears.
12.Choose the table object and click the OK
button. The Choose Source Table Path dialog
box appears.
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13.Select a protocol table and click the OK button.
The Preselection of fields for a line definition
dialog box appears.
14.Expand the protocol table in the Insertable
fields list box.
15.Select a field and click the right arrow icon
to display it in the Columns list box.
16.Repeat the previous step for each field,
which you need to include in the report.
17.Click OK. The Table Contents dialog box
appears.
18.Click the Header Line tab. The Choose a
Table Line Definition dialog box appears.
19.Click OK to display the Table Contents dialog
box again.
NOTE: You can change the layout of a table
line using the Layout button. You can also
specify conditions for the header line to appear
by using the Appearance Cond button.
20.Click OK. The Design project window
appears.
NOTE: You can put a heading to the report
template in the Design project window.
21.Click the File -> Save menu option in the
menu bar to save the file.
22.Close the window to display the New Template
dialog box again.
NOTE: If your report template contains any
image then you need to import that image by
using the Add button in the Static images
section.
23.Click Save to save the report template and
display it in the Report Templates dialog
box. Now, you can use this report template
to create new reports. For creating new
reports, see “Creating Reports” on page
146.
Editing Report Templates
To edit a report template:
1. Select the report template to be edited in the
Report Templates dialog box.
2. Click Edit to display the Edit Template dialog
box.
3. Edit the template as per your requirements.
4. Click Save to save the changes.
Deleting Report Templates
To delete a report template:
1. Select the report template to be deleted in
the Report Templates dialog box.
2. Click Delete to display a message box,
which asks for your confirmation.
3. Click Yes to delete the selected report template.
Creating Custom Reports
BioAssay lets you create two types of custom
reports: List Style and Label Style. In order to
create a custom report you need to use a report
query and report template.
Creating a Report Query
To create a report query:
1. Select Report > Report Queries from the
menu bar of the BioAssay application. The
Generic Reporting SQL Queries window
appears.
2. Click New. The Create a new Generic
Reporting SQL Query window appears.
3. Enter the query name and description.
4. Enter the SQL query in the SQL text area.
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5. Click Create. The new report query that you
created appears in the Generic Reporting
SQL Queries window.
NOTE: The Edit and Delete buttons in the
Generic Report window allow you to edit and
delete SQL queries, respectively.
6. Click Close.
Creating a List Style Custom Report
To create a List Style custom report:
1. Select Report > Generate > List Style from
the menu bar of the BioAssay application.
The Custom Report window appears.
2. Select a report query.
3. Click the Print/Preview/Export button. The
Generating Report dialog box appears.
4. Select a report template and click Open.
The Print Options dialog box appears.
NOTE: If no report template is available, you
can create it by click the Design button in the
Custom Report window. For more information
about creating report templates, see “Creating
Report Templates” on page 146.
5. Select Preview in the drop down list in the
Export Media section.
6. Click Start to view the report.
Creating a Label Style Custom Report
To create a Label Style custom report:
1. Select Report > Generate > Label Style from
the menu bar of the BioAssay application.
The Custom Report window appears.
2. Perform the step 2 to step 6, as mentioned
in the above procedure for creating List
Style custom reports.
Settings
The Settings folder in the Navigator section of
BioAssay lets you configure the settings
related to the following entities.
• Plate Formats
• Well Formats
• Picklists
• External Picklist
• External Datasource
• Field Dictionary
Editing the settings tables
All the entities in the Settings folder present
the same basic user interface wherein data is
stored in tables. By default, the table of a Settings
folder opens in browse mode. While in
browse mode, you can view the data in the
tables, but can not make any changes. To make
changes to a table, you need to switch to edit
mode. Click the Edit button in the menu bar to
open the table in edit mode. In edit mode, the
Add, Delete, Save, and Cancel buttons are visible.
You need to use these buttons to make
changes in the data contained in the tables.
Adding an Entry
To add an entry to the table of a Settings
folder:
1. Click Add in edit mode. An empty row is
inserted into the table.
2. Enter information in the appropriate columns
of the new row.
3. Click Save.
Deleting an Entry
To delete an entry from the table of a Settings
folder:
1. Open the table in edit mode.
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2. Select the row to be deleted.
3. Click Delete.
4. Click Save.
Canceling/Discarding Changes
If you have made changes to the table of a Settings
folder, but have not saved those changes,
you can discard or cancel the changes. To cancel
the changes, which you made to a table:
1. Click Cancel after making the changes to
the table in edit mode. A warning message
appears.
2. Click Yes.
Plate Setup
Plate Formats
Plate formats are used to define the organization
and general content of wells in a plate. The
following attributes can be defined for a plate
format:
• Name: Specifies the name of the plate format
• Physical Plate Type: Specifies the number of
wells to be included in the plate.
After entering values for the above attributes, it
is necessary to define the general content of
each well. To define the general content of
each well, open a plate format by double-clicking
on it. The plate opens with the number of
wells as specified in the Physical Plate Type
attribute. By default, all wells contain the well
format, Compound. You can change the well
format in edit mode. The various well
format options available, are as follows:
• Compound: Refers to a compound can be
inserted in the well.
• Empty: Refers to the well remains empty.
• Positive Control: Specifies that the well is
reserved for a positive control.
• Negative Control: Specifies that the well is
reserved for a negative control.
More well formats can be defined by you. For
more information about editing the entries in
the plate format tables, see“Editing the settings
tables” on page 148.
To define the general contents of the wells in a
plate format:
1. Double-click the plate format to open it in
browse mode.
2. Switch to edit mode by clicking the Edit
button.
3. Click on a well to display a drop down list
containing options for the well format for
that particular well.
4. Select a well format. The well format of the
cell is updated.
5. Click Save.
Well Formats
Well formats define the general content of a
well. When defining plate formats, the well
formats for each well in the plate are selected
from the available well formats. The well formats
that are available, by default, are as follows:
• Compound: Refers to a compound can be
inserted in the well.
• Empty: Refers to the well remains empty.
• Positive Control: Specifies that the well is
reserved for a positive control.
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• Negative Control: Specifies that the well is
reserved for a negative control.
NOTE: The only well in which a compound
from a database can be inserted, is a well with
the Compound well format.
For more information about editing the entries
in the Well Formats table, see “Editing the settings
tables” on page 148.
Picklist
Picklists allow you to limit the values, which
can be assigned to a field. For example, in Bio-
Assay, a default picklist is Scientist. The Scientists
picklist contains four options, as shown
in the following figure:
6. Click Save.
7. Double-click on the row with the name of
the new picklist. A table defining the
entries in the picklist appears.
8. Click Edit to access the edit mode.
9. Click Add to add a new row to the Picklist
Value table.
10.Enter an entry for the picklist.
11.Click Save.
12.Repeat steps 10-12 until all the entries you
choose to define have been entered.
Using a Picklist
To use a picklist in a protocol's table:
1. Define a table (or choose a defined table).
2. Click a field within the table.
3. Set the field type to Picklist Value.
4. Select a picklist name in the Picklist drop
down list.
5. Click Save.
Defining a Picklist
To define a new picklist:
1. Browse to the Picklist folder in the Navigator
frame.
2. Click on Picklist folder. The items in the
Picklist folder appears in the Content frame
on the right.
3. Click Edit to switch to edit mode.
4. Click Add. An empty row is inserted in the
Picklist Name table.
5. Enter a name for the new picklist in the
empty row.
NOTE: After defining a protocol field as Picklist
Value, if you make changes to the field data
then you will have to click the Recalculate button
twice to update the code for the field. This
is a limitation with the Recalculate button.
External Picklists
External picklists lets you define a picklist by
collecting data from external applications.
After defining an external picklist, you can use
it to assign values to protocol fields, which
have field type set as External Picklist Value.
Defining External Picklists
To define an external picklist:
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1. Expand the Settings folder in the Navigator
frame to display the External Picklists
folder.
2. Right-click on the External Picklists folder
to display a pop-up menu.
3. Select the New External PickList menu item.
The New External Picklist window appears.
4. Enter information in the Name and Description
fields.
5. Select a database type in the Database Type
drop down list.
6. Click the icon corresponding to the Connection
String field. If database type is
selected as Oracle, the following Configure
Connection String window appears:
• If database type is selected as SQL Server,
the following Configure Connection String
window appears:
7. Enter relevant information in the Data
Source, Initial catalog, User Name, and Password
fields.
8. Click OK.
9. Click Test Connection to test the validity of
the connection string.
10.Enter a relevant SQL query in the SQL
field, to fetch data from an external application
or database.
NOTE: The SQL query should be in one of the
two forms: SELECT value FROM table
and SELECT key,
value FROM table
11.Click OK.
Using External Picklists
To use the defined external picklist:
1. Open or create a protocol.
2. Create a field with field type, External Picklist
Value. In the Content frame, the Field
Options section appears.
3. Select the defined external picklist in the
Picklist drop down list.
NOTE: If no external picklists had been
defined then the type of the field will revert back
to Text type because it is the default field type.
4. Click Save Changes to save the changes.
5. Click the Data tab to view the data tables of
the protocol. If the Open Datasource dialog
box appears, click the Retrieve All button.
6. Click Edit to switch to the edit mode of the
protocol data table.
7. Access the column with the field type,
External Picklist Value. When you click on
any row of this column, a drop down list
displays the values returned by the SQL
query defined in the external picklist.
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8. Select the appropriate value in the drop
down list corresponding to each row.
9. Click Save in the menu bar to save the
changes.
Editing External Picklists
To edit an already existing external picklist:
1. Right-click on an external picklist within
the External Picklists folder in the Navigator
frame to display a pop-up menu.
2. Select the Edit External PickList menu item
to display the External Picklist window.
3. Edit the values in the various fields as per
your requirements.
4. Click OK.
Deleting External Picklists
To delete an external picklist:
1. Right-click on an external picklist within
the External Picklists folder in the Navigator
frame to display a pop-up menu.
2. Select the Delete External PickList menu
item to display a message box, which asks
for your confirmation.
3. Click Yes to delete the selected external
picklist.
Field Dictionary
Field dictionary is a collection of pre-defined
fields. The Field Dictionary feature in BioAssay
lets you define and group a number of
desired fields, which you need to include in a
protocol table. After defining and adding a
field to the field dictionary, you can include
that field in any protocol table you want. This
reduces the time and effort required to define
the field each time you create a protocol.
Adding Fields to the Field Dictionary
To add a field to the field dictionary:
1. Expand the Settings folder in the Navigator
frame to display the Field Dictionary folder.
2. Click the Field Dictionary folder. In the Content
frame, the Field Dictionary section
appears.
3. Click Add. The New Field Dictionary Entry
dialog box appears.
4. Enter the name and description of the field
in the corresponding text boxes.
NOTE: BioAssay does not allow you to work
with single character field names that are not
valid ASCII characters (letters and numbers).
For example, you can not use the field names, '
(single quote) and " (double quote). The single,
non-ASCII characters get renamed to S_ and
become useless.
NOTE: BioAssay does allow you to use field
names consisting of a combination of two or
more non-ASCII characters, such as # and %.
However, it is recommended that you use only
valid ASCII characters for field names.
5. Select the appropriate field type in the Field
Type drop down list.
6. Select the desired options in the Field
Options section. For example, if you want
that users must enter some value in the field
then enable the Required Value check box.
NOTE: To specify the maximum value that can
be entered in the defined field, select the
appropriate item in the Lock to Result Column
drop down list and enter the maximum value in
the corresponding text box.
7. Click OK. The newly added field is displayed
in the field dictionary.
Using the Field Dictionary
To add a field to your protocol table by using
the field dictionary:
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1. Open a protocol definition.
2. Right-click on a protocol table to display a
pop-up menu.
3. Select the New Field From Dictionary menu
item. The Choose Field Dictionary Entry
window appears.
4. Select the field, which you need to add to
the selected protocol table.
5. Click OK. The selected field gets added to
the protocol table and the field definition is
displayed on the right side of the Content
frame.
NOTE: When you add a field from a field
dictionary, the attributes of the field get locked.
However, the attributes, which appear within
the Field Options section in the field definition
are editable. Examples of field types whose
attributes appear in the Field Options section
include Picklists, External Picklists, and
Concentration.
6. Click Save Changes in the field definition.
Viewing the Field Dictionary
To view the field dictionary:
1. Select a field in the field dictionary.
2. Click View. The View Field Dictionary Entry
dialog box appears.
3. Click OK.
Removing a Field from the Field Dictionary
To remove a field from the field dictionary:
1. Select the appropriate field in the field dictionary.
2. Click Delete. A message box appears and
asks for your confirmation.
3. Click Yes to remove the field from the field
dictionary.
External Datasource
The External Datasources folder, within the
Settings folder, lets you import data from an
external data source into BioAssay by using
the feature, Structured Data Manager (SDM).
For more information, see “Importing Data
from External Data Source” on page 117.
BioAssay Privileges
BioAssay offers various features related to
protocols and the protocol administrator can
grant different access permissions to different
users. For example, a user may be granted permission
to create reports, but may not be
granted permissions to create external picklists
in a protocol. The access permissions are
granted through the use of pre-defined privileges.
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The following table lists the various privileges,
which can be assigned to a user in BioAssay:
Privileges
Description
Privileges
Description
MANAGE_FIELD
_DICTIONARY
Add/edit/delete field
dictionary entries
CREATE_LIST
Create a Compound List
CREATE_PLATE_
FORMAT
Create a new plate format
MANAGE_PICKL
IST
Add/edit/delete picklists
CREATE_PROTO
COL
DELETE_LIST
Create a new protocol
Delete a compound list
MANAGE_PROT
OCOL_ORGANIZ
ATION
Add/edit/delete folders and
projects in tree
DELETE_PLATE_
FORMAT
DELETE_PROTO
COL
EDIT_PLATE_FO
RMAT
EDIT_WELL_FO
RMAT
Delete a plate format
Delete a protocol
Edit an existing plate
format
Edit an existing well
format
MANAGE_REPO
RT_QUERY
MANAGE_REPO
RT_TEMPLATE
MANAGE_SDM_
DATASOURCE
Create/edit/delete report
queries used in custom
reports
Create/edit/delete report
templates
Create/edit/delete/
configure external data
sources using SDM
GENERATE_CUS
TOM_REPORT
Print a custom report
MOVE_PROTOC
OL
Move a protocol in the tree
GENERATE_PRO
TOCOL_REPORT
Print a protocol report
NOTE: For information about assigning privileges,
see “Managing Users Through BioAssay”
on page 165.
MANAGE_EXTE
RNAL_PICKLIST
Add/edit/delete/configure
external picklists
Actions Menu
The Actions menu in BioAssay provides various
options depending on the table or grid
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eing displayed. The following table lists the
options provided by the Actions menu:
Viewing Options
View Details
View Picklist
View Plate Format
View (from the plate
formats grid)
Viewing Commands
Other Options
Autofit
Change Validity
Coloring Options
Copy
Cut
Hide Invalid Data
Hide Pictures
Import Data
Paste
Recalculate
Save List
Select All
Show Coloring
Show Only Valid
Data
Show Pictures
View Details
The View Details menu item in the Actions
menu can be accessed from any protocol data
table, except from a table found at the bottom
of the table hierarchy. The View Details action
opens the data table holding aggregate data for
the current table. You can also achieve this
result by double-clicking on a row in the current
table. This result makes sense because the
data that makes up a particular row in one table
is formed by the data calculated in the next
lowest table.
View Plate Format
The View Plate Formats action is available
from the Plate Formats folder. This action will
open a table defining the chosen plate format.
To view a plate format:
1. Click the Plate Formats folder in the Navigator
frame to display its content in the
Content frame on the right.
2. Select the plate format whose table you
need to view.
3. Click Actions>View Plate Formats from the
menu bar.
View (from the plate format table)
When accessing a plate format, the View
action helps you to populate the cells in the
plate formats table with the selected data. For
example, selecting Actions -> View ->Well
Formats will populate the cells in the table
with the assigned contents, such as Empty or
Compound.
The following options are available in the
View menu:
•
• Well Format
• Concentration
• Well Name
View Picklist
The View Picklist action is available from the
table containing assay picklist definitions. This
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action will open a table containing the values
available in the currently selected picklist.
To view the values stored in a picklist:
1. Click the Picklists folder in the Navigator
frame to display its content in the Content
frame.
2. Select the row defining the picklist to be
viewed.
3. Select Actions>View Picklist menu item.
AutoFit Off
The following figure shows the display result
when the AutoFit action is inactive:
Other Commands
AutoFit
The AutoFit action is available from any grid
view. If the AutoFit action is active, the grid
will automatically resize to fit in the current
window. If the window is resized, the grid will
resize accordingly.
AutoFit On
The following figure shows the display result
when the AutoFit action is active:
Change Validity
The Change Validity action is available from
any data table. By default, the BioAssay application
assumes that data is not validated. Data
that is not validated is denoted by the letter, N
in the leftmost column of the data table. After
validating some data, it is possible to view only
valid data in the tables. In addition, by using
the Security tab, you can specify that valid data
may not be edited or recalculated.
To change the validity of data in certain rows
in the table:
1. Browse to the table holding the appropriate
data, in the Data tab of a protocol.
2. Select the rows holding the data.
3. Click Actions -> Change Validity from the
menu bar. The Change Validity dialog box
appears.
4. Select the appropriate validity. The validity
options available are as follows:
• Not Validated
• Icon: N
• Description: Specifies that no validation
decision has been made.
• Used in Calculation?: Yes
156 BioAssay Desktop & Workgroup
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• Valid
• Icon: V
• Description: Specifies that data is found
to be valid.
• Used in Calculation?: Yes
• Invalid
• Icon: I
• Description: Specifies data is found to be
invalid. Invalid data is not used in calculations
or curve fits.
• Used in Calculation?: No
• Request Review
• Icon: R
• Description: Specifies that data must be
reviewed before making a validation decision.
• Used in Calculation?: Yes
NOTE: If you are validating data in a summary
table, you can also choose to cascade the
validity change to the summary data by using
the options in the Cascading section.
5. Click OK.
Coloring Options
The coloring options are used to implement
heat maps. The Coloring Options dialog box
lets you select a parameter on which a heat
map will be based and specify the color values
for that parameter. The Coloring Options dialog
box can be accessed using the Actions
menu in a Wells table.
To set coloring options:
1. Browse to a Wells table in the Data tab of a
protocol.
2. Click the Plates tab.
3. Click Actions -> Coloring Options from the
menu bar. The Coloring Options dialog box
appears.
4. Select a parameter on which the heat map
should be based.
5. Enter maximum and minimum values corresponding
to each color.
6. Click OK.
Copy
The Copy action can be used when a table is
accessed in edit mode as well as in browse
mode. This action lets you copy selected information
in a table.
Cut
The Cut action can be used only when a table
is accessed in edit mode. This action lets you
cut selected information in a table.
Import Data
The Import Data action can be performed from
any data table of a protocol by using the File
Import wizard. The wizard assists in importing
data through the use of a defined File Import
Template.
Paste
The Paste action can be used only when a table
is accessed in edit mode. This action lets you
paste the already copied data on a selected area
in a table.
Recalculate
The Recalculate action will run all calculations
defined in the chosen table again. The Recalculate
action is useful when you change a key
piece of data and you are interested to see how
the calculations will be affected by the change.
Save Compound List
The Save Compound List action, available
from a data table or search data table, lets you
save the currently selected rows to a list.
Chem & Bio Office 2010 User Guide 157
BioAssay

Select All
The Select All action lets you select all the
rows in a table. The Select All action is helpful
when you need to apply a similar set of actions
to all the rows in a table.
Show Coloring
This action shows the heat map coloring.
When this action is selected, each cell in the
grid will be filled with a color representing a
value defined in the Coloring Options dialog
box.
Show Only Valid Data
The Show Only Valid Data action will display
validated data in a data table of a protocol.
Prohibited Field Names
The keywords that can not be used as field
names in BioAssay are as follows:
A
• ACCESS
• ACCOUNT
• ACTIVATE
• ADD
• ADMIN
• ADVISE
• AFTER
• ALL
• ALL_ROWS
• ALLOCATE
• ALTER
• ANALYZE
• AND
• ANY
• ARCHIVE
• ARCHIVELOG
• ARRAY
• AS
• ASC
• AT
• AUDIT
• AUTHENTICATED
• AUTHORIZATION
• AUTOEXTEND
• AUTOMATIC
B
• BACKUP
• BECOME
• BEFORE
• BEGIN
• BETWEEN
• BFILE
• BITMAP
• BLOB
• BLOCK
• BODY
• BY
C
• CACHE
• CACHE_INSTANCES
• CANCEL
• CASCADE
• CAST
• CFILE
• CHAINED
• CHANGE
• CHAR
• CHAR_CS
• CHARACTER
158 BioAssay Desktop & Workgroup
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• CHECK
• CHECKPOINT
• CHOOSE
• CHUNK
• CLEAR
• CLOB
• CLONE
• CLOSE
• CLOSE_CACHED_OPEN_CURSORS
• CLUSTER
• COALESCE
• COLUMN
• COLUMNS
• COMMENT
• COMMIT
• COMMITTED
• COMPATIBILITY
• COMPILE
• COMPLETE
• COMPOSITE_LIMIT
• COMPRESS
• COMPUTE
• CONNECT
• CONNECT_TIME
• CONSTRAINT
• CONSTRAINTS
• CONTENTS
• CONTINUE
• CONTROLFILE
• CONVERT
• COST
• CPU_PER_CALL
• CPU_PER_SESSION
• CREATE
• CURRENT
• CURRENT_SCHEMA
• CURRENT_USER
• CURSOR
• CYCLE
D
• DANGLING
• DATABASE
• DATAFILE
• DATAFILES
• DATAOBJNO
• DATE
• DBA
• DBHIGH
• DBLOW
• DBMAC
• DEALLOCATE
• DEBUG
• DEC
• DECIMAL
• DECLARE
• DEFAULT
• DEFERRABLE
• DEFERRED
• DEGREE
• DELETE
• DEREF
• DESC
• DIRECTORY
• DISABLE
• DISCONNECT
• DISMOUNT
• DISTINCT
Chem & Bio Office 2010 User Guide 159
BioAssay

• DISTRIBUTED
• DML
• DOUBLE
• DROP
• DUMP
E
• EACH
• ELSE
• ENABLE
• END
• ENFORCE
• ENTRY
• ESCAPE
• ESTIMATE
• EVENTS
• EXCEPT
• EXCEPTIONS
• EXCHANGE
• EXCLUDING
• EXCLUSIVE
• EXECUTE
• EXISTS
• EXPIRE
• EXPLAIN
• EXTENT
• EXTENTS
• EXTERNALLY
F
• FAILED_LOGIN_ATTEMPTS
• FALSE
• FAST
• FILE
• FIRST_ROWS
• FLAGGER
• FLOAT
• FLOB
• FLUSH
• FOR
• FORCE
• FOREIGN
• FREELIST
• FREELISTS
• FROM
• FULL
• FUNCTION
G
• GLOBAL
• GLOBAL_NAME
• GLOBALLY
• GRANT
• GROUP
• GROUPS
H
• HASH
• HASHKEYS
• HAVING
• HEADER
• HEAP
I
• IDENTIFIED
• IDGENERATORS
• IDLE_TIME
• IF
• IMMEDIATE
• IN
• INCLUDING
160 BioAssay Desktop & Workgroup
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• INCREMENT
• IND_PARTITION
• INDEX
• INDEXED
• INDEXES
• INDICATOR
• INITIAL
• INITIALLY
• INITRANS
• INSERT
• INSTANCE
• INSTANCES
• INSTEAD
• INT
• INTEGER
• INTERMEDIATE
• INTERSECT
• INTO
• IS
• ISOLATION
• ISOLATION_LEVEL
K
• KEEP
• KEY
• KILL
L
• LABEL
• LAYER
• LESS
• LEVEL
• LIBRARY
• LIKE
• LIMIT
• LINK
• LIST
• LOB
• LOCAL
• LOCK
• LOCKED
• LOG
• LOGFILE
• LOGGING
• LOGICAL_READS_PER_CALL
• LOGICAL_READS_PER_SESSION
• LONG
M
• MANAGE
• MASTER
• MAX
• MAXARCHLOGS
• MAXDATAFILES
• MAXEXTENTS
• MAXINSTANCES
• MAXLOGFILES
• MAXLOGHISTORY
• MAXLOGMEMBERS
• MAXSIZE
• MAXTRANS
• MAXVALUE
• MEMBER
• MIN
• MINEXTENTS
• MINIMUM
• MINUS
• MINVALUE
• MLS_LABEL_FORMAT
Chem & Bio Office 2010 User Guide 161
BioAssay

• MLSLABEL
• MODE
• MODIFY
• MOUNT
• MOVE
• MTS_DISPATCHERS
• MULTISET
N
• NATIONAL
• NCHAR
• NCHAR_CS
• NCLOB
• NEEDED
• NESTED
• NETWORK
• NEW
• NEXT
• NOARCHIVELOG
• NOAUDIT
• NOCACHE
• NOCOMPRESS
• NOCYCLE
• NOFORCE
• NOLOGGING
• NOMAXVALUE
• NOMINVALUE
• NONE
• NOORDER
• NOOVERRIDE
• NOPARALLEL
• NORESETLOGS
• NOREVERSE
• NORMAL
• NOSORT
• NOT
• NOTHING
• NOWAIT
• NULL
• NUMBER
• NUMERIC
• NVARCHAR2
O
• OBJECT
• OBJNO
• OBJNO_REUSE
• OF
• OFF
• OFFLINE
• OID
• OIDINDEX
• OLD
• ON
• ONLINE
• ONLY
• OPCODE
• OPEN
• OPTIMAL
• OPTIMIZER_GOAL
• OPTION
• OR
• ORDER
• ORGANIZATION
• OSLABEL
• OVERFLOW
• OWN
162 BioAssay Desktop & Workgroup
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P
• PACKAGE
• PARALLEL
• PARTITION
• PASSWORD
• PASSWORD_GRACE_TIME
• PASSWORD_LIFE_TIME
• PASSWORD_LOCK_TIME
• PASSWORD_REUSE_MAX
• PASSWORD_REUSE_TIME
• PASSWORD_VERIFY_FUNCTION
• PCTFREE
• PCTINCREASE
• PCTTHRESHOLD
• PCTUSED
• PCTVERSION
• PERCENT
• PERMANENT
• PLAN
• PLSQL_DEBUG
• POST_TRANSACTION
• PRECISION
• PRESERVE
• PRIMARY
Q
• QUEUE
• QUOTA
R
• RANGE
• RAW
• RBA
• READ
• READUP
• REAL
• REBUILD
• RECOVER
• RECOVERABLE
• RECOVERY
• REF
• REFERENCES
• REFERENCING
• REFRESH
• RENAME
• REPLACE
• RESET
• RESETLOGS
• RESIZE
• RESOURCE
• RESTRICTED
• RETURN
• RETURNING
• REUSE
• REVERSE
• REVOKE
• ROLE
• ROLES
• ROLLBACK
• ROW
• ROWID
• ROWNUM
• ROWS
• RULE
S
• SAMPLE
• SAVEPOINT
• SB4
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BioAssay

• SCAN_INSTANCES
• SCHEMA
• SCN
• SCOPE
• SD_ALL
• SD_INHIBIT
• SD_SHOW
• SEG_BLOCK
• SEG_FILE
• SEGMENT
• SELECT
• SEQUENCE
• SERIALIZABLE
• SESSION
• SESSION_CACHED_CURSORS
• SESSIONS_PER_USER
• SET
• SHARE
• SHARED
• SHARED_POOL
• SHRINK
• SIZE
• SKIP
• SKIP_UNUSABLE_INDEXES
• SMALLINT
• SNAPSHOT
• SOME
• SORT
• SPECIFICATION
• SPLIT
• SQL_TRACE
• STANDBY
• START
• STATEMENT_ID
• STATISTICS
• STOP
• STORAGE
• STORE
• STRUCTURE
• SUCCESSFUL
• SWITCH
• SYNONYM
• SYS_OP_ENFORCE_NOT_NULL$
• SYS_OP_NTCIMG$
• SYSDATE
• SYSDBA
• SYSOPER
• SYSTEM
T
• TABLE
• TABLES
• TABLESPACE
• TABLESPACE_NO
• TABNO
• TEMPORARY
• THAN
• THE
• THEN
• THREAD
• TIME
• TIMESTAMP
• TO
• TOPLEVEL
• TRACE
• TRACING
• TRANSACTION
• TRANSITIONAL
164 BioAssay Desktop & Workgroup
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• TRIGGER
• TRIGGERS
• TRUE
• TRUNCATE
• TX
• TYPE
U
• UB2
• UBA
• UID
• UNARCHIVED
• UNDO
• UNION
• UNIQUE
• UNLIMITED
• UNLOCK
• UNRECOVERABLE
• UNTIL
• UNUSABLE
• UNUSED
• UPDATABLE
• UPDATE
• USAGE
• USE
• USER
• USING
V
• VALIDATE
• VALIDATION
• VALUE
• VALUES
• VARCHAR
• VARCHAR2
• VARYING
• VIEW
W
• WHEN
• WHENEVER
• WHERE
• WITH
• WITHOUT
• WORK
• WRITE
• WRITEDOWN
• WRITEUP
X
• XID
Security
BioAssay implements two levels of security.
The first level controls access to different parts
of the application, such as plate setup and user
management. The second level is more granular.
It lets you control users' abilities to view
and edit protocol data for each protocol. For
more information about controlling access to
protocol data, see “Defining Security” on page
110.
Managing Users Through
BioAssay
In BioAssay, you can manage users by using
the Security menu item, which is available in
the menu bar of the main window of the application.
The Security menu lets you add,
remove, and update user related information. It
also allows the currently logged-on user to
change his/her login password.
Chem & Bio Office 2010 User Guide 165
BioAssay

Adding Users
To add a user:
1. Log on to the BioAssay application as an
admin user.
2. Click the Security -> Manage Users menu
item in the menu bar. The Manage Users
window appears.
3. Click Add User. The Add User window
appears.
4. Enter relevant information about the user to
be created in the various text boxes.
NOTE: To assign administrative rights to the
user to be created, select the Admin User check
box. An administrator user has full access to
protocol data. However, non-administrator
users have to be assigned appropriate rights to
view and edit data specific to a protocol. For
more information, see “Defining Security” on
page 110.
5. Assign permissions to the user as per your
requirements using the Add and Remove
buttons.
NOTE: For more information about the
available permissions, see“BioAssay
Privileges” on page 153.
6. Click OK. The newly created user will be
added to the Select a User list box in the
Manage Users window.
7. Click Close.
Updating Users
To update user related information:
1. Log on to the BioAssay application as an
admin user.
2. Click the Security -> Manage Users menu
item in the menu bar to display the Manage
Users window.
3. Select a user in the Select a User list box.
4. Click Update User. The Edit User window
appears.
5. Edit the user related information and the
permissions assigned, as per your requirements.
6. Click OK. A success message appears.
7. Click OK. The Manage Users window
appears.
8. Click Close.
Deleting Users
To delete a user:
1. Log on to the BioAssay application as an
admin user.
2. Click the Security -> Manage Users menu
item in the menu bar to display the Manage
Users window.
3. Select a user in the Select a User list box.
4. Click Delete User. A message appears and
asks for your confirmation.
5. Click the Yes button to delete the user. A
success message will be displayed.
6. Click OK. The Manage Users window
appears.
7. Click Close.
Changing Password
To change the password of a user:
1. Log on to the BioAssay application as the
user whose password you need to change.
2. Click the Security -> Change Password
menu item in the menu bar. The Change
Password dialog box appears.
3. Enter the existing password and the new
password in the corresponding fields.
4. Click Save. A success message appears.
5. Click OK.
166 BioAssay Desktop & Workgroup
Chapter

Inventory
Desktop & Workgroup

Inventory Desktop & Workgroup
CS Inventory has long been the preferred tool
for managing chemical inventory.
Inventory is an application designed to manage
the chemical and reagent tracking needs of laboratories
and research centers. The system
manages data associated with both commercially
procured and internally produced chemical
substances from their procurement or initial
production through their depletion and disposal.
To meet the needs of institutions of all sizes,
CS Inventory comes in the following editions:
• Desktop Editions
• CS Inventory Pro
• CS Inventory Ultra
• Workgroup Edition: CS Inventory Workgroup
The advantages of CS Inventory include multiuser
access to data, with the ability to share the
same database across sites on the same network.
The application is designed to prevent
data access conflicts. For example, you can
lock a container for a set period to prevent
other users from editing the same container.
In addition, CS Inventory consists of one
installed database that includes samples. When
you have finished testing, you can delete the
test data and use the database for production.
You may also use CS Inventory as a simple
desktop application, with both the client and
database being installed on a single machine.
CS Inventory Pro . It is a complete desktop
package. It includes Microsoft SQL Express,
which is the redistributable database engine for
SQL Server 2005. No additional licensing is
required. Furthermore, SQL Server Express
has self-tuning capabilities to respond to
changing usage characteristics.
CS Inventory Ultra . It is also a SQL Expressbased
product, but includes a subscription to
the online version of ChemACX. The ChemACX
application is CambridgeSoft’s catalog
of chemical products and suppliers.
CS Inventory Workgroup . It is a thick-client
SQLServer- based product. This application is
suitable for larger organizations that do not
have the ability or do not want to maintain an
Oracle server. CS Inventory Workgroup
requires, but does not include, a SQLServer
license.
What’s new
Inventory Desktop for Chem & Bio Office
2010 introduces a variety of improvements and
new features not found in earlier versions. The
new features in this latest version of CS Inventory
are briefly described below. You can find
more information on these and other features
throughout the manual and online help.
Managing Container Requests. This feature
lets you request for containers, view requested
containers, and approve/reject requested containers.
For more information, see “Request
Container” on page 181, “Approve Request”
on page 182, and “Reject Request” on page
183.
Chem & Bio Office 2010 User Guide 169
Inventory

Using Shopping Cart to Request and Order
for Containers and Substances. This feature
lets you search the ChemACX database, select
compounds from the search result and add
them to shopping cart. Later you can request,
order, and receive the containers/substances
added to the shopping cart. You can also generate
reports and purchase orders. For more
information, see “Placing Request” on page
178, “Placing an Order” on page 178, “Receiving
an Order” on page 179.
Login and Logout
The first screen you see when starting CS
Inventory is a login screen.
Enter your username and password to log into
the application. Usernames are assigned roles,
which are defined by privileges. The specific
tasks that a user with a particular role can perform
is determined by the privileges associated
with the role. “Managing Roles” on page 191
for more details.
To allow administrators to test new roles, CS
Inventory provides the Logout feature. This
feature allows an administrator to log out and
log in again with a different username. The
Logout command is on the File menu. The Log
Out menu item is available in the File menu.
Terminology
The three primary entities in a CS Inventory
system are: Locations, Substances, and Containers.
Location
A CS Inventory location represents a physical
location where one or more containers may be
stored. Locations can be nested within other
locations to produce a hierarchy. The location
hierarchy is represented as nested folders on a
tree control analogous to that found in the
Windows file explorer.
Substance
A CS Inventory substance represents a single
pure chemical entity, which can be expressed
as a two-dimensional chemical structure drawing.
The system maintains its own internal
chemical structure database containing unique
substances that can be associated with CS
Inventory containers. Highly advanced duplicate
checking is incorporated into the system.
Only a single substance may be associated
with each CS Inventory container.
In addition to structure and name, substances
can be identified based on unique registry
numbers, such as CAS and ACX ID. Custom
fields may also be defined.
For information on defining mixtures as substances,
“Mixtures” on page 176.
Container
A CS Inventory container represents a physical
container capable of storing chemical substances.
While a container may physically contain
a complex mixture of chemical substances,
CS Inventory is ideally suited for the assignment
of a single (primary) chemical substance
to each container. Additional text fields are
available to track other chemical contents, such
as the solvent. Typical containers include: bottle,
vial, tube, cylinder, and box.
The User Interface
The basic user interface of CS Inventory application
is divided into three main areas or
frames, which are as follows:
• Location tree
170 Inventory Desktop & Workgroup
Chapter

• Container list
• Substance details
The preceding areas support browsing the
inventory. You can view locations, the containers
present in them, and details of the substances
in the containers, as shown in the
following figure:
In the preceding figure:
1- Location Tree area
2- Container List area
3- Substance Details area
The Location Tree area shows all the locations
in the inventory. It is a collapsible hierarchical
tree structure similar to the Windows Explorer
folders list.
The Container List area displays the containers
in the selected location. Use the scroll bar to
view all the containers in a location.
The Substance Details area is a tabbed frame
that shows the details for the selected container.
By default. the Substance Detail area
contains five tabs, which are as follows:
• Summary
• Substance
• Supplier
• Quantities
• Comments
The preceding tabs are common to all versions
of CS Inventory.
In addition to the preceding tabs, there are tabs
that are unique to a particular CS Inventory
version or the way it is set up. For example, the
Custom tab will appear only if you have
defined custom fields.
Forms
In addition to the basic user interface, CS
Inventory provides a number of forms for creating
and editing locations, containers, and
substances. Also, you can create forms to
search substances and containers. You can perform
the form-specific operations using
menus.
Locations
The New Location form has the following basic
fields in all versions of CS Inventory: Parent
Location, Location, Location Name, Location
Type, Location Owner, Grid Format, and
Description.
The Edit Location form is same as New Location,
but without a Parent Location field. You
can edit the parent location using the Move
Location feature.
The forms related to managing locations are
accessed using the Manage menu.
Containers
New and Edit Container are tabbed forms with
many optional fields defining the container and
the substance in it. The top-most tab contains
the required fields.
The forms related to creating and editing containers
are accessed using the Manage menu.
The Search Container form is accessed from
the Search menu. See “Searching for Containers”
on page 184 for more information.
Chem & Bio Office 2010 User Guide 171
Inventory

Substances
New substances are usually created along with
new containers. For this reason, there is a link
to the New Substance form on the New Container
form. You can also create new substances
using the Manage menu. However,
inserting substances into containers becomes a
separate process when you create substances
using the Manage menu.
There are two options for inserting a substance
into a container: create a new substance, or
import from an existing database, such as ACX
or the existing Inventory database. The following
figure shows the New Container form with
New Substance and Select Substance buttons:
The following figure shows the Select Substance
form:
In the preceding figure:
1- Preferences
2- Select database options
3- Additional fields
Managing Locations
A location is defined as any place that can hold
a container, plate, or another location. This
includes a laboratory, a refrigerator, or even a
particular shelf. Different facilities can decide
the best way to organize locations according to
their needs. CS Inventory comes with five special
locations: Root, Disposed, Missing, On
Order, and Trash Can. You may edit the names
and other data associated with any of these
special locations, but may not delete them.
Privileges associated with managing locations
are: create, edit, delete, and move.
Location Tree
The Location Tree lets you navigate through
the Location hierarchy. Click on the +/- symbols
to expand/contract location folders. Clicking
on a location name displays its contents in
the container list frame. Right-clicking on a
location displays a context menu of Location
commands.
Creating a New Location
To add a new location:
1. Click Manage > New Location. The Create a
New Inventory Location form appears.
NOTE: Plate types are not currently supported
in the Pro/Ultra or Workgroup versions.
2. Enter the parent location (the folder that is
one level up from your new folder). If you
pointed to the parent folder before opening
the dialog box, the correct location will be
entered automatically. You may use the
Browse button for single-click entry of the
correct location.
3. Enter the remaining information. Location
Name is the only required field. CS Inventory
will fill in the Location barcode field
automatically unless you enter your own
172 Inventory Desktop & Workgroup
Chapter

value. In either case, it will assign an internal
location ID number.
4. Click OK. The new location appears in the
Location Tree under the parent location, in
alphabetical order.
Editing a Location
After a location is created, its properties may
change. For example, when a particular laboratory
was initially set up, a number of containers
were placed on a shelf. As the laboratory
grew, it was necessary to move the containers
to a cabinet. The simplest way to reflect this
change in CS Inventory is to change the location
type. Rather than creating a new location,
you can edit the existing location.
To change the properties of a location:
1. Browse to the location to be edited in the
Location Tree.
2. Click Manage > Edit Location. The Edit an
existing Inventory Location form appears.
3. Make sure the information listed in the window
that opens is for the correct location.
4. Enter the desired new information in the
window.
5. Click OK.
Moving a Location
After a location is created, it may be necessary
to move the location to somewhere else in the
tree. For example, a refrigerator may have
been located in a lab on the first floor, but is
being moved to a lab on the third floor. Of
course all the containers inside the refrigerator
are moved along with it. It is easy to move a
location along with all of its contents in the CS
Inventory system.
To move a location:
1. Browse to the location to be moved in the
Location Tree.
2. Click Manage > Move Location. The Move
an Inventory Location form appears.
3. Make sure the information listed in the window
that opens is for the correct location.
Enter the new parent location in the Destination
text box.
4. Click OK. The location and all its sublocations
and containers is moved to the new
parent location.
Deleting a Location
If a location needs to be removed from the
inventory system, you should use the Delete
Location feature. If the location is merely
being moved, see “Moving a Location” on
page 173.
To delete a location:
1. Browse to the location to be deleted in the
Location Tree.
2. Click Manage > Delete Location. The Delete
an Inventory Location form appears.
3. Click OK to delete the location.
NOTE: As a safety precaution, a location can
only be deleted if it is empty. You can override
this precaution by selecting the Recursively
delete related locations and containers check box.
Use this check box with caution. You cannot
undo the deletion of a location.
Refreshing the Location Tree
If CS Inventory is being used by more than one
concurrent user, the Location Tree you see
may not be the latest one. The Refresh command
repopulates the tree with the most recent
available location data and returns it to its fully
contracted position. If, however, you have a
location open when you choose to refresh, that
branch of the tree is not contracted: the location
will remain open for you to work with.
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To refresh the Location Tree, click View >
Refresh.
Reconciling Locations
All inventories must be checked from time to
time, to verify that the database reflects what is
actually on the shelves. The Rectify Contents
feature aids you in performing this task. The
reconcile function is designed to work with a
barcode reader, but may also be done manually.
To reconcile a location:
1. Browse the database to the location to be
reconciled.
2. Click Manage > Rectify Contents, or rightclick
the location in the Location Tree, and
click Rectify Contents. The Reconcile
Location dialog box appears. The lower
section displays the containers that should
be in that location.
3. Scan in barcodes of each container, or type
in the numbers in the Scan Barcodes text
box. Click Scan. Results of the scan are displayed.
There are three possibilities:
• The container ID entered matches the
location list. The container is checked off,
and Number of containers verified text
box increments by one.
• The container ID does not match the location
list. CS Inventory searches for the
location, and displays it in a new window.
The Number of containers misplaced
text box increments by one.
• The container is not found at the location.
In this case, the check box in the Existing
containers window remains unchecked.
4. Click OK. A warning appears asking if you
have scanned all containers found at the
location.
5. Click OK. Missing containers are moved to
the Missing folder. Misplaced containers are
moved to the Reconciled Location folder.
In both cases, the container status is
changed to Moved During Recon.
Managing Substances
Substance records store the chemical structure,
formula, and molecular weight information of
the compounds in your inventory. Each record
is identified with a substance ID number, and
may also contain a CAS number and/or ACX
number for cross-reference purposes. If you
have administrator privileges, you can also add
up to five custom fields, which users can subsequently
populate when defining a new substance.
Privileges associated with managing
substances are: Create, Edit, Delete, Create
MSDS, Delete MSDS.
Each substance has only one record in the database.
If you create a new substance that
matches an existing one in any field (except
supplier) a conflict resolution window appears,
showing you the fields that match (see “Conflict
Resolution” on page 177). To avoid conflicts,
it is a good idea to perform a search
before creating a new substance.
Creating a New Substance
There are three ways to create a new substance,
which are as follows:
• Create directly, from the Manage menu.
• Create a new container, then click the New
Substance link on the New Container form.
• If you are using CS Inventory Ultra or
Workgroup, search ACX for the substance,
then add it to the inventory database.
To create a new substance:
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1. Click Manage > New Substance or click the
New Substance button in the Create a
New Inventory Container window. The
Create/Edit Inventory Substance form
appears.
2. Fill in the fields. Substance Name is the
only required field.
NOTE: Custom fields may also be designated
as required.
3. To add a structure, click in the Structure
field. The structure field box is outlined in
blue, and the ChemDraw toolbar appears.
4. Click OK.
To create a new substance from the ACX database:
1. Search the ACX database. To perform the
search, do one of the following:
• Click Search > Substances.
• Click Select Substance in the Create a
New Inventory Container window.
2. Select the ChemACX option in the Databases
section.
NOTE: For CS Inventory 11 and later, you
must have an Internet connection to search
ChemACX. The ChemACX application, which
is included in CS Inventory Ultra and
Workgroup, is supplied online, rather than on a
DVD. ChemACX is available at the following
site: chemacx-di.cambridgesoft.com.
3. Select the search type, if you are doing a
structure search.
NOTE: The default Substructure is generally
used for this type of search.
4. Enter data in at least one of the fields. Usually
either a name or formula or structure is
used.
5. Click Search.
In a few seconds, you will see the results in
the Search Results form.
NOTE: The search is limited to 50 hits, with a
hint to refine the search input data for better
accuracy.
6. Click the Show Suppliers link to see the
suppliers from the ChemACX list. The supplier
list for that substance appears.
7. Click Insert to add the substance to the
inventory database.
When you create a new substance record, CS
Inventory searches the database for duplicates,
and gives you an opportunity to resolve any
conflicts. The substance will be added automatically
only if there are no conflicts. If a
conflict is found in the database with any field
entry, the Conflict Resolution page appears. See
“Conflict Resolution” on page 177.
Material Safety Data Sheets
When you have created a new substance, you
can link a Material Safety Data Sheet (MSDS)
to the substance.
To attach a MSDS, obtain the CAS number of
the substance and/or catalog number.
1. Click Manage > MSDS > Add. The Add
MSDS dialog box appears.
2. Enter the required information. You may
enter:
• a CAS number
• a CAS number plus supplier
• a CAS number plus supplier and catalog
number
• a supplier and catalog number.
3. Browse to the file containing the MSDS
data.
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4. Select the Add an http link or a link to a file
check box to create a link to the file.
If you do not select the Add an http link or a
link to a file check box, the file will be copied
into the database. This is the safest way
to make sure that the MSDS will be available.
You may also enter a link to a web page or
intranet page by using the link option.
The ability to define MSDS by CAS number,
supplier, and catalog number lets you view different
data sheets from different containers of
the same substance.
To view an MSDS file:
1. Select a container.
1. Click the blue MSDS link on the container
details window. A split screen window
appears, displaying local MSDS files:
NOTE: If there are no local files, a dialog
box appears instead, and prompts you to
search the ChemACX website.
2. Click Search, if you would like to search
for MSDS files in the ChemACX database
as well as view local files.
NOTE: In order to search in ChemACX for
data sheets,
File>Preferences>MSDS>Search ACX
option must be checked.
Using ACX
A subscription to the ChemACX online service
is included with the Ultra and Workgroup versions
of CS Inventory. The default ChemACX
server is
chemacx-di.cambridgesoft.com
If your company has a locally installed ChemACX
database, you can change the default
server in the Application Configuration dialog.
This is accessible from the Setup menu of the
Login screen.
Mixtures
Normally, a Substance is defined as a pure
chemical compound. However, CS Inventory
can be customized to define mixtures. Depending
on the approach that makes the most sense
for your users, you could choose to use either
the custom substance fields or the custom container
fields.
For example, to define solvent mixtures commonly
used in reversed phase chromatography,
in which the solvent mixtures contain various
percentages of methanol, acetonitrile and tetrahydrofuran,
use the custom substance fields.
The Substance name would identify the mixture
(e.g. Name = “HPLC Mixture 10% Methanol”),
and the custom compound fields would
identify the exact composition (e.g. Mixture
Component 1 = “10% methanol”, Mixture
Component 2 = “6% acetonitrile”, Mixture
Component 3 = “4% THF”).
This is not, however, the only way to handle
mixtures. Anything you can draw with the
ChemDraw toolbar can be stored in a structure
field, including reactions and labels. While this
might cause problems when searching, it gives
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you the flexibility to draw multiple structures
and define them as a single substance.
NOTE: The Molecular Weight and Chemical
Formula, which are generated automatically
will be for the total of all structures in the field.
Conflict Resolution
The Conflict Resolution process flags and corrects
duplicates in the system. When creating a
new substance in CS Inventory, the Conflict
Resolution process runs automatically. You
may also search for duplicates at any time.
If a conflict is found, the following page
appears with conflicting field(s) highlighted in
red:
Conflict Resolution - Select
To select one of the existing substances rather
then adding a new substance, click Select. The
Create a New Inventory Container form will
appear with the substance inserted.
Conflict Resolution - Edit
To edit the duplicate substance or an existing
substance:
1. Click Edit for the appropriate substance.
The substance record appears.
2. Edit the appropriate fields.
3. Click OK.
Conflict Resolution - Create Duplicate
To create the duplicate, click Create Duplicate.
You will be allowed to continue creating a new
container with the substance inserted.
Creating a duplicate is not recommended. You
must have appropriate permissions to delete
duplicate substances.
Editing a Substance
To edit a substance:
In the example above, the existing substance
and the new substance share the same Substance
name and structure.
In this case, you have three options:
• Select an existing substance (thus canceling
the new substance).
• Edit the conflicting substance or the existing
substance so there is no longer a conflict.
• Create a duplicate substance and resolve the
conflict later.
1. Click Search > Substances. The Inventory
Manager window appears.
2. Fill in the desired field(s) and click Search.
A hit list of matching substances appears.
3. Select a substance. The substance details
appear in the lower pane.
4. Click Edit. The Create/Edit Inventory Substance
form appears.
5. Make the desired changes, and click
Update.
If a duplicate for any required field is found
in the system, the conflict resolution page
appears. See “Conflict Resolution” on page
177 for more information. If there are no
duplicate fields, CS Inventory saves the
changes to the database.
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Placing Request
The Placing Request 1 feature allows you to
search for substances in ChemACX database
and place requests using shopping cart.
To search for substances and place request:
1. Click Search > Substances. The Inventory
Manager window appears.
2. Click the ChemACX radio button in the
Database section.
3. Enter the search criteria by filling in the
various fields, such as Search Type, Substance,
and Molecular Formula.
4. Click Search to perform the search. The
Search Substance window appears.
5. Expand the desired substance to display the
list of its suppliers and catalogs.
6. Expand the desired supplier name to display
the details of the substance provided
by the supplier.
7. Click Add to Cart under the Action column.
The Shopping Cart section in the
Search Substance window displays the
substance added to the shopping cart.
8. Click the hyperlink under the Required At
column and specify the destination location
of the substance added to the shopping cart.
NOTE: You can select and add multiple
substances to your shopping cart. You will have
to specify the destination location for each
substance.
NOTE: You can remove a substance from the
shopping cart by clicking the corresponding
Remove from Cart button under the Action
column.
9. Click Save Cart to save the list of selected
substances.
Placing an Order
To place an order 2 :
1. Click View > Shopping Carts >
Requested. The Shopping Cart View window
appears and displays a list of substances
added to the shopping cart.
NOTE: The Update button can be used to
update the quantity and date.
2. Expand the substance to be ordered.
3. Click the Approve checkbox corresponding
to the selected substance. The Approve
Request button is enabled.
NOTE: The Approve check box is visible to you
only if you have INV_MANAGE_REQUEST
privilege.
1. The Placing Request feature is available
only in Inventory Desktop 12.0.
2. The Placing Order feature is available only
in Inventory Desktop 12.0.
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4. Click Approve Request. A message box
appears and confirms the approval.
NOTE: The Approve Request button is visible
to you only if you have
INV_MANAGE_REQUEST privilege.
5. Click Yes to approve the request and order
the substance.
NOTE: You can generate a Purchase Order
(PO) for the ordered substance by clicking the
Generate P.O. menu in the Shopping Cart View
window. The process of generating PO is similar
to the process of generating reports. For
more information, see “Printing Labels and
Reports” on page 186.
Receiving an Order
To receive 1 an order:
1. Click View > Shopping Carts > Ordered.
The Shopping Cart View window appears
and displays a list of shopping carts.
2. Expand the shopping cart that contains the
substance to be received.
3. Click the Mark Received hyperlink corresponding
to the selected substance. The
substance is received. You can view the
received substance by clicking View >
Shopping Carts > Received.
Managing Containers
1. The Receiving Order feature is available
only in Inventory Desktop 12.0.
Containers are the main focus of CS Inventory.
You track your use of chemicals, ordering,
reordering, and disposal by tracking the containers.
Privileges associated with managing
containers are:
• Create
• Edit
• Checkin
• Change status
• Print container label
• Delete
• Move
• Checkout
• Change quantity
• Request container
• Add to cart
Creating a New Container
To create a new container:
1. Click Manage > New Container. A window
appears with the following tabs: Required,
Substance, Supplier, Contents, Optional,
Owner, and Comments.
2. Enter information about the new container.
Required fields are highlighted with color.
NOTE: Substance is not a required field. This
lets you enter supplies such as glassware or
disposables into the inventory. If you don’t enter
a substance, you will get a warning when you
try to create the new container. You may safely
click OK and ignore the warning. If you don’t
want to see the warning, create a dummy
Substance (such as a letter or word) for nonchemical
supplies.
3. Click OK.
Editing a Container
To edit a container:
1. Select a container to edit.
2. Click Manage > Edit Container. The Edit an
existing Inventory Container form appears.
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3. Enter new values and click OK.
Moving a Container
To move a container to another location:
1. Select a container to move.
2. Click Manage > Move Container.
3. Enter the destination location in the Move
an Inventory Container form and click
OK.
NOTE: Right-click on a container icon to get a
context menu of Container commands. You can
also drag-and-drop containers to move them
from location to location.You may select multiple
containers to move simultaneously. See
“Multi Select” on page 182 for details.
Deleting Containers
To delete a container, drag or move it to the
Trash Can. To remove containers completely
from the database, click Manage > Empty Trash
Can.
Check-in/out, Changing Quantities, and
Other Shortcuts
CS Inventory offers several shortcuts for the
most common operations. For example, you
can check-in and check-out chemicals of a central
storeroom, and update quantities when
compounds are used up.
Check-In/Check-Out Containers
Containers can be checked in and out of locations.
If you routinely work at a specific location,
you can set a default Destination Location
by clicking File > Preferences > Default Checkout
Location.
If you do not set a checkout location preference,
the default will be “Root”. Since Root
can hold only locations, not containers, you
will need to change the Destination Location
every time you check out a container. Failure
to do this will result in an error message, which
reminds you to change the location.
To check out a container:
1. Select a container.
2. Click Manage > Check Out Container. The
Check out an Inventory Container window
appears
NOTE: You can also right-click on the
container and use the context menu.
3. Review the default settings; change as
required
4. Click OK. The container is removed to the
selected location, and its status is reset.
NOTE: The default status is “in use”, the
default user is the one checking the container
out.
Checking a container back in follows a similar
process. By default, the container status in the
Check in an Inventory Container window is set
to “Available” and the container is returned to
the location from which it was checked out.
The default current user does not revert to the
previous user.
Duplicate Container
The Duplicate Container item in the Manage
menu lets you duplicate an existing container.
The duplicate contains an exact copy of all
fields, except the Quantity Remaining field,
which defaults to the container size, Container
ID, and Barcode fields. The Duplicate Con-
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tainer feature is useful when restocking chemicals
from the same supplier.
NOTE: All the new Manage menu items are
also available on the context menu displayed
when you right-click in the Container Grid.
Change Quantity
To change the amount of material left in a container:
1. Select a container.
2. Click Manage > Change Quantity. A window
appears where you can enter either the
amount remaining or the amount used.
3. Click OK. The quantity field in the container
is updated.
Change Status
To change the status of a selected container,
click the Change Container Status menu item in
the Manage menu and select a status from the
Change Container drop-down list.
There are 23 pre-defined status types including
backordered and requested. The list may be
edited from the Data > Edit submenu.
Status is displayed in the container details, and
can also be changed from the Edit Container
dialog box.
You may search containers on the basis of status
by selecting Container Status on the
Advanced Search tab of the Search Inventory
window.
Request Container
The Request Container 1 feature lets you place
a request for a container, and specify the location
where it needs to be delivered.
To request a container:
1. Navigate to the location containing the
desired container.
2. Select the location to view the list of existing
containers.
3. Select the container, which is to be
requested. The details of the container are
displayed in the Substance Details frame.
4. Right-click on the container id of the
selected container and select Request. The
Add Request dialog box appears.
5. Select the destination location in the location
tree. The requested container will be
delivered to the selected location.
6. Specify the amount of substance required,
in the Quantity text box.
7. Click OK. A success message appears and
confirms that the request has been placed.
1. The Request Container feature is available
only in Inventory Desktop 12.0.
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Add to Cart
To add a container to the shopping cart:
1. Navigate to the location containing the
desired container.
2. Select the location to view the list of existing
containers.
3. Select the container, which is to be added to
the shopping cart. The details of the container
are displayed in the Substance
Details frame.
4. Right-click on the container id of the
selected container and select Request
Duplicate Container (Add to Cart). The
Add To Cart dialog box appears.
5. Click Browse to identify and specify the
destination location.
6. Specify the quantity of substance required,
in the Quantity text box.
7. Click Add to add the container to the shopping
cart. You can order for the containers
added to the cart. For more information, see
“Placing an Order” on page 178.
Multi Select
The Multi-Select Containers menu item places a
check box next to each Container ID in the
container list. This lets you select more than
one container and perform one action on all
those containers at once. The actions that can
be performed on multi-selected containers are:
• Move
• Delete
To enable multi-select:
1. Click View > Multi-Select Containers. A
check appears next to the option, and a row
of check boxes appears in the Container
Grid.
2. Select the containers, then right-click in the
Container Grid. From the context menu,
select Move Selected Containers or Delete
Selected Containers. If you select Move
Selected Containers, a browse window
opens to help you navigate to the new location.
If you select Delete Selected Containers,
a message box appears and prompts
you to confirm the deletion operation.
Approve Request
To approve 1 a request:
1. Click View > Request > Requested. The
Shopping Cart View window appears.
2. Select the Select Request checkbox corresponding
to the request to be approved.
3. Select the Approve checkbox corresponding
to the selected request. The Approve
Request button is enabled.
NOTE: The Approve check box and Approve
Request button are visible to you only if you
have INV_MANAGE_REQUEST privilege.
4. Click Approve Request to approve the
request and deliver the requested container
to its destination.
NOTE: You can view the list of received containers
by clicking View > Request > Received.
NOTE: You can also generate a report based
on the received containers. To generate a
report, click the Generate Report tab to display
the Inventory Report window. For more information,
see “Printing Labels and Reports” on
page 186.
1. The Approve Request feature is available
only in Inventory Desktop 12.0.
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Reject Request
To reject 1 a request:
1. Click View > Request > Requested. The
Shopping Cart View window appears.
2. Select the Select Request checkbox corresponding
to the request to be rejected.
3. Select the Reject checkbox corresponding
to the selected request. The Reject Request
button is enabled.
4. Click the Reject Request button. A message
box appears to confirm whether the
request needs to be rejected.
5. Click the Yes button to reject the request.
The rejected request disappears from the
Shopping Cart View window.
Managing EHS Data
CS Inventory has forms for attaching Environmental
Health and Safety (EHS) data to Substances
and Containers. Privileges associated
with managing EHS Data are:
• Edit EHS Data
• Edit SQL Report
The Edit EHS Data privilege is required for both
creating and editing forms.
EHS data has two levels: Substance and Container.
You begin by creating substance-level
data. You may then modify it at the container
level to allow for differences due to different
suppliers or product IDs.
To create EHS data:
1. Click Search > Substances, or on the main
page, browse to a container of a substance
for which you want to create EHS data.
1. The Reject Request feature is available only
in Inventory Desktop 12.0.
2. Click the EHS tab on the Container Details
form. The EHS tab appears.
3. Click the Add Substance EH&S link. The
Add EH&S Data window appears.
4. Enter the EHS data. Observe that the only
required fields are automatically filled in.
NOTE: The names of the three EHS groups can
be modified on the EHS tab of the Custom
Fields preferences. You can also add up to ten
Custom Fields.
To modify EHS data in a container, click the
Edit EH&S link in the EHS tab of the container
details form.
The EHS tab has a Help link that brings up a
document explaining the EHS categories. The
default glossary is a Word document with UN
Numbers, NFPA categories, and ACGIH carcinogens.
You can edit this document, or
replace it.
To replace the EHS glossary:
1. Click Data > Update > EHS Glossary Doc.
The Update EH&S Glossary Document
window appears.
2. Enter the file path in the File text box or
click Browse to locate the file.
3. Click Add.
NOTE: If you do not select the link check box,
the file will be added to the inventory database.
Enter data in the EHS data form. If you have
entered data for the supplier and catalog number,
the edited EHS data will apply to every
container pertaining to the supplier and catalog
number.
The supplier information will appear at the top
of the form if you have entered it. If you have
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not entered supplier information, your modifications
apply to the container you are modifying.
To edit the EHS queries:
1. Click SQL > Edit EHS Report SQL. The EHS
Reporting SQL Queries window appears.
2. Select the report to edit in the Query Name
drop-down list.
3. Click Edit. A duplicate window opens with
an editable copy of the SQL query.
4. Make changes and click Update.
Searching CS Inventory
Searching is the easiest way to find the
required substances or containers in CS Inventory.
The system allows for combined chemical
and text searches of all attributes associated
with a container or substance. Several search
forms are available to accommodate the search
preferences of different users. For example, the
Substructure Search form is particularly well
suited for use by chemists because it allows
searches based on chemical structure, substance
name, CAS number and other attributes.
Searching for Containers
To begin a search:
1. Click Search > Containers. A tabbed search
form appears.
2. Click on the tab indicating the type of
search you would like to perform, and enter
your search parameters.
Simple Search
The Simple Search tab lets you use any combination
of basic criteria, such as CAS Registry
number, Container Barcode, Location Barcode,
Catalog Number, Substance Name, Substance
Synonym, Container Name, Container
Comments, and/or Location ID.
To perform a simple search:
1. Enter the search criteria.
• Select the Search Sublocations check box
to search all sublocations of the chosen
location.
• Select the Multiple Barcode Search check
box if you are looking for more than one
container. A text window opens to allow
barcode entry.
2. Click Search.
NOTE: CS Inventory always does “substring”
searches on text queries. Thus, entering benz in
Substance Name will return Benzene, Benzyne,
Bromobenzene, and so forth.
A list of containers matching your search
parameters is returned. Clicking one of the
containers will allow you to view the location
of the container in the left frame, container
information in the upper right frame, and the
contents of the container in the lower right
frame. The following figure shows a search
result:
:
184 Inventory Desktop & Workgroup
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Advanced Search
The Advanced Search tab adds a number of
categories to the basic Simple Search, such as
Purity, Concentration, Grade, Container Size,
Container Status, Unit of Measure, and Quantity
Remaining.
This search concentrates more on container
properties as opposed to substance properties.
To perform an advanced search:
1. Enter the search criteria.
Custom fields, if defined, will appear on
this search form. Any additional fields have
been defined for your site. Please contact
you system administrator for more details.
2. Select the Search Sublocations check box,
to search all sublocations of the chosen
location.
3. Click Search.
A list of containers matching your search
parameters is returned. Clicking on one of the
containers will allow you to view, the location
of the container, container information, and the
contents of the container. See “Managing Containers”
on page 179 for more information.
Substructure Search
The Substructure Search tab includes most of
the criteria in the Advanced Search, in addition
to Substance Name, Molecular Formula, Mol-
Weight Range, and Substructure.
To draw a structure, double-click in the structure
box. Use the ChemDraw toolbar to draw
your substructure. For more information about
using the ChemDraw toolbar, see “Drawing
Chemical Structures” in the ChemDraw User
Guide.
You may include generic atom types, such as
“X” for any halogen, or “R” for an unspecified
organic group, in your query structure. In fact,
you can include any query specifications
(except those specific to reactions) available in
ChemDraw. For more information, see “Drawing
Query Structures” in the ChemDraw user
guide.
You can specify how CS Inventory will match
the structure you draw to the structures in the
CS Inventory database, by selecting the correct
type from the Search Type drop-down list.
Substructure
Substructure searches find structures that contain
the query, plus any additional attachments
at the open positions. Use this search type to
find classes of compounds.
Exact
Exact searches find structures that completely
match the query. You may get more than one
hit if there are stereo-isomers in the inventory
and you did not specify a particular one to be
matched, or if you included a generic atom
type.
Identity
The Identity search type is intended for use in
compound registration, when you must know if
a perfectly identical copy of your query compound
is already present in the database. It is
similar to an exact search, except that generic
atom and bond types in the query must match
corresponding atom and bond types in the target
exactly. Moreover, stereochemistry must
match precisely between query and target.
Similarity
A Similarity search finds structures that have
structural features, which are similar to the
structural features specified in the query. Similarity
searches are, by their nature, “fuzzy”.
For this reason, similarity searches are useful if
you have a general idea of the types of compounds
you are looking for, but do not have a
precise conception of the target compound.
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Search Preferences
You can set a number of defaults values that
will make CS Inventory perform structure
searches according to your preferences. To set
search preferences, click File > Preferences or
Preferences> Structure Search on the Search
form.
For information about Searching for substances
and their properties, “Searching for
Substances” on page 186.
Searching for Substances
Searching for substances is the same as the
Substructure search option for containers,
except that you begin from a different window,
and fewer fields are displayed. Perform a substance
search to edit a substance record or
search for duplicates.
To search for substances:
1. Select Search > Substances menu item.
The Inventory Manager window appears.
NOTE: Your form may not have the same number
of fields, depending on whether or not custom
fields have been created.
2. Enter search criteria and click Search. A hit
list appears.
If you are searching for duplicate substances,
select the check box at the top of
the form. CS Inventory will search for
duplicates according to the fields you enter.
For more information on resolving duplicates,
see “Conflict Resolution” on page
177.
3. Select a substance from the hit list. A
details frame opens in the lower pane.
4. Click Edit to edit the substance details. For
more information, see “Editing a Substance”
on page 177.
5. Click OK.
NOTE: Right-click on a substance icon to
delete a substance or locate its containers.
Printing Labels and
Reports
CS Inventory Pro/Ultra/Workgroup uses the
List & Label reporting utility from Combit
GmbH. Detailed information on creating customized
reports can be found in List & Label’s
Help, available from the CS Inventory Report
dialog box. This document describes how to
use the built-in templates to produce basic
reports and barcode labels, as well as how to
design more advanced reports.
The CS Inventory Report dialog box is used
for printing both labels and reports. Several
sample label/report templates are provided, or
you can design your own. You can sort the
generated reports by up to three fields (see figure
below). More complex reporting, such as
EHS reports, can be produced by defining custom
SQL queries. Once a user with SQL privi-
186 Inventory Desktop & Workgroup
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leges defines a custom SQL query, it can be
used by other users.
:
4. Select a label template and click Open. The
Print Options dialog box appears.
NOTE: If you click Open without selecting a file, you
will activate the template Wizard to help you design a
new template.
NOTE: In the Reporting tab of the Application
Configuration dialog box, you can set the
default format for Help to either PDF or
MSWord doc.
Privileges associated with managing printing
are: Print report and Print container label. You
can print labels and barcodes to almost any
printer as long as you have the printer driver
installed.
Labels
The standard CS Inventory installation
includes the following sample templates:
• Eight barcode label
• Four standard label
• Four EHS-data label.
You may also design your own labels.
To print labels with a standard template:
1. Select a location.
2. Click Report > Labels. The Inventory
Report window appears, with Label
selected as the Report Type.
3. Click the Print/Preview/Export button. The
Generating Labels dialog box appears.
5. Use the Direct to drop-down list to select
Preview mode, or to send the output to a
file instead of printing.
6. Click Start. Labels are printed for all the
containers in the selected location.
NOTE: The Start Position option allows you
utilize partially used label sheets by adjusting
the start position.
To print a label for a single container:
1. Select a container, either by browsing or
searching.
2. Click the Print Label link on the Summary
tab of the Substance Details section.
The Inventory Report window appears,
with Label selected as the Report Type. Proceed
in the similar way with multiple
labels. The only difference is that the data
for a single label only has been passed to
the print utility.
To skip the Inventory Report window and
its associated tasks:
a. Define a template DefaultLabel.lbl at
the following location: C:\Documents
and Settings\All Users\Application
Data\CambridgeSoft\Inventory12\Print.
NOTE: In Windows Vista, the location is:
C:\ProgramData\CambridgeSoft\Inventory12\
Print.
NOTE: If the Print folder is not there at the
above mentioned location, you need to create it.
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. Click the Print Label link, on the Summary
tab of the Substance Details section
or on the Search Containers result
form.
OR
Select the Print barcodes immediately
check box on the New Container form.
To create a new label template:
1. Select a location.
2. Click Report > Labels.
NOTE: If there are no containers in the
location you have selected, you will get an error
message.
3. Click Design in the Inventory Report window.
The Labels dialog box appears.
4. Enter a new file name in the File name text
box of the Labels dialog box and click
Open. A wizard appears to walk you
through the new label creation process.
8. Adjust the label components to fit the new
label size as necessary, then close and save
the changes to the label file.
NOTE: You may test the positioning of the
printed labels by printing a sample page and
adjusting the dimensions in the designer.
EHS Labels
You can produce EHS labels for one or more
containers.
1. Select a location or a container.
3. Select the appropriate label option from the
Report > EHS sub-menu, as shown in the
following figure.
:
To change the label style:
1. Select a location.
2. Click Report > Labels.
3. Click Design on the Inventory Report window.
4. Select an existing label template and click
Open. A wizard appears.
5. Click Project > Page Setup. The Layout
dialog box appears.
6. Click the Templates tab.
7. Locate your label style and double-click to
select it, then click OK.
:
On selecting a label, the Inventory Report
dialog box appears.
4. Use one of the sample queries provided, or
a custom query created in-house.
5. Click the Print/Preview/Export button. The
Generating Labels dialog box opens
wherein you can select the report template.
188 Inventory Desktop & Workgroup
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6. Select the file GenericEHSQuery.lbl, or
create your own custom template.
7. Click Open. The Print Options dialog box
appears.
8. Select your print options and click Start.
:
NOTE: You can preview the labels by selecting
Preview in the Direct to drop-down list. If you
are printing a large number of labels, Preview
may take several seconds to produce results.
Printing reports is similar to printing labels. You
need to select a location, select the style of
report to print from the Report menu, and step
through the dialog boxes. As with printing
labels, you can design your own template
rather than selecting one of the existing ones.
NOTE: The Print Preview option in the Print
Options dialog box lets you print, save to file,
or send an email of the report in PDF, text, or
graphic format.
Reports
CS Inventory can print reports in two basic
styles: with structures and without. When you
choose Location Report (include structures), CS
Inventory creates graphic files (*.emf) from
the structural data to import to the print utility.
This can be a time-consuming process, especially
for a large inventory. You should consider
the time factor when deciding which
report command to use.
NOTE: The names of all the available report
templates appear when you select either report
type. If you select a template with structures,
but are using the command that does not save
images of the structures, the Structure column
of the report will be blank.
CS Inventory includes many sample report
forms, including EHS report templates. When
selecting a report template based on a userdefined
SQL query (whether for design or
printing) such as the EHS templates, you must
choose one that matches the defined query. If
the fields in the report template do not match
the fields in the selected SQL query, you will
get an error message.
EHS Reports
EHS reports are produced in a similar manner
to EHS labels.
NOTE: You must select a query that matches
the report you wish to produce. If you do not,
you will get an error message.
A typical report for total quantities of EHS
materials would be done as follows:
1. Select a location. Select Root, if you want
the report to be for the entire database.
2. Select the appropriate report option from
the Report > EHS sub-menu. You can get a
report broken down by location and sublocation
if you wish. The Inventory
Report dialog box appears.
Chem & Bio Office 2010 User Guide 189
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3. Select the default query from the dropdown
menu, or create your own custom
query.
4. Click the Print/Preview/Export button. A
dialog opens to select the report template.
5. Select a sample file or a customized template.
6. Click Open. The Print Options dialog box
appears.
7. Select the desired print options and click
Start. The generated report appears:
:
• Edit SQL report
• View Audit Trail
• Delete container
• Move container
• Change container quantity
• Checkout container
• Delete location
• Move location
• Delete substance
• Edit EHS data
• Delete MSDS
• Print reports
NOTE: If you do not have access to something
you need access to, please contact your system
administrator.
CS Inventory Tasks
The following tasks may be performed by
users who have been assigned the appropriate
privileges:
• Search (Browse)
• Create container
• Edit container
• Change container status
• Checkin container
• Create location
• Edit location
• Create substance
• Edit substance
• Create MSDS
• Print labels
The tasks specifically limited to the CS Inventory
Administrator are:
• Manage Users
• Lock/unlock records
• Backup the database
• Manage Roles
• Define custom fields
Managing Users and Roles
CS Inventory applies the concept of security
levels based on Roles. Roles are lists of privileges
that determine what a user can and cannot
do in the database. When you create a new
user, you must assign the user to at least one
Role. The predefined roles in CS Inventory
are:
• Inv_Admin
• Inv_Browser
190 Inventory Desktop & Workgroup
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• Inv_Chemist
The Inv_Admin role cannot be deleted, though
it can be modified. Other roles and users may
be added, modified, or deleted only by the
database owner, invadmin. Users can change
only their own passwords.
NOTE: There is a difference between the role
“Inv_Admin” and the user with the name
“invadmin”. User “invadmin” is the database
owner, and has security permissions in CS
Inventory database. Users with the
“Inv_Admin” role can make changes in the CS
Inventory database, but cannot administer
users and roles.
Managing Roles
To create or edit a Role:
1. Click Security > Manage Roles. The Manage
Roles window appears.
2. Click the appropriate button at the bottom
of the Manage Roles window. The following
table describes the buttons:
Button
Close
Add Role
Update
Role
Users
Function
Closes the dialog box.
Creates a new role.
Edits the selected role.
Adds users to the selected
role. Used to populate new
roles or change user assignments
to existing roles.
Button
Roles
Delete
Function
Assigns all the privileges of
one or more roles to the
selected role in a single step.
This nesting capability gives
you a consistent way of
assigning hierarchies of privileges.
Deletes the selected role.
When you add or edit a role, you work with the
same dialog box. The only difference is that
you have to type in a role name when adding a
new role. When editing, the name is grayed
out, and cannot be changed.
Check the privileges that will define the role.
NOTE: The INV_BROWSE_ALL privilege is, by
default, assigned to all roles. It cannot be
unchecked.
To nest roles within other roles:
1. Click Security > Manage Roles.
2. Select a role, and click Roles on the Manage
Roles dialog box.
3. Select a role, and add or remove it with the
Add or Remove buttons.
The role named in the Role Name text box
includes all the privileges of those roles that
appear in the Current Roles list.
NOTE: If you inspect the privileges list for that
role, you will not see additional boxes checked.
The checked privileges are only those that have
been assigned directly.
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To assign users to a role:
1. Click Manage Roles on the Security menu.
2. Select a role and click Users on the Manage
Roles window.
3. Select users, and add or remove them from
the role.
Managing Users
To create, modify, or delete a user account:
1. Click Manage Users on the Security menu.
The Manage Users window appears.
NOTE: These Security menu items only appear
when you log in as the database owner
(invadmin).
2. Click the appropriate button at the bottom
of the Manage Users window.
When adding or modifying users, the Edit
User window appears. When modifying a
user, the Username and Password text
boxes are grayed out and cannot be
changed.
NOTE: Normally, users maintain their own
passwords. Thus, the Password text box is
blocked from editing to prevent accidental
changes. You can, however, override this by
checking the Change Password check box.
3. Enter appropriate data in the text boxes.
User Name and Last Name are the only
required fields. Blank passwords are
acceptable.
There is no specific requirement for a user
name or last name, but the text boxes cannot
be left blank. Any alphanumeric or
symbol may be used. A user name, once
created, cannot be modified. To change a
user name, you must delete the user and
create a new name.
NOTE: Deleting a user name in CS Inventory
does not delete the corresponding SQLServer
‘login’.
4. Add or remove user roles by selecting a
role and clicking the Add or Remove buttons.
Every user must have at least one role
assigned.
Managing Tables
Some fields in CS Inventory forms are entered
from drop-down menus rather than by typing
in text. CS Inventory stores these pre-set field
entries in tables that can be edited by an
administrator. If, for example, you want to
specify a type of container that is not on the
container type menu, the new type can be
added. You can also delete items from the
tables, provided they are not being referenced
by any records in the CS Inventory database.
To edit a table:
1. Select the table to edit from the Data menu.
2. Fill in the attributes in the form that
appears, and click OK. CS Inventory stores
the changes to the table.
To edit or delete a table entry:
1. Click Data > Edit, and select the table to
edit. The table is displayed.
2. Do one of the following:
• Edit the text as required.
• Select the entire row you wish to delete,
and press the Delete key.
3. Click Save. CS Inventory stores the
changes to the table.
192 Inventory Desktop & Workgroup
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Suppliers
The default supplier list has over 300 entries.
To make it easier to find the correct supplier
from the list, an administrator can not only add
new suppliers, but can abbreviate the displayed
list.
To abbreviate the supplier list:
1. Click Data > Abbreviate > Supplier List. The
Abbreviate Supplier List window appears.
2. Deselect suppliers that will not be used in
the Show column.
NOTE: The deselected suppliers are not
removed from the database. They are merely not
displayed. They can be restored at any time by
reselecting them on the list.
3. Click Save Changes when you have completed
the edit.
Custom Fields
If you have CS Inventory administrative privileges,
that is, if you are logged in as invadmin,
you can add custom fields to compound, container,
and EHS records. Compounds can have
up to five custom fields. Containers can have
up to ten custom fields and five custom dates.
You may also add up to ten custom fields for
EHS data. Custom fields and dates can be designated
as required fields. Custom compound
fields can be marked for duplicate checking.
To add custom fields:
1. Click File > Preferences > Custom Fields.
The Define Custom Fields window
appears.
The Custom Fields dialog box has three
tabs: Compounds, Containers, and EHS.
2. Click the appropriate tab, and enter the
name of the new field(s).
The fields will appear on the blank forms
when you open them.
NOTE: The custom fields appear directly on
the Compound form. For containers, they
appear on the tab labeled “Custom”, and when
applicable, on the tab labeled “Substance”.
When browsing containers, the first custom
field defined is displayed on the “Summary”
tab.
Record Locking
Administrators can turn record locking on or
off. When record locking is turned on (the
default), a record (that is, a container or a substance
that’s being edited) can only be
accessed by one user at a time. An administrator
can unlock records to allow immediate concurrent
access. When records are locked, a
second user attempting to edit an open record
will receive a notification message that the
record is currently open, and cannot be
accessed.
If a user leaves a record open, but inactive, for
more than 10 minutes, the lock times-out, and
other users can access the record. When the
original user returns to the record, a message is
displayed warning the user to resave any
changes.
Managing the Container list
display
You can adjust the display of fields in the Container
list. Changes will be viewed by all users.
Click File > Preferences > Container Grid Display.
The Container Grid Display Preferences
window appears.
You can change the Field Name, Column
Order, and Column Width. You can also select
which fields will be displayed. Clicking the
name of a column in the grid form sorts the
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entries by that column. This is to facilitate
rapid editing; it does not affect the display.
The following table lists the default names of
custom fields in the Grid Display form:
Custom Field
Container Fields
Container Dates
Substance Fields
Field_1 etc.
Date_1 etc.
Field Name
ALT_ID_1 etc.
Backup/Restore Database
CS Inventory includes a backup/restore utility
for your database. The utility requires you to
quit the application in order to run.
To backup a database:
1. Click Data > Backup/Restore DB. A message
appears and shows that you need to
quit the CS Inventory application to continue.
2. Click Yes to continue. The application quits
and a Backup/Restore Inventory Database
window appears.
3. Click Connect to connect the utility to
SQLServer. A message appears at the bottom
of the window, recommending that you
back up both the CS Inventory
(CHEMINVDB2) and CSSecurity databases.
4. Type in the path, or browse to the location
of the backup CS Inventory database file.
The default location is C:\Documents and
Settings\All Users\Application
Data\CambridgeSoft\Backup\CHEMINVD
B2.bak.
5. Browse to the location of the MstFiles
Backup Folder. The default location is in
the C:\Documents and Settings\All
Users\Application
Data\CambridgeSoft\Backup\Mstfiles.
Type in the path, or browse to the location
of the CSSecurity DB Backup File. The
default location is in the C:\Documents and
Settings\All Users\Application
Data\CambridgeSoft\Backup\ folder.
6. If you check the Append timestamp... check
box, you will create a new backup DB file
with the date and time in the file name. If
you deselect the check box, the backup process
will append data to the existing backup
database file, if there is one.
7. Click Backup. After a brief delay, a message
appears and shows that the backup
process was successful.
To restore a backed up database:
1. Repeat steps 1-3 of the backup procedure.
2. Click the Restore tab of the dialog box.
3. Type in the path, or browse to the previously
created backup file. You must select
the correct file to restore.
4. Browse to the location of the backup Mst-
Files folder.
5. Browse to the folder to receive the restored
MstFiles.
6. Type in the path, or browse to the backup
CSSecurity DB file.
7. Click Restore to restore the database.
Audit Trail
CS Inventory logs all changes relating to Locations,
Containers, and Substances. You can
view this log and print out reports, filtering the
data according to your needs. Output can be
directed to a printer or to a file. Output file formats
include PDF, Excel, text, HTML, and
RTF. You must be assigned the View Audit
Trail privilege in order to do this.
194 Inventory Desktop & Workgroup
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Viewing the Audit Trail
You must view the Audit Trail before printing.
To view the audit trail, click Data > Audit Trail.
The Audit Trail window appears.
:
Use Filter...
Action
To...
view a specific type of
change: Insert, Update, or
Delete
The filter settings both limit the data that
appears in the report, and determine how it is
presented. Each setting has a blank position
that signifies no filtering on that parameter.
The following table describes the filter settings:
Use Filter...
Table
From Date
To Date
To...
view changes for just
Containers, Substances, or
Locations.
view changes by
date. Select filter
dates from a
calendar display
or type in the text box.
Note that when you create a new Container,
Substance, or Location, you “insert” data for
every field. Every edit or move is logged as an
“update” to the field(s) that have changed.
When you delete a Location or Substance, or
empty the Trash Can, each field in the item
affected is “deleted”.
When you have selected the filters you want to
apply to the data, click the Filter button to view
the results. You can reset the filters, or change
them individually, to view a different data set.
The filters also give you two controls over the
output format:
• Results per Page
• Order Results By
These affect both the view and the printout.
Printing an Audit Report
You must view the data before printing. When
you click the Filter button to view a report, two
more buttons appear: Design and Print, as
shown in the following figure:
:
Current User
Container
Barcode
Location
Compound ID
view changes by a specific
user.
view the changes for a
specific container.
view the changes for a location.
view the changes for a
specific substance.
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A new template, AuditTrailReport, has been
added to the default report templates listed
when you click the Design or Print buttons.
When you are reviewing changes to Structures,
the Audit report displays only a structure code.
The View link in the last column on the right
lets you display the structures, as shown in the
following figure:
:
To deploy MolServer assemblies to the database:
1. Register the MolServer11.dll file.
NOTE: If you have the Inventory client already
installed on the database server,
MolServer11.dll will have been already
registered.
2. Register the RegCodeCom11.dll file.
For more information on designing and printing
reports, see “Printing Labels and Reports”
on page 186.
Securing Structure Files
Inventory permits users to have a shared database
containing structure files. However, you
can choose to stop sharing your structure files
over the network and prevent other users from
directly accessing your structure files. The
benefit of not sharing structure files is that,
access to your data will be through SQL Server
and other users will not be able to copy the
data.
To stop sharing structure files over network
and allow access through SQL Server, you
need to perform the following tasks:
• Ensure that the TRUSTWORTHY database
property of SQL Server is set to ON. This
property is used to indicate whether the
instance of SQL Server trusts the ‘Inventory’
database and the contents within it.
• Deploy MolServer assemblies to the database.
NOTE: Both the files can be found in “C:\Program
Files\CambridgeSoft\ChemOffice2010\Common\DLLs”,
or in the appropriate folder on
Windows Vista.
3. Set write/modify permissions to the appropriate
usergroup so that users belonging to
the permitted usergroup can access your
structure files. If your network is secure,
you can choose ‘Everyone’ group.
To set the permissions on your structure
file:
a. Right-click on the structure file and
choose Properties.
b. Select the ‘Everyone’ group.
c. Select the check boxes: Modify and
Write.
d. Click OK.
By default, ‘Network Services’ usergroup
has write/modify permissions. If you
change the default setting then ensure that
all users who connect to the SQL Server
database also modify the following Inventory.exe.config
files:
• C:\Documents and Settings\All
Users\Application
Data\CambridgeSoft\Inventory11\ Inventory.exe.config
196 Inventory Desktop & Workgroup
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• C:\Program
Files\CambridgeSoft\ChemOffice2008\In
ventory\ Inventory.exe.config
In the above files, users need to change
to
4. Execute the application: DeployMolServer/
CambridgeSoft.Inventory.Deploy-
MolServerDBO.exe on the database server.
The Deploy MolServer Database Objects
dialog box appears:
NOTE: The MolServer related .NET
assemblies are marked as UNSAFE to allow
these modules to access resources outside the
database.
5. Select the location of your structure (.mst)
files.
6. Click the Deploy button.
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198 Inventory Desktop & Workgroup
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Chem & Bio Office
Enterprise

15
Informatics Directions
OVER RECENT YEARS a number of seemingly
conflicting trends have emerged from the
pharmaceutical, biotechnology and chemical
industries. One particular trend that
CambridgeSoft has observed is the movement
away from custom solutions and towards commercial
“off the shelf” software. This movement
has been accompanied by a drive towards
integration of disparate enterprise software and
other chemical and biological informatics solutions.
The trend away from custom software
has clearly been driven by the ongoing cost of
maintenance and general upkeep. Companies
in the business of drug development or chemical
manufacture are now hesitant to also
become experts in software development and
maintenance as well, preferring instead to
focus on their core competency and reduce
costs wherever possible.
The number of Enterprise software companies
serving the science industry has expanded dramatically
in the past decade. From broad applications
such as SAP and Siebel to LIMS, Data
Management and purely Science based applications;
companies now have a broad array of
software solutions available that are capable of
being deployed across the entire enterprise. As
more of these applications are deployed, a corresponding
need has increased for these disparate
applications to communicate and share
information with each other. These integration
projects often require custom code since the
applications are from multiple vendors. The
overall result is a high level trend towards
commercial software offerings that is accompanied
by a need for integration solutions that
typically require custom code.
Figure 15.1 Four key offerings of the CambridgeSoft
Business Strategy.
In addition to increased integration and
interoperability across applications, many clients
are also observing a need for increased
flexibility, data visibility across applications as
well as increased simplicity; seemingly contradictory
requests given the current state of the
market.
Chem & Bio Office 2010 User Guide 201
Chem & Bio Office Enterprise

CambridgeSoft has developed a suite of applications
that address many of these seemingly
contradictory issues and provide a scientific
decision support platform on which to build
knowledge, chemical and biological informatics
solutions. This Suite addresses the key
attributes described above for an overall informatics
solution:
1. Ability to integrate across the enterprise
2. Simplify to allow for easier adoption and
maintenance
3. Ability to visualize data across multiple
applications
4. Flexibility to address ongoing changes in
technology and business
In addition, this solution supports the ability to
improve cycle time from gathering raw data to
making an informed business decision.
Collaboration
CambridgeSoft approaches solutions to these
problems from multiple levels. By adopting a
business model that is focused on client collaboration,
CambridgeSoft is able to identify
requirements and provide complete solutions
for clients that address the key elements
described above. Understanding the immediate
underlying market need as well as longer term
trends is a critical component in identifying the
proper solution set. Based upon this collaborative
approach, CambridgeSoft has developed a
suite of applications that include multiple
industry leading enterprise software applications:
Technology and Integration
The CambridgeSoft Enterprise Suite applications
are designed for integration and interoperation.
By deploying the suite in its entirety as
many of our clients have, they realize the following
advantages:
• Commercial integration provided, no custom
code needed between suite application
members.
• Simplified data access between applications
and interoperability.
• Ability to visualize data across multiple
applications using CambridgeSoft visualization
tools.
• Flexibility to integrate with other Enterprise
applications using the same web services
202 Informatics Directions
Chapter 15

and API's used to integrate the
CambridgeSoft suite members.
Figure 15.2 The CambridgeSoft Enterprise Suite of
applications.
For larger clients, it is more typical to deploy
individual suite components and integrate
them as needed. The “designed in” connectivity
allows users to mix and match and provides
the framework to construct a unified informatics
system even if the components are from
multiple vendors.
Professional Services
The role of professional services in the business
strategy is significant. It is the professional
services group that provides the bridge
between the commercial “off the shelf” offering
and the final solution deployed by the client.
In many cases, this involves configuration,
training and deployment services that are
straightforward. However, the CambridgeSoft
professional services group is able to step in
and help with requirements gathering, as well
as solution design, development and deployment
for more sophisticated solutions that
require custom code. The depth and breadth of
professional services available gives
Chem & Bio Office 2010 User Guide 203
Chem & Bio Office Enterprise

CambridgeSoft the ability to offer a complete
solution to our customers.
Figure 3: The CambridgeSoft Enterprise Suite
offers solutions across research, development
and manufacturing.
Summary
By deploying the Enterprise Suite, customers
can take significant steps in satisfying diverse
and seemingly conflicting needs:
1. Integration – Integration between
Enterprise Suite components is designed
into the package. A set of API's and web
services is available that allows each component
to integrate and interact with non
CambridgeSoft applications.
2. Simplification – By using multiple components
of the Enterprise Suite, the overall
workflow is simplified. For example, the E-
Notebook, Materials Management and
Materials Registration systems can all work
together as if they were a single application
allowing for easy compound registration
and retrieval from Inventory.
3. Included in the Suite are data visualization
tools that allow users to access data from
multiple databases and work with the data
both visually and mathematically.
4. Using the API's and web services, clients
retain the flexibility to interoperate between
CambridgeSoft applications and other systems
and retain the ability to change applications
based on technical or business need.
The CambridgeSoft Professional Services
group gives customers the flexibility to do
their own development where needed, or
contract with CambridgeSoft to provide a
complete solution.
Based on a comprehensive architectural and
integration technology, deployment of the
204 Informatics Directions
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CambridgeSoft Enterprise Suite results in
increased productivity, increased IP and compliance
protection while minimizing risk and
reducing cost of ownership.
For more information about Enterprise Solutions,
please send email to solutions@cambridgesoft.com,
or call 1 617 588
9300 in America, in Europe call 00 800 875
20000, or in Japan call 0120 731 800.
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16
Supporting an Informatics Enterprise
Workflow
In a recent CBN article, some of the new
dynamics emerging from the science-based
industries were explored and the advantages of
Platform-based applications, such as the
ChemBioOffice Enterprise Decision Support
Platform, were discussed. (http://chembionews.cambridgesoft.com/Articles/
Default.aspx?articleID=579).
This unique suite of applications provides a
comprehensive base for a corporate Informatics
strategy. This article will provide deeper
insight into how the different applications integrate
and interoperate. Please note that demonstrations
of this workflow are available on the
CambridgeSoft Web site. Please search under
webinars for “Business of Science” for a series
of six webinars that describe the workflow outlined
below.
Experimental workflows cut across multiple
boundaries. A single experimental workflow
may involve both Chemistry and Biology. In
addition, more and more collaborative work
across departments is occurring — for example,
bridging Discovery with Analytical Chemistry
or Methods development with QC/
Manufacturing. To support these real life situations,
the informatics platform needs to have
the integration, interoperability, and flexibility
to meet these changing needs. The
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CambridgeSoft Decision Support platform
provides those capabilities.
Figure 16.1 A high level experimental workflow that
supports multiple scientific disciplines as well as
multiple departments.
In this article, the workflow described above
will be explored and the integration between
the applications will be discussed.
Data Visualization
Science by nature is an iterative process and
the workflow represented supports this concept.
At the beginning of any experiment, scientists
have a need to identify the data set they
are working with and identify particular items
of interest. The ability to link data in different
databases together through common metadata
is quite valuable and allows the scientist to better
identify compounds or other substances that
may be of value. This holds true whether the
company designs its own compounds, purchases
compounds from an outside source, or
is working with an already predefined compound
set.
The ChemBioViz application provides an
excellent method of connecting these data
types and visualizing them in a way that helps
identify valuable data. The ChemBioViz application
is also directly integrated with Chem-
BioDraw such that after a compound of
interest is identified, a user can launch Chem-
BioDraw directly. At this point, the user can
use ChemBioDraw to either determine strategies
for synthesizing the compound, perform
predictive modeling to identify how the com-
208 Supporting an Informatics Enterprise Workflow
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pound will behave under certain types of analysis,
or otherwise modify the compound to suit
the investigators needs.
For Workflows where compound structural
work is not required, please skip to the “Experimental”
section of this article.
available or if a compound is already known in
the literature.
Figure 16.3 Search for new IP or reagent sources
directly from ChemBioDraw.
The Database Gateway Hotlink is directly
accessible from the ChemBioDraw View
Menu.
Figure 16.2 Use the ChemBioViz applications’s
interactive tools to quickly identify prospective
compounds of interest based on your specific
criteria.
Directly from ChemDraw, it is also possible to
explore all of CambridgeSoft’s online databases.
This is extremely useful when trying to
identify whether a reagent is commercially
Experimentation
Having used ChemBioViz, ChemBioDraw,
and the Database Gateway to identify a compound,
reaction, or substance of interest, it is
simple to paste the reaction directly into the
CambridgeSoft E-Notebook. The E-Notebook
provides the framework to do additional experimentation
to properly qualify and quantify the
reaction as well as request Analytical Analysis
and link that analysis directly to the experiment.
Figure 4. Structures and reactions may be
dropped directly from ChemBioViz into E-
Notebook.
Directly from the E-Notebook, it is then possible
to Register a product of a reaction as well
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as create a container within the Inventory system.
Figure 16.4 Create Inventory Containers From E-
Notebook. An E-Notebook reference is inserted
directly into the Inventory System.
For cases where the compound or reaction are
already well defined, E-Notebook can seamlessly
access Registration and Inventory systems
to pull the appropriate references whether
by name or structure into the E-Notebook.
Expanding the Workflow
Across Corporate Boundaries
At this stage in the workflow, a compound or
substance of interest has been identified —
either through Discovery experimentation or
by working with purchased compounds. The
new substance has been registered and a container
created with the new substance for further
work. All of these actions have been done
using the integrated applications within the
CambridgeSoft Decision Support Platform.
Now this substance can be made available to
others within the company who may want or
need to use this substance for additional work.
This may include colleagues in the Biology
department or possibly in other departmental
areas. In this section of the workflow, the ability
to connect scientific disciplines and departments
is illustrated.
Using the E-Notebook, it is possible to access
data within both the Registration system and
Inventory directly. In the example below, a
user pulls a container from Inventory and scans
the bar code directly into an E-Notebook field.
Inventory metadata is immediately retrieved
and also placed within the notebook. The
Investigator may also update the Inventory
Figure 16.5 Directly Register Compounds From E-
Notebook. An E-Notebook reference is inserted into
the Registration System.
210 Supporting an Informatics Enterprise Workflow
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container contents directly from the same E-
Notebook page.
Figure 7. E-Notebook Biology configuration pulling
data directly from Inventory based on bar
code entry.
Note that in a Biology oriented Notebook, the
look and feel of the E-Notebook system is tailored
specifically to the Biologist. Although it
is the same overall E-Notebook platform, different
users may configure the notebook to
their specific needs. Administrators may establish
Templates that scientists work from to
establish consistency while maintaining the
flexibility needed for multiple environments.
The full MS Office suite is supported within
the E-Notebook application. This configuration
capability allows the same E-Notebook
system to be deployed across scientific disci-
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plines as well as across departmental boundaries.
Figure 16.6 Embedded Excel functionality within E-
Notebook. In place Excel editing is supported, Excel
add-ins are supported, and all content is stored
within the E-Notebook database and indexed for
searching.
If assay based analysis needs to be done, Bio-
Assay may be configured and launched
directly from E-Notebook and the Assay analysis
linked to the E-Notebook experiment.
Figure 16.7 Create Assay experiments directly from
E-Notebook and request an analyst to perform the
work.
The Assay experiment raw data may be
accessed directly from E-Notebook. Likewise,
212 Supporting an Informatics Enterprise Workflow
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it is possible to link back to the appropriate E-
Notebook experiment directly from BioAssay.
ChemBioViz provides a significant amount of
interaction with the data and may be more suitable
for scientists in the lab.
Figure 16.8 Figure 10. Use BioAssay to process a
wide variety of assay based data sets and return
results to the E-Notebook system. A bi-directional
link is established.
Decision Support
Having gathered a wide array of chemical and
biological data, scientists and managers can
use the web based BioSAR and/or ChemBio-
Viz to assist with the decision support process
and identify what the next step in the experiment
should be. BioSAR provides a light
weight query and reporting front end. It is
excellent for management reports and inclusion
into corporate portals to make project
information available to a broad audience.
Figure 16.9 Use BioSAR for HTML based data
consolidation and reporting.
Figure 16.10 Use the ChemBioViz applications
interactive tool to manage the new data set in detail
providing Decision Support Capability and ultimately,
additional predictive knowledge for the next
experiment or business decision.
The ability to use the same tools for Decision
Support, Data Visualization and prediction
allows for a clean iteration into the next round
of experimentation and decision making.
Summary
The CambridgeSoft Enterprise Decision Support
platform provides a solid integrated base
from which to establish a global scale informatics
strategy. The fully integrated components
promote seamless data transfer and
simplicity while eliminating the need to manage
integration between disparate applications.
Demonstration webinars illustrating this workflow
are available through the CambridgeSoft
web site (www.cambridgesoft.com), keywords
“Business of Science”.
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17
DocManager Enterprise
Chem & Bio Office DocManager Enterprise
lets you create a central repository for storing
chemical documents for your entire organization
in .doc, .txt, .ppt, .xls, and .pdf formats.
You can then search the repository using Boolean
parameters through a Web browser. Each
document submitted is securely stored in a
database, indexed by both structure and text.
Batch Submission
The Batch Submission tool allows administrators
to schedule the submission of documents
in a specified directory.
Viewing Recent Activities
The Recent Activities tool allows administrators
to view and sort recent document submissions.
Searching for Documents
DocManager Enterprise supports both basic
and advanced searching for text characters and
operators and structure searching.
When performing a text search, you specify the
search criteria by filling in values for the various
fields in the query form. When performing
a structure search, you need to draw a structure
of the compound for which you are looking.
For more information about drawing structures,
the Chem & Bio Draw User Guide.
After entering search criteria, start the search
by clicking the Search button.
For more information about search features,
see the Chem & Bio Office Enterprise User
Guide.
Basic Text Searching
DocManager Enterprise supports two types of
basic text searching:
• Exact Phrase Matching
• Wildcard Searching
Exact Phrase Matching
Exact phrase matching lets you retrieve documents
that contain the exact text or phrase
specified in the search criteria. Exact phrase
matching returns exactly the requested information.
Here are examples:
Searching For ... Returns ...
thymidine
synthesis
The words thymidine
synthesis in that order, with
no words between in a
document’s text.
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Searching For ... Returns ...
cyclohexane
The word cyclohexane in a
document’s text.
Wildcard Searching
Wildcard searching is useful when a prefix or a
suffix of the desired word or phrase is either
unknown or variable. Wildcard searching
returns all words containing the word root
specified in the search criteria. Wildcard characters
can be used in a basic text search when
searching for all documents that contain a part
of a word. Wildcard searching typically returns
more matches to search criteria than Exact
phrase matching.
Advanced Text Searching
Advanced text searching lets you use Boolean
operators. The advanced text searching types
are:
• ABOUT
• AND (&)
• EQUIValence (=)
• fuzzy (?)
• MINUS (-)
• NEAR
• NOT (~)
• OR (|)
• Soundex (!)
• Stem ($)
Escape Characters
To perform a search over words or symbols
that have special meaning to query expressions,
such as & or |, you must escape them.
There are two ways to escape characters in a
query expression, using the curly brackets,
{}and using a backslash, \.
Curly Brackets
Any symbol or string within a set of curly
brackets is a part of the escape sequence. When
you use brackets to escape a single character,
the escaped character becomes a separate
token in the query. The table below lists examples
of using curly brackets to escape an
ampersand (&) and a dash (-).
Backlash
The backlash symbol can be used to escape
only a single character or a symbol. Only the
character/symbol immediately following the
backslash is escaped. Here are examples using
a backslash to escape an ampersand (&) and a
dash (-):
:
Instead of
AT&T
Instead of
AT&T
highvoltage
highvoltage
{AT&T}
{high-voltage}
AT\&T
high\-voltage
Use
Use
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18
E-Notebook Enterprise
E-Notebook is an electronic version of the
familiar paper notebook that scientists have
traditionally used to keep notes in the laboratory.
E-Notebook lets you manage diverse
types of data on electronic pages that are much
like the pages of a paper notebook. The electronic
pages make it easy to organize information
and streamline your workflow. With
E-Notebook, you can set up notebooks and
pages to manage information about organic
syntheses and related information such as stoichiometry
calculations, reaction preps, spectra,
analytical methods, notes, and
spreadsheets.
E-Notebook Features
E-Notebook has many advantages over traditional,
paper notebooks. Since E-Notebook has
electronic rather than paper pages, you can
conduct searches by substructure, keyword,
date, and so on. You can set up templates to
avoid re-entering information that you often
use. E-Notebook fully automates stoichiometric
calculations. E-Notebook also provides a
full audit trail and change tracking features to
maintain compliance with 21 CFR Part 11.
With E-Notebook, you can create a customized
electronic notebook that matches your workflow.
You can develop new fields to manage
specialized types of data, and configure your
own forms to manage the information that is
important to you. You can also add your own
data analysis tools and customized searches to
E-Notebook.
You can use E-Notebook to organize a wide
variety of other information critical to your
work processes as well. For example, common
reactants used in reaction preps can be stored
in the E-Notebook database and shared among
researchers. In large enterprises, E-Notebook
can be configured to both supply and retrieve
information from other Enterprise systems,
such as chemical registration or chemical
inventory management systems.
E-Notebook Collections
E-Notebook information is organized into sets
of related items called collections. Examples of
some common types of collections are:
• Notebook and Page
• Therapeutic Area
• Project
• Experiment
• Reaction Scheme
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• Synthesis
For example, you could create a collection that
contains all of the reaction steps for a specific
synthesis. Typically, primary research data is
stored in Experiments or Pages, which are
organized within Notebooks, just like the paper
pages in paper notebooks. In this case, the synthesis
could be a Notebook, and each of the
steps could be a Page. Each of the Pages may
come from a different Notebook and may have
been created by a different Chemist, but the
Notebook for this, particular synthesis could
collect all of these Pages in a single place.
You can organize collections in other ways,
too. For example, you may want to create a
collection of all of the syntheses that lead to a
certain product, or all of the E-Notebook users
who are working on a specific project. E-Notebook
lets you to set up these relationships easily.
Collections are extremely flexible because
they allow you to organize information to suit
your workflow. E-Notebook allows you to
browse and search collections. You can also
create references to them, duplicate them, and
make them read-only (to prevent changes).
Just as you would use pages in a paper notebook
for recording various types of data, you
can use sections in E-Notebook for recording
reactions, spectra, or any other kind of information.
For example, within an experiment,
there may be sections for Reactions, notes,
reactants, etc. — whatever you need to record
and display your information the way you
would with a paper notebook. You can also
have the option to use templates, so that sections
are set up automatically and uniformly
with each new experiment you create.
Your system configuration determines the
types of collections and sections that you can
create within E-Notebook and the rules that
define their contents.
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System configuration
The permission to view, edit, and create collections
can be set up on a per-collection basis.
Navigation Overview
E-Notebook comprises two main areas —
Browse and Search.
The Browse area displays the collections, organized
in a tree structure. To expand a collection
and view its contents, either double-click it or
click the plus sign next to it. Clicking an individual
collection allows you to view and/or
edit it in the right frame. There are ways to
specify your Collection Tree view.
Browse and search buttons
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From within the Search area, you can construct
a query. For example, you can search for all
the sections that contain a certain structure or
all the collections created by a particular user.
When you run a query, you can save the results
list and the query itself. You can click any item
in the results list to browse to that item.
Figure 18.11 Running a query
Some menus in E-Notebook are available
when in context menus. For example, rightclick
any collection in the Collection Tree to
display the collection menu.
Working with Collections
All information in E-Notebook is organized
into collections. Collections may be notebooks,
folders, experiments, pages, and other
items. E-Notebook lets you browse through
collections and search them for information.
Your system configuration determines the
types of collections that you can create within
E-Notebook and the rules that define their contents.
An E-Notebook administrator can set up
permission to view, edit, and create each collection.
Organizing Collections
You can organize collections in the Collection
Tree to make their order meaningful to you and
other E-Notebook users. You can:
Move collections within a Container
Collection. You can organize collections
within a container collection by moving them
up and down the collection list.
Moving collections between Container
Collections. moving them from one container
collection to another.
Creating a reference within the collection
Tree. Within the collection tree, you can create
a reference to a collection that exists elsewhere
in the tree. The reference acts as a shortcut to
the original collection, and it reflects any
changes that are made to the original.
Duplicating a Collection. You can duplicate a
collection within its container collection in the
Collection Tree. The duplicate you create contains
references to all of the collections that are
contained within the collection at the time the
copy is made.
Renaming a Collection. You can rename a collection
to avoid a duplicate name, or simply to
make the name more meaningful to you and
other E-Notebook users.
Deleting a Collection. You can delete a collection
from the Collection Tree so that you manage
only the information that is relevant to
your current needs. Your system configuration
determines which types of collections can be
deleted.
Viewing Collection Properties
You can see specific information about a collection
by viewing the Collection Properties.
To view properties of a Collection:
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Importing and Exporting
Collections
E-Notebook lets you to export and import collections
as XML files. Each XML file contains
all of the data and formatting associated with
the collection.
Templates
E-Notebook lets you use templates so that to
avoid re-entering information unnecessarily.
For example, you may create a template for a
particular type of Experiment or page. It may
contain data and notes that you often use, or
typical values for various properties.
Form Tools
A form tool is used to perform various types of
function in an E-Notebook form/field. There
are several standard form tools in E-Notebook
that may be associated with the section or collection
types, for example, the New Section
Form Tool associated with Notebook collection
type or Import/Export Form Tool, which is
present in new section types you create.
Collection Security
You can control user access for each E-
Notebook collection.To change the security
properties of a collection, you must have Full
Control privileges to the collection based on
your system configuration.
The default security for any new collection is
Inherits Security, meaning that a collection has
the same security profile as its parent collection
in the Collection Tree. Transition security
is the security applied to the collection transitions.
For example, some users may be allowed
to close a collection while others can also
reopen the collection.
Collection Transition
You can configure collections to have states
associated with them. These states define the
life cycle of the collections. For example, a
notebook may have open and closed states; the
open state may permit editing, and the closed
state may be a read-only state that does not
allow edits. Transitions are the actions you perform
to move a collection from one state to
another, for example, from Open to Closed
Reaction Sections
A section is a form for E-Notebook data. You
use sections for recording reactions, spectra,
and other types of information.
Pre-configured Sections
E-Notebook has several preconfigured sections
that you can add to your pages:
• Reaction sections
• Reactant sections
• Spectrum and spectra sections
• Table sections
• MS Word Sections
• MS Excel Sections
Managing and Organizing
Sections
There are several basic ways to manage and
organize sections:
Creating a Section. You can create a new section
within a collection.
Modifying a Section. Only E-Notebook user
can edit sections in a individual collection at
any given time. If another user is editing a collection
and you attempt to edit it, a message
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will inform you that the collection is locked for
editing by the other user.
Moving a Section within a Collection. You can
move a section within a collection. This allows
you to organize sections in the most effective
way.
Duplicating a Section. When you duplicate a
section, the copy can be in the same collection
as the original or in a different collection.
Exporting Sections to Word. You can export
sections to MS Word, then manage them as
you would other MS Word documents.
Create a new Reaction
Sections
A reaction section shows one step in a reaction.
It contains a stoichiometry grid that analyzes
the reaction drawing. The AutoText feature
updates the preparation text when you change
the reaction drawing and the information in the
stoichiometry grid.
Within a reaction section, you can record:
Chemical Structure. Draw (or import) and
store chemical structures and reactions using
the ChemDraw toolbar.
Reaction Properties List. Record pressure,
temperature, and other reaction properties.
Stoichiometry Table. This table calculates and
stores amount, formula mass, molarity, density,
volume, and other variables. The table is
updated whenever you modify the reaction
drawing.
Drawing and Analyzing Reactions
You can draw a reaction using the ChemDraw
reaction field. When you draw a reaction, the
stoichiometry grid is automatically populated
with the properties of the reactants and products.
If you remove a reactant or product from
the stoichiometry grid, the corresponding
structure will be removed from the reaction
drawing.
Analyzing a Reaction
After you draw a chemical reaction in the reaction
field of a reaction section, you can analyze
the reaction. When you analyze a reaction, the
Stoichiometry Grid of the reaction section is
automatically populated with information
about the reactants and products.
NOTE: This only occurs if information has not
already been added to the Stoichiometry Table
manually.
Based upon the chemical drawing in the reaction
field, new reactants and products are
added to the stoichiometry table. By default,
the names of the reactants and products are
determined from the molecular formulas in the
drawing.
Name=Struct
The names of compounds you draw in a reaction
can be added to the stoichiometry grid
automatically, using the ChemDraw
Name=Struct feature.
NOTE: You need to have Chem & Bio Draw
Ultra installed on your computer to use
Name=Struct.
The Reaction Toolbar
The reaction toolbar provides a number of features
for managing the reactants and products
in your reaction section.
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The reaction toolbar normally appears just
below the reaction field.
Adding Structures
With the reaction toolbar, you can add reactants
and products from your Acronyms collections
in E-Notebook. You can use either the
Add dialog or the Quick Add method to add a
structure with the reaction toolbar.
Filtering Acronyms with the Reaction
Toolbar
The reaction toolbar offers several options for
filtering acronyms before selecting one to add
to your reaction section.
Defining a New Acronym
You can use the reaction toolbar to add new
acronyms to reactants collections.
Deleting a Structure with the Reaction
Toolbar
You can use the reaction toolbar to delete
structures from a reaction.
The Stoichiometry Table
The stoichiometry table calculates and stores
stoichiometric data for a reaction. It is filled in
automatically as you modify a reaction drawing.
You may change values manually as well.
You can also add reactants from the Collection
Tree to the stoichiometry table.
Spectra and Other
Sections
Ancillary Data Sections
You can use an ancillary data section to import
files with an E-Notebook page or experiment.
When you import the file, the checksum,
source path, and source file name are populated
automatically.
Captured Image Sections
With Captured Image Sections, you can
import, export, view, or annotate PDF documents.
The section supports a wide variety of
image file types such as JPG, GIF, PNG, TIFF
and BMP.
Managing Spectral data
You can manage your spectral data using
Spectrum and Spectra sections. There are two
types of sections for spectra. Each type can
contain properties, and notes for each spectrum.
• Spectrum Section – this section can contain
a single spectrum.
• Spectra Section – this section can contain
multiple spectra, organized in subsections.
Table Sections
You can use Table sections to organize the
chemical properties of compounds that interest
you. You can add properties to a Table, pivot a
Table, resize columns and rows, and organize
columns and rows. You can also insert links to
other E-Notebook sections or collections into a
table.
Working with Structures and Images
Tables may contain chemical structure fields,
which you can use to manage data about the
structures that interest you. You can also add
standard image files to the chemical structure
fields.
Changing Information in a Table Cell
The data type of a cell determines what type of
information you add to the cell. For example,
you can only draw a chemical structure in a
cell with a data type of structure.
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Creating a Reference in a Cell
Within a table cell, you can add a link to
another collection/section in E-Notebook or a
link to an external URL. This makes it easy to
browse back and forth between related data.
Word Excel Sections
Use Microsoft Word and Excel sections to
import and edit information that you normally
record in these applications.
Working with Data
E-Notebook lets you work with many, diverse
types of data, and then keep related data
together in collections, such as experiments
and pages.
Chemical Structure Data
The ChemDraw Toolbar lets you to create a
chemical structure by connecting frequently
used substructures together. You can also paste
standard image files into chemical structure
fields and then use the ChemDraw toolbar to
add annotation, such as text and arrows and
searchable text. Text in the chemical structure
fields is searchable.
Database Tables
You can use Database Tables to import data
from an external database and display it in
E-Notebook. The data is for display only and
cannot be edited.
Styled Text
You can use styled text boxes to record notes,
preparation information, etc. A styled text box
is often included in a form with other types of
data, making it possible to combine text notes
with related data. Certain styled text fields in
your configuration may have AutoText associated
with them. You can use the AutoText feature
to populate the styled text field
automatically.
Property Lists
Property Lists are used in forms to record various
types of data properties such as temperature
or pressure.
Property lists lets you to add references to
them. When you add reference to a property,
you can navigate to the collection or section
you have referenced, simply by clicking a link
in the property cell.
Creating a Reference
Within a property list, you can add a link to
another collection/section in E-Notebook or a
link to an external URL. This makes it easy to
browse back and forth between related data.
Rendering
Rendering in computer science is to convert
(graphics) from a file into a visual form., as on
a video display. Here, we are using it to
describe the export of the contents of a collection
to a PDF or MS Word file, or to a printer.
E-Notebook provides several options for rendering
the contents of your experiments and
other types of collections. It also offers the E-
Signatures feature for electronically signing
your experiments.
Searching
E-Notebook offers an extensive array of
searching features. You can search for:
• Chemical structures
• Strings of text
• Values in property lists and tables
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• Collections and sections that meet specific
criteria, such as creation date or owner’s
name
• Unannotated versions of collections.
Searching for Collections
The collection search lets you search for notebooks,
folder and experiments. You can search
for content or for metadata such as owner’s
name or creation date. You can save your queries
and the results lists in the Collection Tree.
Your search for collections may include these
search fields:
Query Text
Use the Query Text field to search for:
• text in Word fields
• styled Text
• Text in Excel spreadsheets
• Text in chemical structure
• Properties in property lists and tables
Chemical Structure Field
You can search for a structure, substructure, or
reaction using the ChemDraw Toolbar.
Search Location Field
The Search Location field lets you specify the
branch of the collection tree for your search.
Collection (Metadata) Properties
Metadata Properties describe the collections
that contain the sections for which you are
searching.
Chemical Structure Search
Substructure searching finds structures that
contain the query and any other attachments at
the open positions. Using the Chem & Bio
Draw toolbar, you can attach features such as
atom lists and variable bond types to a query.
The Chemical Structure search finds structures
in chemical structure fields and tables in
E-Notebook. The results are grouped by structure
for easy analysis and organization. You
can save queries and the results lists to the
E-Notebook Collection Tree.
Note that you may also search for chemical
structures with the Section Search and Collection
Search. These searches allow you to combine
the structure search with other search
criteria. The results of the Section Search and
Collection Search, however, will present the
search results in a list, rather than ordering
them by structure.
In searching substructures, E-Notebook finds
the substructure query regardless of its orientation
or drawing presentation in the targeted
molecules.E-Notebook does its best to follow
your instructions even if those instructions are
contradictory. For example, you can create a
query such as:
• Substituents: Up To
• Substituents: Exactly
• Implicit Hydrogens
• Ring Bond Count
• Unsaturation
• Reaction Change
For links to other properties, see:
• Reaction Stereo
• Translation
• Isotopic Abundance
• Abnormal Valence
• Atom Special Types
• Bond Type
• Bond Topology
• Reaction Type
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Reaction Searching
The chemical structure search in E-Notebook
lets you search for reactions.
Atom-to-Atom Mapping
In chemical structure fields, you can specify
atom maps. These maps can be used during
searching to resolve certain type of structure
hits. By matching numbers across the arrow,
you can see where atoms move during the
course of the reaction. E-Notebook uses atomto-atom
map information to determine the
reacting centers for reactions.
Searching for Reactants
If you know what starting materials you are
interested in but do not know their products,
you might perform a reactants query. A reactants
query is very similar to a reaction search,
except that there is nothing to the right of the
arrow.
If you are doing a substructure search, this
finds any reactions in which maleic anhydride
or a compound containing a maleic anhydride
substructure is consumed or transformed.
Searching for Products
If you know the desired end product but not
how to get there, you can do a products query.
A products query is similar to a reaction
search, except that there is nothing to the left of
the arrow.
Searching with the Search Location Field
The search location field lets you select the
specific branch of the collection tree over
which your search is conducted.
Collection Attributes
You may search for collections and sections in
E-Notebook based on specific attributes, such
as owner’s name and creation date.
Property and Table Queries
The Property Query Field is used to search
over property lists, and the Table Query field is
used to search over E-Notebook tables.
Text Queries
With the Query Text field, you can search for
text that is contained in these E-Notebook
fields:
• Styled Text fields
• MS Word fields
• MS Excel fields
• E-Notebook property lists
• E-Notebook tables
• Text in chemical structure fields
Basic Text Searching
You can use basic text searching, or querying,
to find information in MS Word and Notes
portions of E-Notebook. There are a number of
special characters used in basic text searching
which will help narrow or increase search
results.
Exact Phrase Matching
If a search is meant to find only exact matches
for the text entered, exact word or phrase
matching should be used.
Wildcard Searching
If a prefix or a suffix for a word is either
unknown or variable, wildcard characters
become useful in a free test search to return all
words with the same word root. Wildcard characters
can be used in a basic text search when
searching for all documents that contain a part
of a word. This kind of search typically returns
more matches to search criteria than the exact
phrase search.
226 E-Notebook Enterprise
Chapter 18

Advanced Text Searching
E-Notebook offers a number of advanced text
searching options for searching notes and
Word documents in the application.
Refining a Search
Once you have conducted a search, you can
further refine it — performing a search that is:
• An intersection of two searches
• A union of two searches
• The exclusion of one set of search results
from another
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Chapter 18

19
CombiChem for E-Notebook
With CombiChem, you can set up and manage
combinatorial chemistry libraries in E-
Notebook. You can set up a generic reaction,
add reactants, and automatically enumerate the
products.
Features include:
• Data import/export
• Select reaction sites
• Automatic stoichiometry calculations
• Flexible plate handling
• Navigator and structure palettes
• Configurable data sections
Setting up the Generic Reaction . You can add
a new generic reaction or prepare a reaction
from an existing experiment.
Adding Reactants from a Chemical Database.
After you add a generic reaction, you can add
reactants from a chemical database or draw
them using the Chem & Bio Draw tools.
Checking Reaction Sites. When a reactant has
more than one possible reaction site, CombiChem
lets you choose which site(s) participate
in the product enumeration process.
Editing Reactants. CombiChem performs a
check to ensure that the reactant matches the
generic component you selected. If it does not
match, a message is displayed to that effect,
and you are prompted to change the drawing.
Enumerating Products
After you add reactants to a CombiChem
library, you can enumerate the products using a
template.
CombiChem Navigator
CombiChem offers a color-coded Navigator
palette. When you are viewing the products
portion of a CombiChem library, each location
or well in the Navigator represents an individual
reaction. Selecting a well lets you view its
reaction components.
Combichem Structure Palette
The CombiChem structure palette displays the
structures of the reactants and products in a
well. When you click a well in the navigator
and the structure palette is displayed, the structure
palette changes to display the structures in
the well you selected. When you are viewing
the Reactants portion of a CombiChem library,
the Navigator changes to display the reactants.
Displaying Data
The CombiChem library has a number of settings
that you can modify to present your data
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accurately and effectively. You can modify the
layout of reactants and products in a plate. You
can also modify the naming and numbering
schemes for enumerated products. In addition,
CombiChem makes it possible for you to modify
the way that structures are displayed in the
library.
230 CombiChem for E-Notebook
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20
BioAssay Enterprise
BioAssay Enterprise lets you store, analyze,
and create reports on biological assay data.
BioAssay may be used for high-throughput
screening or managing data related to lowthroughput
and in vivo studies.
Protocols
Protocols are the basic data entities in BioAssay
Enterprise. The BioAssay Enterprise application
enables users to store and analyze assay
data through the use of protocols. The interface
provided by BioAssay Enterprise for managing
assay data is similar to that of Microsoft
Access.
Protocols contain tables in which data is actually
stored. The fields contained in these tables
can be defined as simple text, a piece of
numerical data, a calculation, or an attachment,
such as a picture or document.
Protocol Tasks
You can perform these protocol tasks:
• View and manage experimental data
• Import a data file
• Manage tables, fields, and file import templates
• Get help using the associated help files
Searching Protocol Data
BioAssay Enterprise allows you to perform
search operations over protocol data according
to your specified criteria.
Browsing Protocol Data
The data is arranged in hierarchical tables.
Double-clicking a row in a table displays the
data related to that row in the next table in the
hierarchy. Double-clicking a row in the Plates
table exposes the data in the Wells table associated
with the selected plate. You can view:
• Plate Data (for one or more plates)
• Graphical Data
• Lookup Structure
• Wells in Inventory
Designing a New Protocol
BioAssay Enterprise allows you to design your
own customized protocol using pre-defined
protocol templates.
Importing and Viewing Data
To import data into a BioAssay protocol, you
first defining a file import template compatible
with the data being imported. File import templates
are used to import data from a file and
populate user-defined tables with that data.
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External Data
Data can be imported from an external data
source using Structured Data Manager (SDM).
SDM also lets you validate the data contained
in external sources and populate the protocol
data table based with the result of validation.
Integrating with E-Notebook
BioAssay enables you, as an E-Notebook user,
to request an analysis in a BioAssay protocol
and retrieve the resultant data in E-Notebook.
Data Management and Curve
Fitting
Any set of data can be plotted and fit to a
curve. To plot your data, you first design a
graph template for your protocol. Graph templates
define the data being plotted, the location
from where the graph template is
accessed, and the physical properties of the
graph.
Fitting Data to a Curve
The graphing interface of the BioAssay
Enterprise application will fit any data to any
curve as long as the curve is defined in the
application. By default, two curves are defined
in BioAssay Enterprise:
• Sigmoidal-dose response
• One phase exponential decay
Viewing the Plotted Data
When you plot data in BioAssay Enterprise,
the Data tab available in the menu bar of the
plot, displays the plotted data along with information
about any curves fitted to the data.
Equation. The Equation tab displays the equation
in which the data is fit. The x and y variables
define the x and y coordinates for the
fitted curve. The values for other parameters in
the equation are assigned to fit the data in the
best possible way.
Data Statistics. The Data Statistics tab defines
various statistics for both the X and Y values
Fit Statistics. The Fit Statistics tab records statistics,
which define how well the equation fits
the table data.
Modifying Data Points. BioAssay Enterprise
lets you modify data points to produce a better
curve fit.
External Analysis
Bioassay allows you to create an add-in to perform
calculations or connect to third party
products to perform analysis. Thereafter, you
can store the analysis results in BioAssay data
tables.
You can create these types of add-ins:
• Sample External Analysis
• Prism Analysis
• Statistica Analysis
Reporting
You can create reports using the data in the
protocol data tables.You can use the existing
report templates or create a new report template.
After creating a report you can preview
and print it.
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21
Registration
Registration lets you track and characterize
compounds and store them in a searchable
database. Registration assigns a unique identifier,
a registration number, to the compounds.
Registration numbers are drawn sequentially
from a table. If a compound is removed from
the database, its Registration number is not reused.
Compounds, when submitted, are initially
stored in a temporary table. For those compounds
to be moved to the permanent table, the
compounds must be approved and registered.
This provides an additional qualifying step
before registering the compound. Data entry
error or other human errors can be detected
before registering the compound in the database.
The various characteristics of the registration
process are:
• Batch and analytical data can only be added
to registered compounds.
• Registration numbers are assigned when
compounds are moved from the temporary
table to the permanent table.
• Registration checks for duplicates only
when a compound is being registered in the
permanent table.
Registering Records
When a record in the temporary table is registered,
the record is deleted from the temporary
table and moved to the permanent table. You
can add identifier and analytics data to records
in the permanent table to help easily identify
them.
Adding Identifier Information
Identifier information includes information
about the chemical name, synonym, and CAS
number of a compound.Identifier information
can be added only to the registered compounds.
Adding Analytics Data
Analytics data includes solubility, optical rotation,
and 1H NMR data for a batch record. You
can add analytics data to only registered batch
records.
Query and Reporting
You can search the Registration database using
criteria you specify. A query specifies the
field(s) on the basis of which Registration
Enterprise is to be searched. Reporting allows
you to group records on the basis of the experiment
type and view them in a spreadsheet.
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22
BioSAR Enterprise
The BioSAR Enterprise application lets you
combine data from multiple applications
including Chem & Bio Office Enterprise applications
and subsequently manage the data. The
application is fully customizable; allowing you
to create you own search forms and display
data according to their will.
Terminology
Schema
A schema details the structure of a particular
database that can be accessed using the Bio-
SAR Enterprise application. Each schema is
made up of one or more tables and each table
contains a number of fields.
In addition to describing the content of each
table, a schema also defines the relationships
between tables and fields contained in it. The
relationships between tables and fields of a
schema are automatically generated when you
enable the schema for use.
Relationships across schemas can also exist.
For example, if a registration id number in the
REGDB schema is also included in the
CHEMINVDB2 schema, these two fields can
be linked within the application.
Table
Table refers to a database table that exists in a
schema in the Oracle instance. Tables define
entities in the schema. For example, one
schema may have a table defining a person
with fields, such as person id, last name, and
first name. Similarly, another table might
define an order with fields like customer id,
product, and order date.
View
View refers to a database view that exists in a
schema in the Oracle instance. Views are created
by assigning the results of a query to a
new table in the database.
For example, a view could be made from the
tables defining person and order (mentioned
above within Table). This view could include
the last name and first name of the person as
well as the order date. Now, the view can be
accessed in the same way as the table was
accessed, thereby eliminating the need for
longer, more complicated SQL statements to
access the information.
In database theory, a view is read-only whereas
a table is modifiable. However, in BioSAR
Enterprise, tables and views are treated as synonymous
entities because users do not have
direct access to the tables accessed by BioSAR
Enterprise.
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Formgroup
Each form created in BioSAR Enterprise is
actually a combination of three forms: search
form, list view form, and details view form.
The three forms are interlinked. A formgroup
refers to the group of three forms.
When creating formgroups, users are able to
assign access rights to other users. If users,
other than the creator is given access to a formgroup,
the formgroup is considered public.
Schema Management
The Schema Management feature in BioSAR
Enterprise allows administrators to control the
visibility of information stored in the database.
In other words, the Schema Management feature
allows administrators to control the schemas,
tables, views, and fields that can be used
in forms.
Form Management
BioSAR Enterprise allows users to search
through and view data in multiple application
databases at the same time. In order to accomplish
this, users must define the search criteria
and return values. BioSAR Enterprise's Form
Management interface provides you the tools
to create and customize search criteria and
return values.
Searching
There are three different ways to retrieve
search results. These are as follows:
• Using a Form Group
• Retrieving a Saved Query
• Retrieving a Query in the History
After a search is performed, the results are
always displayed in the same format.
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23
Inventory Enterprise
Overview
Inventory Enterprise 9.0 is a Chem & Bio
Office Enterprise application that allows you
to track the data associated with the reagents
procured or produced by chemical and pharmaceutical
research centers. It keeps track of
all the data from the procurement or initial production
of the reagents to the depletion or disposal
of the reagents.
Searching Inventory
Enterprise
The searching feature of Inventory Enterprise
9.0 enables you to locate a substance, container,
or plate stored in the Inventory
Enterprise 9.0 database.
In Inventory Enterprise 9.0, different types of
users can perform different types of searches,
such as simple search, advanced search, substructure
search, batch search, global search,
and plate search. For example, chemists need
to search Inventory Enterprise 9.0 on the basis
of attributes, such as chemical structure, substance
name, and CAS number. They can perform
the search with the help of the
substructure search. Similarly, stock room or
receiving room personnel can use the advanced
search to search Inventory Enterprise 9.0 on
the basis of attributes, such as container and
location barcode.
Container Management
Inventory Enterprise 9.0 allows chemical and
pharmaceutical research centers to manage the
containers associated with the reagents that are
procured or produced by the research centers.
The container management tasks are performed
in the Container Management area of
Inventory Enterprise 9.0. You can access the
Container Management area by clicking the
Browse link within the Inventory Enterprise
section in the home page of Chem & Bio
Office Enterprise.
Grid Management
The Grid Management feature in Inventory
Enterprise allows you to place plates and containers
in grids, in the same way as they are
physically kept in racks. Before placing place
plates and containers in grids, you need to create
a grid format, which specifies the number
of rows and columns of the grid.
Managing Batching Fields
Batching is a feature in Inventory Enterprise
that allows you to relate containers based on
arbitrary fields, including the custom fields.
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The fields, based on which containers are
related, are called batching fields and a group
of related containers is called a batch. All the
containers in a particular batch have the same
batch id.
Batching is controlled via a GUI interface,
which facilitates searching, requesting, and
reserving of samples in batches. After you
have classified the containers into batches, you
can search for containers in a particular batch.
For example, you can create batches based on
the status of the containers so that the containers
with status, 'available' will be in one batch
while the containers with status, 'backordered
item' will be put in another batch. Therefore,
later on you can easily search for the 'available'
containers based on their status.
Managing batching fields involves specifying
the field/fields based on which the containers
are to be grouped in batches and updating the
container details thereafter.
Plate Inventory
Plates can be defined as means of holding multiple
compounds in an easily transportable unit.
In Inventory Enterprise 9.0, plates are analogous
to containers. Similar to containers, plates
are held in locations and can be managed in the
same way as containers are managed.
Like containers, plates are also managed in the
Container Management area of Inventory
Enterprise 9.0. However, the Container List
frame and Container Details frame of the Container
Management area are termed as Plate
List frame and Plate Details frame when they
are used to manage plates instead of the containers.
Reports Management
The Reports sub-module of the Chem & Bio
Office Inventory Enterprise 9.0 application
enables you to create reports, which can be
used to gather information about the locations,
containers, and substances in Inventory
Enterprise 9.0. The data required for creating
reports is stored in the ReportQueue.mdb and
ChemInv_reports.mdb tables. Inventory
Enterprise 9.0 uses the ReportsQ.dll and
Reports.exe files to manage reports.
In Inventory Enterprise 9.0, there are two types
of reports, which are as follows:
• Standard reports: Refers to the reports that
are already available in Inventory
Enterprise 9.0.
• Custom reports: Refers to the reports that
are not already available in Inventory
Enterprise 9.0 and are created by the users,
as per their requirements.
Both types of reports are driven by the report
layouts, which specifies the format for a report
and the information that is to be included in the
report.
Generating a Standard Report
Inventory Enterprise 9.0 contains various standard
reports, each of which is generated in a
different manner. The various types of standard
reports available in Inventory Enterprise
9.0 are as follows:
• Label report
• Container search result report
• Location report
• Custom report
• Plate location report
• Plate search result report
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• Plate label report
• Batch label report
Managing Organizations
Inventory Enterprise allows you to define
organizations and their constituent users so
that when reserving a sample, you can specify
the organization for which you are reserving
the sample.
Integrating with
Registration Enterprise
Inventory Enterprise seamlessly integrates
with Registration Enterprise and allows you to
directly access compounds stored in the Registration
Enterprise database. However, in order
to integrate, you need to make changes in the
configuration settings of the Inventory
Enterprise application.
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240 Inventory Enterprise
Chapter 23

Databases

24
Scientific Databases
CambridgeSoft offers a library of chemical
information databases, containing compounds
and chemical reactions. Users may search over
the databases with tools provided in the Chem
& Bio Office software suite.
Searching by chemical structure requires the
use of Chem & Bio Draw® or the Chem & Bio
Draw ActiveX/Plugin, which is available for
free from CambridgeSoft for the Internet subscription
version, and is included with the runtime
software.
The Scientific Databases bring a wealth of
chemical information to your desktop. Searching
through these databases by chemical
names, structures, physical data, suppliers,
safety data, and literature references becomes
as easy as clicking a mouse.
ChemBioFinder.Com
Gateway
The ChemBioFinder.Com Gateway lets users
search all non-reaction databases in one easy
step. Searchable fields include structure, substructure,
chemical name and CAS Registry
Number. The search results contain the number
of search results, which databases the results
are found in, and hyperlinks to the appropriate
database record for review.
Database Offerings
Reference Data
• The Merck Index
• R&D Insight/Chemists
• ChemINDEX
• Ashgate Drugs
• NCI
• AIDS
• Traditional Chinese Medicines
• Nanogens Index
Sourcing and Safety Data
• ChemACX
• ChemMSDX
• Sigma-Aldrich MSDS
• EH&S Enterprise
Reaction and Synthesis Data
• ChemRXN
• ChemSynth
• ChemReact
The chemical databases work with Chem &
Bio Office Desktop, an integrated suite of software
tools for chemists and biologists.
Chem & Bio Office 2010 User Guide 243
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ChemBioFinder—The primary application
provides the engine for searching data and the
forms and tables for viewing it. Relational
databases are supported by ChemBioFinder.
Chem & Bio Draw—The chemical drawing
standard allows structures to be drawn and
edited in ChemBioFinder. It can represent individual
structures or chemical reactions, complete
with atom-to-atom mapping and absolute
or relative stereochemistry, for detailed structure-based
queries.
Chem & Bio 3D—A molecular modeling and
computations application offers molecular
mechanical and quantum mechanical computational
capability. Featuring an intuitive graphical
user interface, it displays molecules as
three-dimensional models that you can rotate
and translate to reveal details of a structure not
evident in two dimensions.
ChemBioFinder Tips
Some databases are provided with customized
applications. If the database you are using does
not include such an application:
1. Start ChemBioFinder.
2. Go to File>Open and select a form for one
of the databases.
Help
Additional sources of help for using the databases
include the following:
• Quick Reference Card
• ChemBioFinder online help
• ToolTips
• Status Bar
• CambridgeSoft Technical Support
Online Help
Access to online help is provided from the
ChemBioFinder and Chem & Bio Draw help
menus.
ToolTips
ChemBioFinder and Chem & Bio Draw provide
ToolTips as an additional form of online
Help. Rest your pointer on a tool to display a
message box with a brief description of the
tool.
Status Bar
The bottom left corner of the ChemBioFinder
and Chem & Bio Draw Status Bars display a
slightly more detailed description of the tool
icons.
244 Scientific Databases
Chapter 24

Reference Data
25
The Merck Index
The Merck Index is a one-volume encyclopedia
of chemicals, drugs and biologicals that
contains more than 10,000 monographs. The
entries are not a listing of Merck & Co., Inc.
products, but rather cover a wide range of compounds
that have been selected by the editors
on the basis of present or historic importance
and interest. Since the publication of its Thirteenth
Edition in 2001, over 5,000 monographs
have been significantly revised and updated.
Each monograph is a concise description of a
single substance or a small group of closely
related compounds. The information provided
includes chemical, common and generic
names, trademarks and their associated companies,
Chemical Abstracts Service (CAS) Registry
Numbers, molecular formulas and weights,
physical and toxicity data, therapeutic and
commercial uses, citations to the chemical,
biomedical and patent literature, and chemical
structures.
How Is It Useful?
For more than 100 years, the printed edition of
The Merck Index has been the premier reference
for validated data about many compounds
of general interest. The subjects covered
include human and veterinary drugs, biologicals
and natural products, agricultural chemicals,
industrial and laboratory chemicals, and
environmentally significant compounds. The
electronic version includes all of the information
in the printed edition, and enhances it by
allowing direct and rapid searching over all
data fields. Where the printed edition offers
indexes of names and CAS Registry Numbers,
the electronic version allows the user to enter
them as search terms, and takes you directly to
the relevant monographs without having to flip
through a bulky printed volume. Physical properties
as well as many other attributes can also
be used in the search. The Merck Index allows
searching by structure, substructure, and similarity,
all of which are impossible when using
the printed edition. Users also receive access to
almost 1000 monographs which were retired
from previous printed volumes.
Chem & Bio Office 2010 User Guide 245
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Organic Name Reactions, and Supplemental
Tables are also available to search through.
• 14th Edition: data available on Cambridgesoft.com.
• Included in 13th Edition: 10,250
• Added since 13th Edition: 230
• Archived from 12th Edition: 540
Using The Merck Index
Online
About The Merck Index
Availability:
• CD-ROM
• Internet subscription
• Intranet using Chem & Bio Office
Enterprise
• Number of Monographs
The Merck Index is split into 5 tabs:
• Homepage (below)
• Basic Search
• Structure Search
• Organic Name Reactions
• Supplemental Tables
The Homepage delivers important information
about The Merck Index, user help guides, tech-
246 The Merck Index
Chapter 25

nical support, and how to purchase. Additional
links allow the user to access the major sections
of The Merck Index: Basic Search, Structure
Search, Organic Name Reactions, and
Supplemental Tables.
The complete contents of the chosen record
is displayed.
Compound Searching
The Structure Search section allows searching
for compounds by physical properties, compound
attributes, and structure. The Merck
Index’s compound searching form acts much
like the other search forms found in
ChemOffice Enterprise applications.
To access the Compound Searching section,
click the Compound Search Link or Structure
Search Tab at the top of the page. The
Compound Search Form appears
To search for compounds:
1. Enter the desired information into the fields
provided in the Compound Searching
Form.
NOTE: To search without using structures,
click the Basic Search link or Tab.
2. Click Search.
A list of search results appears
To view the contents of a particular record in
the list, click Show Details.
Organic Name Reactions
The Organic Name Reactions (ONR) section
contains a list of reactions which have come to
be recognized and referred to by name within
the chemistry community. The reaction
descriptions are meant to be informative, but
not comprehensive. The descriptions are composed
of the following:
• name(s) associated with the reaction
• the original and/or primary contributor(s)
connected with the discovery and/or development
of the reaction
• a concise description of the transformation
• a reaction scheme
• key references
• cross references to other ONR based on
commonalities.
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Useful abbreviations can be found on the main
page of this section. To access the Organic
Name Reactions section:
Click the Organic Name Reactions Tab
found at the top of the page.
The Organic Name Reactions homepage
appears.
The Reaction details appear in the right
frame
The Search Tab allows the user to enter a free
text search for the appropriate reaction. To
search for a reaction:
1. Enter keywords into the text box available.
2. Click Search. A list of matches is
returned.
3. Click on the link for the appropriate reaction.
The Reaction details appear in the
right frame.
The left frame of the homepage contains 2
tabs: Browse and Search.
The Browse Tab lists all reaction names
included in The Merck Index. To view the contents
of a record, scroll to the appropriate reaction
and click on the link.
For tips about entering a free text search, click
on the Tips for Searching link found below
the free text search textbox under the Search
Tab.
Supplemental Tables
The Supplemental Tables section lists multiple
tables available to view by the user in PDF format.
To access the Supplemental Tables section,
click on the Supplemental Tables Tab found
at the top of the page.
248 The Merck Index
Chapter 25

The Supplemental Tables homepage appears.
To view a particular table, click on the link
provided. All tables are available in PDF format
and therefore require the Adobe Acrobat
Reader to view. If you do not have the Adobe
Acrobat Reader installed, click on the link provided
to obtain a free copy.
Logging Off
You can end your session with The Merck
Index at anytime by logging off. To log off:,
click Log Off.
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250 The Merck Index
Chapter 25

26
R&D Insight/Chemists
R&D Insight/Chemists (RDIC) is a collaborative
database produced by CambridgeSoft and
Wolters Kluwer Health. RDIC is contains current
information on drug products under development
and is essential for those working in
research and development, licensing and marketing
at pharmaceutical and healthcare institutions.
The database is updated weekly.
About RDIC
Availability: Internet Subscription
Number of drug products: >20,000
Using RDIC Online
Users can search the collection by structure,
substructure, names, partial names and synonyms.
Additional search fields include CAS
Registry Number, Indication, Phase of study,
Country of study, WHO ATC, EphMRA ATC,
Author, Article Title, and Journal Name.
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annual reports, news services, press releases,
and licensed Lehman Brothers' PharmaPipelines
data.
Each record contains key characteristics such
as molecular formula, CAS Registry Number,
ATC codes and Mechanism of Action, as well
as Pharmacokinetics and Pharmacodynamics
statistics. Records also include the Adis Evaluation
of the most significant scientific information
related to a compound and up-to-date
details of phase of development, originator and
licensees and references. For those users who
also subscribe to the full version of Adis R&D
Insight, each record also contains a link to the
full profile and review of the drug and link to
supporting summaries on key studies from
Adis Clinical Trials Insight.
Adis R&D Insight is compiled from information
collected from many sources. The primary
sources are: direct contact with companies
involved with research and development,
information collected from drug and therapeutic
literature published in over 2,300 medical
and biomedical journals, attendance at international
meetings and conferences, company
Benefits to users include:
• The ability to identify compounds of interest
in competitors' pipelines
• The ability to assess the strengths and
weaknesses of competitors based on chemistry
• Evaluation of the safety profiles of related
compounds
• Tracking the stages of development of competing
compounds
• Accessing Pharmacokinetics and Pharmacodynamics
data quickly.
252 R&D Insight/Chemists
Chapter 26

27
ChemINDEX
ChemINDEX Ultra is a collection of these
chemical reference databases: ChemIndex,
NCI Cancer, and AIDS databases. The databases
are available as Internet subscriptions
and on Intranets using Chem & Bio Office
Enterprise.
How Is It Useful?
This class of databases serves as an extensive
chemical reference for finding general information
about commonly used compounds,
such as structure, name, molecular weight,
CAS Registry Number, synonyms, and physical
data (melting point, boiling point, vapor
pressure, etc.). ChemINDEX Net contains
active hyperlinks to Web sites with further
information about the compounds.
About ChemIndex
Availability:
• Internet Subscription
• Intranet with Chem & Bio Office Enterprise
• SDfile
Number of compounds: >78, 000
Key Fields:
• Structure
• Formula
• ACX Number
• SC Number
• Molecular Weight
• Supplier
• Catalog
• Name
• Vapor Pressure
• Synonym
• CAS Registry Number
• Boiling Point
• Melting Point
• Site ID
Using ChemINDEX Ultra
You can access ChemINDEX Ultra at Chem-
BioFinder.com or with Chem & Bio Office
Enterprise.
ChemBioFinder.Com
ChemBioFinder.com is one of the most heavily
used public-access chemical information sites
on the Internet. ChemINDEX is the Chem-
BioFinder database of small molecule information
presented at this site. Many of the
individual compound records also contain lists
of links to other sites containing additional
information about the compound.
Chem & Bio Office 2010 User Guide 253
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Chem & Bio Office
Enterprise
ChemINDEX, available online through a Subscription
uses the same conventions as other
webserver applications.
254 ChemINDEX
Chapter 27

28
Ashgate Drugs
Ashgate Drugs is fully searchable database
created from the popular book, Drugs: Synonyms
and Properties, published by Ashgate
The online database has 7,922 drugs which are
currently in common use worldwide. It
includes all drugs approved by FDA prior to
2004. These drugs all have recognized applications,
and are classified into one or more of
201 therapeutic categories.
Each entry is accompanied by:
• The CAS Registry Number
• The European Inventory of Existing commercial
Chemical Substances (EINECS)
number
Each field is fully searchable. Thus an entry
may be located on the basis of structure or substructure,
synonyms, biological activity, physical
properties or manufacturer.
A key component of this reference is the extensive
coverage of synonyms. The electronic version
adds almost 70,000 synonyms and trade
names that did not fit into the print version
bringing the total number to nearly 100,000.
This reference will be invaluable to research
chemists, biologists, and physicians and to
anyone interested in drugs who, starting with a
single synonym for a drug, will be able to
quickly find a thumbnail sketch of the essential
information concerning that agent.
About Ashgate Drugs
Availability:
• Internet Subscription
• Intranet on Chem & Bio Office Enterprise
• SDfile
Number of Record: 7,922
Key Fields:
• Chemical Structure
• CAS Registry Number
• EINECS Number
• Chemical name
• Molecular formula
• Synonyms, including tradenames
• Medical application
• Manufacturer
• Physical Properties
Using Ashgate Drugs
You can open Ashgate Drugs online or with
Chem & Bio Office Enterprise.
When you open Ashgate Drugs in Chem-
BioFinder, the application starts in Monograph
view. In this view, users can browse records
using the navigation buttons on the Chem-
Chem & Bio Office 2010 User Guide 255
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.
BioFinder Menu. To search, click the “Search
Monographs” button
Online or Chem & Bio Office
Enterprise
Ashgate Drugs is split into four tabs:
• Introduction
• Compound Searching
• Browse
• System Requirements
Data that can be searched includes chemical
structures, synonyms, CAS Registry Number;
the European Inventory of Existing Commercial
Chemical Substances (EINECS) Number;
the physical properties of each compound; and
the known biological activity and indicated
applications.
The Introduction and System Requirements
tabs deliver important information about Ashgate
Drugs, compatibilities, and how to navigate
the site. The Compound Searching and
Browse tabs bring the Ashgate Drugs data to
the user.
Compound Searching
Search results are displayed in Monograph
view and can be browsed using Chem-
BioFinder’s record navigation tools.
The Compound Searching section allows
searching for compounds by physical properties,
compound attributes, and structure. The
Ashgate Drugs compound searching form acts
much like the other search forms found in
ChemOffice Enterprise applications.
256 Ashgate Drugs
Chapter 28

To access the Compound Searching section,
click on Compound Search Tab found at the
top of the page.
The Compound Search Form appears.
The complete contents of the chosen record is
displayed.
To search for compounds:
1. Enter the desired information into the fields
provided in the Compound Searching
Form.
2. To search without using the structure
search, click Click Here for Non-Plugin
Searching.
3. Click Search.
A list of search results appears
Browse
The Browse Tab lists therapeutic categories in
alphabetical order. Click on a link to view the
record for compounds with the listed therapeutic
category.
To view the contents of a particular record in
the list, click Show Details.
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258 Ashgate Drugs
Chapter 28

29
NCI
NCI (National Cancer Institute) is a database
of potential anti-cancer screening compounds
provided by the National Cancer Institute.
The NCI database is provided with
CambridgeSoft-generated 2-dimensional structures.
Number of compounds: >223,000
NOTE: The National Cancer Institute’s AIDS
database can be accessed through the NCI
database
Using NCI
Availability: Part of ChemIndex
• Internet Subscription
• Intranet on Chem & Bio Office Enterprise
Using the NCI Forms
The NCI Database ChemBioFinder form consists
of three tabs:
• Basic Chemical Information, searchable by:
• Chemical Structure
• Molecular Formula
• Molecular Weight
Chem & Bio Office 2010 User Guide 259
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• NSC Number
• CAS Registry Number
• Synonym
• Human Tumor Cell Line
• AIDS Antiviral Screen.
A box appears under the Basic Chemical
Information tab if data is available.
Using NCI Online
ChemINDEX, available online through a Subscription
uses the same conventions as other
ChemOffice Enterprise applications.
A box appears under the Basic Chemical
Information tab if data is available.
260 NCI
Chapter 29

30
AIDS
AIDS (The National Cancer Institute’s AIDS
database) is a library of potential HIV screening
compounds provided by the National Cancer
Institute.
The AIDS database is provided with
CambridgeSoft-generated 2-dimensional structures.
is available for the substance retrieved, a box
appears under the Basic Chemical Information
tab.
Using AIDS Online
The AIDS database is available through the
NCI search forms online.Please see “NCI” on
page 259 for more information.
Using AIDS on CD
The AIDS database is available through the
NCI search forms. Please see “NCI” on page
259 for more information. If AIDS information
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262 AIDS
Chapter 30

31
Traditional Chinese Medicines
Compiled by NiceData, Traditional Chinese
Medicines (TCM) has monographs for over
10,000 chemicals isolated from 4,636 natural
sources used in traditional Chinese remedies.
The monographs feature bio-activity data for
many of the compounds, effects and indications
of the medicines, English, Latin, and Chinese
names for the natural sources, and over
2,000 references.
About TCM
users to choose one or both methods. Users
need to simply click the desired check box on
the search form and then search away! (Note:
The CD-ROM version allows the user to perform
both searches independently.)
The chemical substructure search shown,
drawn in the Chem & Bio Draw Active X control,
has a ring position with the [N,O,S] label
which allows for any of the three elements
nitrogen, oxygen, or sulfur at that position.
Availability:
• CD-ROM
• Internet Subscription
• Intranet with Chem & Bio Office Enterprise
• SDfile
Number of compounds: 10,458
Number of natural sources: 4,636
ChemOffice Enterprise
The Traditional Chinese Medicines database is
designed to allow users to choose different
views of the dataset, which can be called
"Chemistry Space" and "Natural Sources
Space". Some might wish to search over the
chemical information database. Others will
prefer searching over the natural sources database.
The enhanced search interface allows
The search found 165 records in "Chemistry
Space", or 165 chemical compounds that contain
the substructure that was searched. The
Chem & Bio Office 2010 User Guide 263
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search also found 175 records in "Natural
Sources Space", which means that there 175
natural sources that contain a chemical compound
with the substructure that was searched.
Selecting the Natural Sources radio button will
display the results in Natural Sources Space.
The view of the search results is selected by
choosing the radio button next to the view
results section of the screen.
Search results from either view may be
expanded. For example, selecting “Show
Details” for the sixth record from the "Chemistry
Space" result list will display the monograph
for that record.
264 Traditional Chinese Medicines
Chapter 31

The monograph contains chemical information
about the compound, including when available,
CAS Registry Numbers, synonyms, and
physical properties. Also in the monograph is a
list of all the natural sources containing the
compound (in this case there is only one),
along with the uses, effects and indications,
English, Latin and Chinese names, and bioactivity
when available. The bottom part of the
monograph contains the references.
All the “Chemistry Space” monographs are
cross referenced with the “Natural Sources
Space” monographs. Clicking on the View
Details hyperlink found after the natural
sources section of the monograph will bring up
the “Natural Sources Space” monograph for
that particular source. This view repeats the
information found in the “Chemistry Space”
monograph, and then includes a list of all
active chemical compounds that have been isolated
from the source.
Each of the chemical compounds is cross referenced
back to the “Chemistry Space” monographs,
and can be accessed by clicking on the
associated View Details hyperlink.
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266 Traditional Chinese Medicines
Chapter 31

32
Nanogens
The Nanogen Index is useful scientists in the
pharmaceutical, chemical and biotech
industries, and academia who need information
on pesticides, agricultural chemicals
and environmental contaminants
which are currently or were previously
available globally or in development.The
Nanogen Index contains data on over 3000
pesticides and other environmental contaminants.
It contains authoritative and up-to-date
information on all pesticides and agricultural
chemicals in world-wide use. Data is included
not only on currently used pesticides, but also
those that are in the R&D pipeline and compounds
that were once marketed or reached a
development status. The Nanogen Index is an
online, fully searchable Nanogen Database
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268 Nanogens
Chapter 32

33
Off-Label Database
Established in 2002, Off -Label Ltd is a UKbased
company dedicated to maintaining a
constantly-updated database on the off-label
use of drugs. The company’s core product is an
online searchable resource that provides rapid
access to information detailing the latest off -
label uses of over 400 licensed drugs.
The Off-Label database is available to licensees
via the Internet at CambridgeSoft’s Chem-
BioFinder.com portal, and can also be
accessed via the Database HotLink in Chem-
BioDraw. All that is required is a supported
web browser, and for structure searching, the
appropriate ChemDraw plug-in (available for
free download). The database can also be
placed on your internal network. The database
is licensed annually, and shorter term evaluations
can be arranged.
Each record in the Off -Label database contains
the original literature citation to the
reported off -label study, and a hyperlink to the
corresponding abstract on PubMed for further
details.
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270 Off-Label Database
Chapter 33

34
Martindale for Scientists
For scientists in the pharmaceutical, chemical
and biotech industries, and academia who need
unbiased, and reliable information on drugs
and medicines used globally, Martindale for
Scientists is a drug reference database that provides
detailed, up-to-date information on the
world’s pharmacopeia. Martindale for Scientists
covers over 6,500 substances, including
human and veterinary drugs, diagnostics, vaccines,
herbal medicines, drugs of abuse, excipients,
pesticides and nutritional agents. It covers
approved and discontinued drugs and published
compounds in Phase III clinical studies.
Database Contents
• Drug names, systematic names, international
trade names, “street” names, CAS
Registry Numbers, synonyms and codes
• Structure, molecular formula and weight
• Salts and derivatives
• Summary of clinical properties, physical
properties and pharmacokinetics
• Uses and administration
• Over 6600 substances
• Details of almost 180,000 proprietary and
nonproprietary medicines
• Details of 17,700 manufacturers
• Trade names from 40 countries
Accessibility
Martindale for Scientists is available to licensees
via the Internet at CambridgeSoft’s Chem-
BioFinder.com portal, and via the Database
HotLink in ChemBioDraw. All that is required
is a supported web browser, and for structure
searching, the appropriate ChemDraw plug-in
(available for free download). The database
can also be accessed via CambridgeSoft’s E-
Notebook, or placed on your internal network.
The database is licensed annually, and shorter
term evaluations can be arranged.
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272 Martindale for Scientists
Chapter 34

35
Encyclopedia of Reagents for Organic
Synthesis
The Encyclopedia of Reagents for Organic
Synthesis is a fully searchable database that
provides systematic and exhaustive coverage
of reagents used in organic synthesis, including
classical reagents, new “designer” reagents and
catalysts.
Reagents and Catalysts
EROS, covering over 4000 reagents and catalysts,
surveys, exemplifies, and discusses their
use in some 70,000 reactions, complete with
literature citations. In addition to listing chemical
and physical properties, EROS editors provide
expert commentary on the scope and
limitations of reagents and catalysts through
unbiased assessments of the most appropriate
compound to use for the synthesis in hand, taking
into account factors such as stereo- and
regio-specificity and potentially interfering
functional groups.
Searchable Reactions
EROS can be searched by reaction name (e.g.
“Mannich”) as well as reaction type (e.g. “ring
formation”). Searches can be refined by querying
by yield and/or experimental conditions.
EROS can also be searched by structure,
including molecules and reactions, so that syntheses
of specific molecules can be planned, as
well as transformations of partial structures
and functional groups.
Database Contents
• Reagent/catalyst name and other identifiers
• Physical properties
• Solubility
• Physical form
• Reaction name and type
• Reaction conditions (solvent, temperature,
pressure) and yield
• Graphical structure
• Hyperlink to full text literature
• ~4000 reagents and catalysts
• ~70,000 reactions
• Updated with new reagents/catalysts and
new uses of existing compounds
Ready Accessibility
The EROS database is available to licensees
via the Internet at CambridgeSoft’s Chem-
BioFinder.com portal, and can also be
accessed via the Database HotLink in Chem-
BioDraw, requiring only a supported web
Chem & Bio Office 2010 User Guide 273
Databases

owser, and for structure searching, the
appropriate ChemDraw plug-in (available for
free download). The database can also be
accessed via CambridgeSoft’s E-Notebook, or
placed on your internal network. The database
is licensed annually, and shorter term evaluations
are available.
274 Encyclopedia of Reagents for Organic Synthesis
Chapter 35

Sourcing & Safety Data
36
Sourcing & Safety Databases
The following databases comprise
CambridgeSoft’s Sourcing and Safety Data
offerings:
• ChemACX
• ChemMSDX
• Sigma-Aldrich MSDS
• EH&S Enterprise
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276 Sourcing & Safety Databases
Chapter 36

37
ChemACX
ChemACX (Available Chemicals Exchange) is
a database of chemicals available from chemical
manufacturers and distributors, featuring
complete catalogs of major world suppliers of
fine research, specialty, and industrial chemicals.
ChemACX is a read-only database.
ChemACX Database
Availability:
• Internet Subscription
• Intranet with Chem & Bio Office Enterprise
• SDfile
Number of Catalogs: >535
Number of Unique Chemical Entities:
>530,000
Number of Chemical Products: > 1.6 Million
Key Fields:
• Structure
• Formula
• ACX Number
• Product Name
• Molecular Weight
• CAS Registry Number
• Synonym
• Product ID
• Catalog Number
• Supplier ID
• Property
• Supplier Name
How Is It Useful?
ChemACX is your guide to commercially
available chemicals worldwide. Whether you
are planning a bench synthesis, scale-up, or a
commercial process, you can search these databases
to determine the availability and sources
for the chemicals you need.
You can search ChemACX by any of the following:
• Chemical structure
• Chemical substructure
• Compound name
• Molecular formula
• CAS Registry Number
• Molecular weight range
• Combinations of the above criteria
For information about searching, see the
ChemBioFinder section in the Chem & Bio
Office manual.
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Using ChemACX with
ChemOffice Enterprise
ChemACX allows the user to search for particular
chemicals, view a list of vendors providing
what was searched for, and save the
products desired to a Shopping Cart.
Opening ChemACX
To open ChemACX:
1. Type http://servername into your web
browser.
NOTE: Servername is the name of the
ChemOffice Enterprise machine. For more
information about your server, please contact
your system administrator.
The main ChemOffice Enterprise window
appears.
2. Click ChemACX. The ChemACX Query
Input Form appears.
Searches for chemicals in ChemACX can
include a combination of any of the following
fields:
• Substance Name (text search)
• CAS Registry Number
• ACX Number
• Mol. Formula (formula search)
• MW Range (molecular weight search)
• Catalog Number
To search for information from ChemACX
vendors:
1. Open ChemACX.
2. Enter search criteria.
3. Select the appropriate Search:
• If you would like to search over all of the
vendors in ChemACX, select Search all
vendors.
• If you would like to search over a previously
generated list of favorite vendors,
select Search your favorite vendors.
4. Click Search.
The Search Results page appears. The following
illustration shows part of the results from a
substructure search for cyclohexane.
Searching ChemACX Catalogs
Searching ChemACX is similar to searching
all other ChemOffice Enterprise applications.
278 ChemACX
Chapter 37

Searching Without the Plug-in
A Chem & Bio Draw plug-in is available from
the ChemACX Query Input Form. This plug-in
lets you search by substructure. If searching by
substructure is not necessary, searching without
the plug-in may be appropriate.
Searching without the plug-in allows the user
to simplify the search to a chemical name or a
CAS Registry Number only.
To search without the plug-in:
From the ChemACX query input form,
click Click for Non-Plugin Search.
The Non-Plug-in Search page appears.
results to include products from only your
“favorite vendors”.
To create or edit a list of favorite vendors to
search over:
1. From the ChemACX Query input form,
click Edit Favorite Vendors List.
The Vendor Selector box appears.
1. Take the appropriate action:
If you want to
search
by chemical name
by CAS Registry
Number
with the full query
page, including
structures and other
criteria
Then
in the text box, enter
a chemical name.
in the text box, enter
a CAS Registry
Number.
click Advanced
Query with Plugin.
2. Click Search. The Search Results page
appears.
Creating and Editing Favorite Vendors
It is possible for the user to search for substances
from a shorter list of preferred or
favorite vendors. This shorter list limits search
2. Select the checkbox next to any vendor that
should be included in the favorite list. To
remove a vendor, deselect the checkbox.
3. Click Save as Preferred List.
4. A list of favorite vendors is saved and the
Vendor Selector box closes.
Viewing Search Results
Similar to other Chem & Bio Office Enterprise
applications, search results can be viewed in
two major formats: List View and Details
View.
• List View - lists all results in a compact
manner, giving only summary information
for each result. You are able to register and
lookup MSDX data from this view.
• Details view allows users to view all information
in the selected record. You are able
to register and lookup MSDX data from this
view as well as add items to your shopping
cart.
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To view a record's entry:
1. Search for a chemical on ChemACX. For
more information about searching in ChemACX,
see “Searching ChemACX Catalogs”
on page 278.
2. To view vendors for a specific record, click
Details.The detailed view appears.
6. In the list, select the checkbox next to Add
to Cart and enter a quantity.
The order is added to your Shopping Cart.
7. To view the full catalog listing, click Catalog
Details, and a new window will appear
displaying catalog information.
8. In the list, select the checkbox next to Add
to Cart and enter a quantity. The order is
added to your Shopping Cart.
Viewing Search Results in List View
Results of a search are returned in list view by
default. The maximum total number of records
returned and the number of records returned on
each page is controlled by user preferences.
3. Select one of the tabs: Online Vendors,
Your Favorite Vendors, or Other Vendors.
4. Highlighting a vendor name in the list
found in the tabs will display a catalog listing
to the right. To compare more then one
vendor, hold down CTRL when highlighting
vendor names.
5. Clicking Catalog View or Compact View
will toggle between the two viewing
options. Select whichever view you are
most comfortable with.
The following functions can be performed
from this view:
• Zoom in on the structure.
• List all Synonyms for the substance.
• Access the record in details view.
• Mark the record.
• Register the compound in Registration
Enterprise.
• Access the MSDX data for the compound.
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To view results in list view, perform a search.
Use the browsing buttons to browse through
the pages of result.
• Add products to your shopping cart.
Viewing Search Results in Details View
Clicking on the Details button for a record in
List View brings you to details view for that
record. Details view makes available all of the
tools to browse through vendor catalogs and
add products to your shopping cart.
The following functions can be performed
from this view:
Browsing Vendor Information
Records in details view are displayed with both
structure and vendor information.
To find the vendor catalog you are looking for:
1. Select one of the tabs: Online Vendors,
Your Favorite Vendors, or Other Vendors
depending on your preference.
Highlighting a vendor name in the list
found in the tabs will display a catalog listing
to the right.
• Zoom in on the structure.
• List all Synonyms for the substance.
• Return the List View.
• Mark the record.
• Register the compound in Registration
Enterprise.
• Access the MSDX data for the compound.
• Browse Vendor information.
NOTE: To compare more then one vendor, hold
down CTRL when highlighting vendor names.
2. Select the appropriate viewing option by
clicking on one of the following buttons:
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Catalog View
when the data is not available, the MSDX link
will appear greyed out.
To access a substance's MSDX data, click the
MSDX link in list or details view.
To view the full catalog listing, click Catalog
Details, and a new window will appear displaying
catalog information.
Compact View
• If there is more then one data sheet for the
substance, an option window appears.
• If there is only one MSDS available, or as a
result of selecting one of the options, the
MSDS appears in PDF format.
NOTE: For details about using the shopping
cart, please see “Using the Shopping Cart” on
page 283.
Accessing MSDX Data
MSDX Data, when available, can be accessed
from the MSDX link found in list and details
view on a substance's record. MSDX data is
not available for all substances. By default,
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Using the Shopping Cart
The Shopping Cart is a convenient way to save
a list of chemicals to be ordered. For more
information, about ordering the chemicals in
your shopping cart, see “Ordering Chemicals
in Shopping Cart” on page 283.
You can add items in the shopping cart from
details view of any record.
To view a record's entry:
1. Search for and access a record in details
view.
2. Browse to the product you would like to
add to your shopping cart.
3. In the list, select the checkbox next to Add
to Cart and enter a quantity. The order is
added to your Shopping Cart.
Viewing Your Shopping Cart
Your Shopping Cart list can be retrieved from
the ChemACX Query Input form or the Search
Results page.
To view your Shopping Cart, click either
• On the Shopping Cart page, click Remove.
To remove all items from your Shopping Cart,
click Remove all on the Shopping Cart page,.
Ordering Chemicals in Shopping Cart
There are three options in saving the
ChemACX shopping cart information gathered
during a session: Print, Export to Excel, and
Export to Word.
• To print your shopping cart, click Print.
• To export shopping cart data to Excel or
Word, click Export to Excel (or Export to
Word).
NOTE: Exporting to MS Excel or MS Word are
options configured by your system
administrator. See your system administrator
for more details.
The Requisitioner Information Form
appears.
• OR
•
Your Shopping Cart list appears.
Enter appropriate information in the space
provided.
Removing Items from Shopping Cart
To remove an item from your Shopping Cart:
• Click
Excel (or Export to Word).
Export to
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Your shopping Cart information is saved to
an Excel workbook or Word Document
with one sheet for each vendor.
Registering and Creating
Containers
ChemACX can be integrated with Registration
Enterprise and Inventory if they are installed.
If the system is configured to utilize these features,
the Register link (on search results
pages) and the Send Hits to Inventory button
(on the shopping cart page) are visible. Otherwise,
these tools will not be available.
For more information about configuring your
system to link to Registration Enterprise and/or
Inventory, please see your system administrator.
Registering Products
When this feature is available, a Register link
appears in List View.
1. Click the Register link. A registration window
appears.
2. Adjust the information as desired.
• Change the CAS Registry Number in the
CAS textbox.
• Select a name from the Chemical Name
listbox. The names listed are all names
associated with the record in ChemACX.
3. Click OK.
The compound is added to the Temporary
Table in Registration Enterprise by default.
Creating Containers for Products
When this feature is available, a Send Hits to
Inventory button is found on the shopping cart
page.
To register the compound:
To Send the contents of your Shopping Cart to
Inventory and make containers for them:
1. Click Send Hits to Inventory.
284 ChemACX
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.
An Inventory window appears.
• To commit the data to Inventory, click
Commit Click View to view your new
containers in Inventory.
2. Enter the appropriate information about the
containers being created for each ChemACX
product.
3. Click OK.
Saving Hitlists and Exporting
SDfiles
ChemACX uses the hitlist management and
SDfile Export Features of the ChemOffice
Enterprise.
Logging Off
You can end your session with ChemACX at
anytime.To log off, click the Log Off button.
4. From this screen, you can commit the information
you have entered or test the commit
process before committing the data.
• To test the data before committing, click
Test
Supplier Requests
An updated list of participating vendors can be
found on CambridgeSoft’s corporate website
at:
http://chemacx.cambridgesoft.com/chemacx/
suppliers.asp
CambridgeSoft is always adding new companies
to ChemACX. Contact your supplier and
ask them to participate in ChemACX. To participate,
your supplier sends CambridgeSoft its
product list. The preferred format for submission
is a ChemBioFinder database with structures.
They can also use other electronic
formats such as Access databases or Excel
spreadsheets. They can use a brochure for short
product lists. Send the information to:
Chem & Bio Office 2010 User Guide 285
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ChemACX Data, CambridgeSoft Corporation,
100 CambridgePark Drive, Cambridge,
MA 02140 (USA)
286 ChemACX
Chapter 37

38
ChemMSDX
CS ChemMSDX is a collection of over 21,000
Material Safety Data Sheets presented through
ChemACX in PDF format.
How is it Useful?
Access MSDX data from ChemACX by clicking
the MSDS Database button in the record’s
form.
ChemMSDX provides rapid access to comprehensive
health and safety information to aid in
the safe handling, storage, and transportation
of materials, and provides precautionary and
emergency medical information.
Availability:
• DVD as part of ChemACX Ultra
• Internet Subscription as part of ChemACX.com
• Intranet with ChemACX on Chem & Bio
Office Enterprise
Number of Compounds: > 21,000
Using ChemMSDX
You can access ChemMSDX from the ChemACX
Ultra DVD or Chem & Bio Office
Enterprise.
Access MSDX data from ChemACX on Chem
& Bio Office Enterprise by clicking on the
blue MSDX hyperlink. If the MSDS is not
available, the hyperlink will be grayed out.
Chem & Bio Office 2010 User Guide 287
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Selecting “View MSDS” will cause the MSDS
record to appear in a new browser window in
PDF format.
If multiple MSDS records are available, users
are able to choose which record they wish to
view.
288 ChemMSDX
Chapter 38

39
Sigma-Aldrich MSDS Collection
Extend the coverage of safety information with
this collection of over 130,000 MSDSs for the
products of the Sigma-Aldrich family of catalogs
(Sigma, Aldrich, Fluka, Supelco, Riedelde
Haën) in HTML format. This information is
smoothly integrated with CambridgeSoft's
Enterprise and Workgroup products.
With a click of a hyperlink, users will be able
to view the Sigma-Aldrich MSDS using their
browser.
Availability:
• Intranet with Chem & Bio Office Enterprise
and
• ChemACX Enterprise
• Inventory Enterprise
• E-Notebook Enterprise
• Available with Inventory Workgroup
Number of records: >130,000
Chem & Bio Office 2010 User Guide 289
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290 Sigma-Aldrich MSDS Collection
Chapter 39

40
EH&S Enterprise
EH&S Enterprise is a complete package for
handling Environmental, Health, and Safety
Data and Report Management
How Is It Useful?
Environmental, Heath and Safety (EH&S)
groups are critical to research institutions
because they help to ensure compliance with
laws, regulations and an organization's own
safety policies. As part of the basic function,
these groups often play a key role in the procurement,
inventory, transport, storage, and
disposal of chemicals throughout the organization.
EH&S Enterprise is a fully developed and
proven system to provide clients with information
that allows all departments, from the
receiving clerk to the company's waste disposal
contractor, to properly segregate chemicals
for delivery, storage, handling and
disposal. Chemical structure and substructure
searching provides intuitive access for chemists.
Non-chemists can correctly segregate
chemicals using the chemical segregation
module.
The backbone of EH&S Enterprise is a data
system which has been fully developed by a
certified industrial hygienist with over 24 years
of experience. The data is integrated into the
application using CambridgeSoft Chem & Bio
Office Enterprise technology.
Key Benefits
• Help to segregate reactive chemicals in
compliance with OSHA regulations
• Integrated Department of Transportation
and IATA regulatory information
• Deliver in-depth right-to-know information
to all employees with a few keystrokes.
• HMIS/NFPA hazard warning
• Is the compound a carcinogen or sensitizer?
• Material Safety Data Sheets
• A complete DEA regulated compound database
• Purchases can be pre-approved
• Comply with shipping and storage
requirements
• OSHA and EPA threshold planning lists
• Ensure quantities purchased will not
exceed the threshold planning quantity
• No more process safety management
reports
• Integration with Inventory Enterprise and
Workgroup
Chem & Bio Office 2010 User Guide 291
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• Integration with ChemACX Enterprise and
Workgroup
• Integration with the Sigma-Aldrich MSDS
collection
292 EH&S Enterprise
Chapter 40

Reaction & Synthesis Data
41
Reaction & Synthesis Databases
This section provides information about
CambridgeSoft’s Reaction and Synthesis Data
Chemical Databases.
The following databases comprise
CambridgeSoft’s Reaction and Synthesis Data
Offerings:
• ChemSynth
• ChemReact
• ChemRXN
Chem & Bio Office 2010 User Guide 293
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294 Reaction & Synthesis Databases
Chapter 41

42
ChemReact
ChemReact500 contains essential information
on almost 500,000 reactions referenced in literature
published from 1974-2001. These reactions
have been selected from the parent
InfoChem database with an eye towards
emphasizing those reactions that have been
proven to be synthetically useful. All of these
reactions have been reported as having greater
than 50% yield. ChemReact68 further refines
the selection by adding the criteria that have
been cited in leading journals at least five
times.
About ChemReact
Availability:
• Solvent Structure
• Author
• Title
• Journal Reference
ChemReact68 is a ChemBioFinder database.
No software is included with the database.
When you open ChemReact68 in Chem-
BioFinder, the application starts in browse
view. In this view, users can browse records
using the navigation buttons on the Chem-
BioFinder Menu. To search, click on the
“Search” icon or menu in ChemBioFinder button
• ChemReact68 (ChemBioFinder database
only - no software is included)
• Internet Subscription
• Intranet on Chem & Bio Office Enterprise
Number of Record:
• ChemReact500: 445,717 Reactions
• ChemReact68: 67,926 Reactions
Key Fields:
• Reaction Structure
• Yield
• Reaction Conditions
• Catalyst Structure
Data that can be searched includes chemical
structures and reactions. You can search for
particular templates for starting materials or
Chem & Bio Office 2010 User Guide 295
Databases

products by placing an arrow to the left (product)
or right (reactant) of the structure you
wish to search.
Other searchable fields include yield, reference
information and comments.
Searching
The search page lets you search by reaction,
product or reactant, compound, or literature
reference information.
1. Enter the reaction into Chem & Bio Draw
box provided in the Search Form.
2. Click Search.
To search a structure only as a reactant
1. Enter the structure into Chem & Bio Draw
box provided in the Search Form.
2. Place an arrow to the right of the structure
3. Click Search.
To search a structure only as a product
1. Enter the structure into Chem & Bio Draw
box provided in the Search Form.
2. Place an arrow to the left of the structure
3. Click Search.
When the search is complete, a list of search
results appears.
To search for compounds anywhere in the
reaction
1. Enter the structure into the Chem & Bio
Draw provided in the Search Form.
2. Click Search.
To search for a complete reaction transformation
296 ChemReact
Chapter 42

To view the contents of a particular record in
the list, click Show Details. The complete contents
of the chosen record is displayed.
Chem & Bio Office 2010 User Guide 297
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298 ChemReact
Chapter 42

43
ChemRXN
ChemRXN is a database of chemical reactions
that includes literature citations, products,
reactants, solvent and catalyst data, yields, and
reaction conditions. ChemRXN consists of
ChemPrep and ChemSelect.
How Is It Useful?
ChemRXN provides ready access to information
useful in planning a chemical synthesis. A
reaction query can search for all reactions that:
• Yield a particular product
• Use a particular catalyst or solvent
• Consume a particular reactant
• Have been published by a certain author
For example, you can search for reactions
which produce benzofurans in greater than
90% yield.
ChemPrep
ChemPrep is a carefully prepared chemical
reaction database from the Institute for Scientific
Information (part of Thomson Reuters).
ISI is one of the largest and most reputable
providers of scientific information, and has a
several scientific databases available including
exhaustive reaction and molecular literature
databases.
Directory: ChemPrep
Filenames: Chemprep.cfw, Catalyst.cfw,
Reaction.cfw, Solvent.cfw
Number of Reactions: 16,761
Key Fields:
• Structure (reaction)
• Reaction Formula
• Abstract
• Molecular Weight (components)
• Atmosphere
• Reaction text
• Time
• Key phrases
• Pressure
• Reflux
ChemPrep has a principal form or main screen,
Chemprep.cfw, and three associated forms:
• Reaction.cfw
• Solvent.cfw
• Catalyst.cfw
Reaction.cfw shows the reaction diagram in a
larger window. It is useful in case the reaction
is complicated or has large molecules or many
components. Reaction.cfw is called from the
main screen by clicking the zoom Reaction
button. The “view Solvents” and “view Catalysts”
buttons provide larger views of the sol-
Chem & Bio Office 2010 User Guide 299
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vent (form Solvent.cfw) and catalyst (form
Catalyst.cfw) molecules which appear in the
scrolling lists on the right of the main screen.
Each of these associated forms has a button to
return to the main screen.
The reactions in ChemPrep were selected by
ISI from their larger reaction databases and
were provided with full literature references.
The reaction centers and atomic transformation
matrices were computed with ChemBioFinder.
• Structure (reaction)
• Reaction Formula
• Year
• Molecular Weight (components)
• PageNumber
• Journal
• Yield
• Reaction Text
• Pressure
• Reflux
• Literature text
• Author
• Type
• Title
• Language
• Volume
ChemSelect has a main form, ChemSelect.cfw,
and three associated forms:
ChemSelect
ChemSelect is a collection of the most commonly
cited reactions from the literature,
selected by InfoChem GmbH of Germany. The
ChemSelect data is taken from the VINITI
project of the former Soviet Union, in which
over 2 million chemical reactions were compiled.
The 13,037 reactions of ChemSelect
were obtained using a defined statistical methodology
which selects the most representative
reactions from the database. All reactions contain
full literature citations.
Directory: ChemSelect
Filenames: ChemSelect.cfw, Catalyst.cfw,
Reaction.cfw, Solvent.cfw
Number of reactions: 13,037
Key Fields:
• Reaction.cfw
• Solvent.cfw
• Catalyst.cfw
The associated forms show the data in a larger
window.
To access Reaction.cfw:
• From the main screen, click Zoom Reaction.
To display larger views of Solvent.cfw and
Catalyst.cfw molecules:
• Click Zoom Solvent(s) or Zoom Catalyst(s).
To return to the main screen:
• Click Return or Return to main screen.
InfoChem is a major provider of scientific
information, and has also created selections
called ChemReact68 (68,000 reactions),
ChemSynth (180,000 reactions), and
300 ChemRXN
Chapter 43

ChemReact500 (500,000 reactions). These are
also be available as ChemBioFinder databases.
For further information, contact
CambridgeSoft or InfoChem GmbH.
Selection Criteria
For inclusion in ChemSelect, each reaction
must typify at least five different reactions.
Two reactions are considered to be of the same
type if the reaction centers and the groups
around the reaction centers are identical. Each
reaction in ChemSelect has been cited in at
least five different journal articles, has a yield
of at least 50%, and has been published in a
generally available journal.
Chem & Bio Office 2010 User Guide 301
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302 ChemRXN
Chapter 43

44
ChemSynth
ChemSynth contains essential information on
180,000 reactions referenced in literature published
from 1974-2001. These reactions have
been selected from the parent InfoChem database
with an eye towards emphasizing those
reactions that have been proven to be synthetically
useful. All of these reactions have been
reported as having greater than 50% yield, and
all have been sited in leading journals at least
twice.
About ChemSynth
Availability:
Using ChemSynth
You can use ChemSynth online or with Chem
& Bio Office Enterprise.
ChemSynth is a ChemBioFinder database. No
software is included with the database.
When you open ChemSynth in Chem-
BioFinder, the application starts in browse
view. In this view, users can browse records
using the navigation buttons on the Chem-
BioFinder Menu. To do a search, click on the
“Search” icon or menu in ChemBioFinder button
• ChemBioFinder database only - no software
is included
• Internet Subscription
• Intranet on Chem & Bio Office Enterprise
Number of Record: 178,842 Reactions
Key Fields:
• Reaction Structure
• Yield
• Reaction Conditions
• Catalyst Structure
• Solvent Structure
• Author
• Title
• Journal Reference
Data that can be searched includes chemical
structures and reactions. You can search for
particular templates for starting materials or
products by placing an arrow to the left (prod-
Chem & Bio Office 2010 User Guide 303
Databases

uct) or right (reactant) of the structure you
wish to search.
Other searchable fields include yield, reference
information and comments.
Other Search Methods
You can also search online or with Chem &
Bio Office Enterprise
The Search Page allows searching by reaction,
by product or reactant, by compound, and by
literature reference information. The Chem-
Synth searching form acts much like the other
search forms found in ChemOffice Enterprise
applications.
1. Enter the reaction into Chem & Bio Draw
box provided in the Search Form.
2. Click Search.
To search a structure only as a reactant
1. Enter the structure into Chem & Bio Draw
box provided in the Search Form.
2. Place an arrow to the right of the structure
3. Click Search.
To search a structure only as a product
1. Enter the structure into Chem & Bio Draw
box provided in the Search Form.
2. Place an arrow to the left of the structure
3. Click Search.
The example shows a search for a structure as
a product. When the search is complete, A list
of search results appears.
To search for compounds anywhere in the
reaction
1. Enter the structure into the Chem & Bio
Draw box provided in the Search Form.
2. Click Search.
To search for a complete reaction transformation
To view the contents of a particular record in
the list, click
Show Details. The com-
304 ChemSynth
Chapter 44

plete contents of the chosen record is displayed.
Chem & Bio Office 2010 User Guide 305
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306 ChemSynth
Chapter 44

Index
A
A (any), special atom type 225
A Sample Protocol - IC50 131
abnormal valence 225
About this Guide 87
access privileges 5
acronyms
adding 33, 223
filtering 33, 223
Actions Menu 154
active document sections 53, 224
Adding a new Reactant Collection 13
Adding a Notes Attachment Field 143
Adding a Structure with the Add Dialog 32
Adding an Entry 148
Adding and Mapping an External Data
Source to a Protocol 118
Adding Fields to the Field Dictionary 152
Adding Graph Attachment Fields 141
Adding Items from the AutoText Pane 37
Adding New Solvates and Salts 36
Adding Structures 223
adding structures to reactions 32
Adding Users 166
Additional Tables 99
Advanced Search 185
Aggregate Calculations 106
Allow Editing 104
analyzing reactions 31, 222
ancillary data sections 45, 223
Assigning a Calculation to a Field 105
atom properties
abnormal valence 225
exactly 225
implicit hydrogens 225
indicators 225
isotopic abundance 225
reaction changes 225
reaction stereo 225
ring bond count 225
translation 225
unsaturation 225
up to 225
atom to atom mapping 226
attributes, searching with 226
audit report, printing 195
Audit Trail 194
audit trail
analyzing 194
viewing 195
AutoFit 156
AutoFit Off 156
AutoFit On 156
Auto-Numbered Collections 16
AutoText 36
based on other fields 39
custom 38
field type definition 39
from property lists 39
from section names 40
from tables 40
inserting links 38
item definition 39
keyword definition 39
new definitions 38
section type definition 39
Autotext Based on Other Fields in the Section
39
AutoText pane 37
Avery labels, selecting 188
Chem & Bio Office 2010 User Guide 307

Administrator
B
B 158
backup see database 194
Backup/Restore Database 194
batch import commands
alert 77
batch 75
childReference 76
collectionType 75
import 75
log 76
refresh 77
source 76
target 75
BioAssay Privileges 153
BioAssay User Guide 87
bond properties
reaction center 225
bonds
topology 225
browse 219
Browsing at a Higher Level 16
Browsing from Home 15
Browsing Protocol Data 93
Browsing the Collection Tree 14
browsing the entire collection tree 16
Browsing up to the User Group 10
C
C 158
Calculating IC50 Values 139
Calculation Tables 98
Canceling/Discarding Changes 149
captured image sections 46, 223
CAS registry number 253
Change Quantity 181
Change Status 181
Change Validity 156
changes to collections, saving 59
Changing Collection Security Properties 24
Changing Password 166
changing passwords 190
changing quantities 181
check-in/check-out 180
Check-In/Check-Out Containers 180
Check-in/out, Changing Quantities, and
Other Shortcuts 180
Chem & Bio Office 244
ChemACX 176, 255, 277
opening 278
ordering chemicals 283
removing from shopping cart 283
saving search results 279
searching 278
using 278, 285
viewing search results 283
ChemACX-SC 255
chemical structure fields 30, 222
chemical structure search 225
chemical structures
automatic naming 31, 222
deleting 33, 223
drawing 30, 61, 224
Chemical synthesis database 251, 261, 263,
289, 291, 299
Chemicals database 255, 277
ChemIndex 253, 271, 273
ChemMSDX 287
ChemPrep 299, 300
ChemRXN 251, 261, 263, 291, 299, 303
ChemSelect 300
collection attributes, in queries 226
collection properties 225
Collection Security 221
collection security 24
collection tree
browsing 14, 219
browsing all 16
hiding 15
308 Index

hiding collections 15
home collection 15
limiting browsing 15
reactants folder 13
references in 220
root collection 15
showing collections 15
collections
behaviors 16
container 220
copying 21
deleting 220
duplicating a section in 222
exporting 23
home 15
importing 23, 221
limitations on 16
links from table cells 52
managing 220
moving 220
moving sections in 56, 222
organizing 19, 220
reactants 13
renaming 22, 220
saving changes 59
searching for 225
security properties 24
table of contents 13
templates 23, 221
transition 25, 221
unlocking 81
user 9
viewing properties 22, 220
Coloring Options 157
Commonly cited reactions 300
Compound Lists 145
compounds, acronym lists 33, 223
compounds, adding to stoichiometry table
35
compounds, automatic naming 31, 222
compounds, removing from stoichiometry
table 35
Conditional Calculations 110
Conflict Resolution 177
conflict resolution 177
create duplicate 177
edit 177
select 177
Conflict Resolution - Create Duplicate 177
Conflict Resolution - Edit 177
Conflict Resolution - Select 177
Container 170
container grid 193
Containers 171
containers 171
changing status 181
creating 179
definition 170
deleting 180
duplicating 180
editing 171, 179
managing 179
multiple select 182
new 171
searching for 184
Copy 157
Copying a Collection 21
copying collections 21
creating
containers 179
experiments 10
new locations 172
notebooks 10
pages 10
substances 174
Creating a Folder 12
Creating a Graph Template 122
Creating a New Container 179
Creating a New Location 172
Creating a New Substance 174
Creating a Notebook 10
Creating an IC50 Protocol 131
Chem & Bio Office 2010 User Guide 309

Administrator
Creating Graphs 138
Creating New Autotext Definitions 38
Creating Report Templates 146
Creating Reports 146
CS Inventory
adding non-chemical items 179
tasks 190
terminology 170
user interface 170
CS Inventory Tasks 190
Curve Fit Calculations 108
Curve Fit Templates 124
custom AutoText 38
Custom Fields 193
custom fields 193
Cut 157
cut and paste, sections 56
D
D 159
data
chemical structure 61, 224
from external databases 224
images 62
in table cells, editing 51, 223
properties 63, 224
text 62, 224
working with 224
Data Manipulation and Curve Fitting 121
Data Statistics 125
database tables 224
database, backup and restore 194
default units
in property lists 79
in tables 79
Defining a New External Data Source 117
Defining a Picklist 150
Defining a Primary Protocol Table 101
Defining External Picklists 150
Defining Fields in a Table 101
Defining Security 110
Defining Tables and Fields 100
deleting
containers 180
locations 173
Deleting a Collection 22
Deleting a Location 173
Deleting a Structure with the Reaction
Toolbar 33
Deleting an Entry 148
Deleting Annotation 124
deleting collections 220
Deleting Containers 180
Deleting External Picklists 152
Deleting Report Templates 147
Deleting Users 166
Designing a New Protocol 100
drag-and-drop of containers 180
drawing structures and reactions 30
drawing window, expanding 30
Duplicate Container 180
Duplicating a Collection 220
duplicating a container 180
Duplicating a Protocol 92
E
E 160
Editing
favorite vendors list 279
editing
containers 179
locations 173
sections 221
substances 177
Editing a Container 179
Editing a Location 173
Editing a Substance 177
Editing External Picklists 152
editing information in table cells 51, 223
310 Index

Editing Report Templates 147
Editing the settings tables 148
EHS
labels 188
reports 189
EHS data 183
EHS help file 183
EHS Labels 188
EHS Reports 189
ending a session 81
E-Notebook Features 217
E-Notebook, collections 217
E-Notebook, introduction 7, 217
E-Notebook, refreshing 79
environmental, health, and safety see EHS
data 183
Equation 125
Exact 185
exact phrase matching 226
experiments
closing 11
creating 10
exporting
collections 23
Exporting Data to Excel 90
External Analysis 130
External Calculations 110
External Datasource 153
External Picklists 150
F
F 160
Field Dictionary 152
field type, in AutoText definitions 39
Field Types 102
fields
chemical structure 30, 222
fields, custom 193
File Import Data Source Options 114
File Import Templates 99, 111
Filtering Acronyms with the Reaction
Toolbar 33
Filtering Data 90
Fit Statistics 125
Fitting Data to a Curve 124
folders
adding a reference 12
autotext definitions 12
reactants 12, 13
template 12
user configuration 12
form tools 24, 221
Form, see Query Input Form
Forms 171
forms 171
G
G 160
Getting Help 91
Graph Images 123
Graph Options Additional Content Tab 128,
129
Graph Options General Tab 127
Graph Templates 99
Graphing Options 127
H
H 160
history pane 60
home collection 15
hydrates, adding to stoichiometry grid 35
hydrogens, implicit 225
I
I 160
Identity 185
images
annotating 62
in chemical structure fields 62
Chem & Bio Office 2010 User Guide 311

Administrator
in tables 51, 223
implicit hydrogens
in queries 225
Import Data 157
importing
MS Excel spreadsheets 54
MS Word document 53
spectra 47
Importing and Exporting Collections 23
Importing and Viewing Data 111
Importing Data 115
Importing Data from External Data Source
117
Importing the Data File 135
Indexed Fields 104
Input form, see Query Input Form
Inserting Annotation 123
Installation 244
Integrating with Excel 120
Interactive Graphs 123
Inventory Desktop & Workgroup 169
Inventory Workgroup & Desktop 12.0 169
isotopic abundance 225
items, in AutoText definitions 39
K
K 161
Key Fields 104
keywords, in AutoText definitions 39
L
L 161
Labels 187
labels 186
labels, EHS 188
labels, printing 187
limiting browsing 15
Limiting Collection Browsing 15
links
from property lists to collections 65
from property lists to sections 65
from table cells to collections 52
from table cells to sections 52
links, inserting with AutoText 38
LN (link node), special atom type 225
Location 170
location
definition 170
Location Tree 172
location tree 172
location tree, refreshing 173
Locations 171
locations 171
creating 172
deleting 173
editing 171, 173
moving 173
new 171
locked collections, releasing 81
locking records 193
Logging in to BioAssay 87
Login and Logout 170
login and logout 170
M
M 161
M (metal), special atom type 225
managing
container list display 193
containers 179
locations 172
substances 174
tables 192
users 192
users and roles 190
Managing Containers 179
Managing EHS Data 183
Managing Locations 172
Managing Organizations 237
312 Index

Managing Roles 191
Managing Spectral data 223
Managing Substances 174
Managing Tables 192
Managing the Container list display 193
Managing Users 192
Managing Users and Roles 190
Managing Users Through BioAssay 165
Manipulating Compound Lists 145
Manipulating Data Points 125
mapping, in reaction queries 226
Material Safety Data Sheets 175
material safety data sheets see MSDS
Mathematical Calculations 106
misplaced containers 174
missing containers 174
Mixtures 176
mixtures 176
Modifying the File Import Template 143
moving
locations 173
Moving a Container 180
Moving a Location 173
Moving a Protocol or Project 92
moving containers 180
moving containers, with drag-and-drop 180
MS Excel sections 54
MS Word
displaying toolbars 53
exporting sections to 222
importing a document from 53
spell check 54
MS Word sections 53, 224
MSDS
attaching to substances 175
viewing 176
MSDS database 287
Multi Select 182
Multi-select feature 182
N
N 162
Name=Struct feature 31, 222
National Cancer Institute database 259
Navigation 88
navigation
browsing 14, 16
home collection 15
table of contents 13
Navigation Overview 4
navigation, in E-Notebook 219
New Features 87, 169
non-chemical items, adding to the database
179
Normalizing Values 137
Notebooks 10
notebooks
creating 10
O
O 162
Online help 244
Opening
ChemACX 278
Ordering chemicals through ChemACX
283
organizing sections 221
organizing tables 49
Other Commands 156
Overview 131
P
P 163
pages
closing 11
creating 10
passwords, defining 190
Paste 157
Performing a Collection Transition 25
Chem & Bio Office 2010 User Guide 313

Administrator
permissions 5
Picklist 150
Plate Block Data Format 114
Plate Formats 149
Plate Setup 149
Plate Template Manager 96
Plotting Data using a Graph Template 122
preconfigured sections 29, 221
Primary Tables 98
Printing 90
printing 186
labels 187
reports 189
template wizard 187
Printing an Audit Report 195
Printing Labels and Reports 186
privileges 190
products, searching for 226
Prohibited Field Names 158
properties
adding to property lists 63
reaction center 225
removing from property lists 64
properties, of collections 22, 220
properties, see also atom properties
property lists 63, 224
adding properties to 63
default values 79
editing values 64
in spectrum sections 47
linking to a URL 53
linking to collections 65
linking to sections 65
linking to URLs 66
references in 65, 224
removing properties from 64
Protocol Data 93
Protocol Data and Definitions 92
Protocol Definitions 97
Protocol Navigation 91
Protocol Security 99
Protocol Tasks 93
Protocols 91
Q
Q 163
Q (heteroatom), special atom type 225
quantities
changing 181
queries 224
abnormal valence 225
atom properties 225
collection 225
exactly 225
implicit hydrogens 225
isotopic abundance 225
location 225
metadata 225
product 226
reactant 226
reaction change 225
reaction stereo 225
ring bond count 225
special atom types 225
structure 225
text 226
text, advanced 227
text, exact phrase 226
translation 225
unsaturation 225
up to 225
wildcards 226
queries, refining 227
Query Input form
accessing 278
opening 278
R
R 163
R, special atom type 225
reactant collections 13
adding 13
314 Index

eactants
adding new to collection 41
searching for 226
reactants collection 41
reactants collection, adding new 42
reactants folder 13
reaction center 225
reaction changes 225
reaction searching 226
reaction sections 222
reaction stereo 225
reaction toolbar 31, 33, 222, 223
reactions
adding structures 32
analyzing 31, 222
drawing 30
reagents, see collections, reactants 13
Recalculate 157
Reconciling Locations 174
reconciling locations 174
Record Locking 193
record locking 193
rectify contents 174
references
adding to folders 12
references, in property lists 65, 224
references, in table cells 52, 224
refining a search 227
refreshing E-Notebook 79
Refreshing the Data View 90
Refreshing the Location Tree 173
refreshing the location tree 173
Removing
ChemACX shopping cart 283
Removing a Field from the Field Dictionary
153
Removing a Filter 33
removing a section 56
Removing Reactants and Products 35
Renaming a Collection 22
renaming collections 22, 220
renaming sections 57
Reporting 145
Reports 189
reports 186
EHS 189
matching fields 189
printing 189
Required Fields 104
Resizing and Moving Columns 89
resizing columns or rows in tables 49
resolving conflicts 177
restore see database 194
ring bond count 225
roles 190
managing 191
roles, assigning users to 191
roles, nesting 191
root collection 15
Running the External Data Source Manually
119
S
S 163
safety data see EHS data 183
Salts and Solvates 35
salts, adding to stoichiometry grid 35
Sample External Analysis 130
Save Compound List 157
Saving
ChemACX search results 279
to Shopping cart 279
saving changes to collections 59
search 219
search location field 225, 226
Search Preferences 186
searches 184
advanced techniques 185
Chem & Bio Office 2010 User Guide 315

Administrator
for containers 184
for substances 186
preferences 186
simple 184
searches, refining 227
Searching
ChemACX 278
searching
for collections 225
for locations 225
for metadata 225
for products 226
for reactants 226
for reactions 226
for structures 225
for text 226
for text, advanced 227
for text, exact phrase 226
with collection attributes 226
with wildcards 226
Searching CS Inventory 184
Searching for and Viewing Data in Tables
115
Searching for Containers 184
Searching for Substances 186
Searching Protocol Data 93
section type, in AutoText definitions 39
sections
active document 53, 224
ancillary data 45, 223
captured image 46, 223
creating 55, 221
cut and paste 56
duplicating 222
editing 221
exporting to MS Word 222
links from table cells 52
managing and organizing 221
moving 56, 222
MS Excel 54
MS Word 53, 224
overview 221
preconfigured 29, 221
reaction 222
removing 56
renaming 57
Security 165
security
collection 24
security, overview 5
Select All 158
selecting multiple containers 182
session manager 81
sessions, ending 81
Setting Calculation Options 136
Setting up a File Import Template 133
Setting up Plate Format 132
Setting up the Wells Table 132
Settings 148
Shopping cart
removing entries 283
saving to 279
viewing 283
Show Coloring 158
Show Field 104
Show Only Valid Data 158
Showing Columns 14
Similarity 185
Simple Search 184
solvates, adding to stoichiometry grid 35
Solvents 40
solvents folder 40
solvents, in reaction sections 40
Sorting Data 89
sorting, data in tables 49
special atom types 225
spectrum
adding to a section 47
replacing 47
zooming in on 47
spell check, in MS Word fields 54
316 Index

spreadsheets 54
SQL queries, editing 184
Start Menu Login 5
status, of containers 181
stoichiometry grid 34, 222, 223
adding salts or solvates 35
adding to 35
removing reactants or products 35
structure query field 225
structure searches 185
exact 185
identity 185
similarity 185
substructure 185
structures
deleting 33, 223
drawing 30
in tables 51, 223
styled text 62, 224
subsections 63
Substance 170
substance
definition 170
Substances 172
substances 172
creating 174
editing 177
managing 174
new form 172
searching for 186
select form 172
substituents
exactly 225
up to 225
Substructure 185
Substructure Search 185
substructure search see structure searches
Summary Tables 99
supplied reactants 13
Supplier Information Form 279
supplier list, abbreviating 193
Suppliers 193
suppliers, adding from the ChemACX link
175
Suppliers, requesting 285
supplies, adding to the database 179
Synthesis database 251, 261, 263, 289, 291,
299
T
T 164
Table and Form View 90
table of contents 13
hiding columns 14
showing columns 14
sorting 14
table sections 48, 223
tables
adding columns or rows 48
changing information in 51, 223
default values 79
managing 192
moving columns or rows 49
organizing 49
references in 52, 224
removing columns or rows 48
resizing 49
sorting 49
templates
for experiment creation 23, 221
Terminology 87, 170
terminology, in E-Notebook 83
text, adding with AutoText feature 36
text, styled 62, 224
The Reaction Toolbar 31
The Stoichiometry Table 34
The User Collection 9
The User Configuration Folder 12
The User Interface 170
Tool Tips 244
Chem & Bio Office 2010 User Guide 317

Administrator
toolbars
reaction 31, 222
topology, of bonds 225
transition security 25
transitions 25, 221
translation (query property) 225
U
U 165
units, numerical 79
unsaturation, in queries 225
up to, in queries 225
Updating Users 166
URL, linking to 53, 66
user collection 9
user configuration folder 12
users, assigning to roles 191
users, managing 192
Using
ChemACX 278, 285
Shopping cart 279
Using a Picklist 150
Using ACX 176
Using Annotation in Graphs 123
Using External Picklists 151
Using Quick Add to Add a Structure 32
Using the Field Dictionary 152
V
V 165
Validating Data 119
Validating Protocol Data 116
Verifying Results 137
View (from the plate format table) 155
View Details 155
View Picklist 155
View Plate Format 155
Viewing
ChemACX shopping cart 283
Viewing and Browsing Data 116
Viewing Collection Properties 22
Viewing Commands 155
Viewing Data of Attachment Fields 142
Viewing Protocol Properties 92
Viewing the Audit Trail 195
Viewing the Field Dictionary 153
Viewing the Plotted Data 125
visual display of changes
effect of 56
W
W 165
Well Formats 149
What’s New 7
wildcards
in searches 226
X
X 165
X (halogen), special atom type 225
318 Index

CambridgeSoft
Solutions
featuring
E-Notebook
DESKTOP SOFTWARE
ENTERPRISE SOLUTIONS
CHEMICAL & BIOLOGICAL
RESEARCH INFORMATICS
LABORATORY, DEVELOPMENT &
MANUFACTURING INFORMATICS
KNOWLEDGE MANAGEMENT
SCIENTIFIC DATABASES

CAMBRIDGESOFT
Vision, Passion
Research, Discovery, Development,
CambridgeSoft Software, Solutions and Databases

SOLUTIONS
& Innovation
Trials and Manufacturing
Motivated by Vision
Innovation is an organizational must in pharmaceutical, biotechnology, and chemical industries.
Effective new ideas, developed through collaboration and communication, free from organizational
boundaries, will determine your long-term success. In today’s connected world, information flow
within organization can be overwhelming. Large amounts of data—some structured and some
unstructured—can cloud an R&D organization’s ability to focus on what is important. Since 1986,
CambridgeSoft has been solving the problem of electronic storage and communication of chemical structures, models, and information.
Starting with ChemDraw, then broadening to ChemOffice in 1992 and BioOffice in 2004, CambridgeSoft extended its software to
include enterprise wide solutions with ChemOffice Enterprise in 1998, E-Notebook in 2000 and biology with BioAssay in 2001. Today,
CambridgeSoft products are used by hundreds of thousands of chemists, biologists, scientists, and engineers who work in pharmaceutical,
biotechnology, and chemical industries, including government and academic research. These systems work within your research, discovery,
development, trials and manufacturing, and information technology to help you capitalize on your organization’s intellectual assets. By
turning information into explicit knowledge, you accelerate innovation and drive organizations forward.
Created with Passion
Chemists, biologists, scientists, and engineers need timely, convenient access to critical information,
whether structured or unrefined. CambridgeSoft, which began by helping scientists manage desktop
chemical and biological information with Chem & Bio Draw, now addresses enterprise-wide scientific
information problems with Chem & Bio Office Enterprise and Workgroup. These solutions are flexible
and powerful to deal with today’s complex projects which span functional organizations and geographical
boundaries. Eliminating data barriers and bringing information to all—in the form they need to interpret it—aligns all of the members
of your teams, focusing their collective knowledge and diverse skills toward the common goals of problem solving and innovation.
The results can be dramatic:
· Information transparency and group collaboration improve productivity and reduce costs.
· Faster and smarter research decisions cut time to market and increase productive efforts.
· Empowered employees contribute increased value to the research, discovery, development, trials and manufacturing organization.
Advanced through Innovation
When your research, discovery, development, trials and manufacturing organization is
able to respond swiftly and effectively to opportunities and market changes, promote innovation and
accelerate product delivery, you are working smarter to outpace your competitors. As the speed of business
continues to accelerate, leading organizations constantly seek faster and better informed decision
making as well as new business efficiencies. For the individual chemist, biologist, scientist, and engineer
who needs to capture, organize, and communicate chemical and biological data, through the complex and widespread workgroup
and enterprise scientific information systems needs, CambridgeSoft Solutions can help.

CAMBRIDGESOFT
Chem & Bio Office Desktop
KNOWLEDGE
MANAGEMENT
CHEMICAL,
BIOLOGICAL
Desktop
Chemistry
E-Notebook
Biology
E-Notebook
BioAssay &
ChemBioViz
Process
E-Notebook
Workflow
LIMS
BioSAR
Enterprise
Enterprise
Compliance
E-Notebook
DocManager
Enterprise
Chem & Bio Office
Enterprise
E-Notebook Enterprise
Chemistry & Biology
Analytical Services
Sample Management
Workflow LIMS
Compliant DB
Oracle Cartridge
BioAssay Enterprise
BioDraw
BioSAR & BioViz
Registration Enterprise
ChemBioFinder
Enterprise
KNOWLEDGE MANAGEMENT
Research organizations thrive when information is easily captured, well organized and readily available.
E-Notebook Enterprise streamlines record keeping with rigorous security and efficient archiving,
and facilitates text and structure searching. E-Notebook provides organizations with a powerful
mechanism to transfer mission criticalwork product from shared drives to a well-organized, compliant
and searchable Oracle application. MS Office, chemical structures and workflow support
modules are provided for the full range of research and development activities.
LABORATORY INFORMATICS
Laboratory Informatics includes Workflow LIMS for instrumentation automation, Compliant DB for storage
of your data and the Oracle Cartridge which is the industry’s only enterprise content management
system developed by a large pharmaceutical company.
BIOLOGICAL INFORMATICS
Finding structural determinants of biological activity requires processing masses of biological
assay data. Scientists use BioAssay Enterprise and BioSAR Enterprise to set up biological models
and visualize information. The BioViz application allows you to create graphical representations
of data.
CHEMICAL INFORMATICS
Managing huge data streams is a key challenge. Registration Enterprise organizes information
about new compounds according to an organization's business rules.

SOLUTIONS
to Enterprise Solutions
LABORATORY &
MANUFACTURING
SCIENTIFIC
DATABASES
Inventory
Enterprise
ChemACX
Database
The Merck
Index
Registration
Enterprise
GxP
Validation
Sigma-Aldrich
MSDS
Oracle Cartridge
or SQL DB
Compliant
SDMS
ChemBioFinder
Gateway
Inventory Enterprise
Materials Management
Compliance Management
ChemDraw & Chem3D
ChemFinder & ChemInfo
BioDraw, BioAssay &
BioViz
Inventory & E-Notebook
ChemBioFinder Gateway
The Merck Index
ChemACX Database
Development
Training & Support
MANUFACTURING INFORMATICS
CambridgeSoft’s Inventory Enterprise application is designed to manage the
chemical, reagent, sample and compound tracking needs of large multi-site
chemical and pharmaceutical laboratories. Inventory Enterprise is an Oracle-based,
ChemOffice Enterprise product that is designed for multiple users with diverse
container types, racks, and multi-well plate formats.
DESKTOP SOFTWARE
Success begins at the desktop, where scientists use ChemOffice, ChemDraw, BioOffice and
BioDraw to pursue ideas and communicate with the natural language of chemical structures,
biological pathways, and models. Scientists organize information and manage data with E-
Notebook and Inventory. ChemBio3D provides modeling, ChemBioFinder aids searching, while
BioOffice adds BioDraw, BioAssay and BioViz. All are integrated with Microsoft Office to speed
research tasks.
SCIENTIFIC DATABASES
Good research depends on reference information, starting with the structure-searchable
ChemACX Database of commercially available chemicals and Sigma-Aldrich MSDS. The Merck
Index and other scientific databases provide necessary background about chemicals, their properties,
and reactions.
PROFESSIONAL SERVICES
CambridgeSoft's scientific staff has the industry experience and the chemical and biological
knowledge to maximize the effectiveness of your information systems.

ENTERPRISE &
Chem & Bio Office Enterprise
Integrated Research, Discovery, Development,
Desktop to Enterprise
Since the company's founding, CambridgeSoft's desktop software,
starting with its industry-leading Chem & Bio Draw, has
been the cornerstone application for scientists who draw and
annotate molecules, reactions, and pathways. This suite of enterprise
applications has developed and now provides solutions in all
areas of discovery.
Research and Discovery
Researchers can record and share their experimental
information using E-Notebook, while protecting intellectual property
with digital signatures and 21 CFR Part 11 compliance. They
can design both single experiments or design combinatorial
libraries of compounds. They can find and purchase reagents in
ChemACX database, store and use them from Inventory, record
newly made compounds within a proprietary Registration system,
record the results in BioAssay, analyze the results with BioViz, and
generate reports linking activity and structure with BioSAR.
Virtually every aspect of discovery, from synthesis planning,
library enumeration, reagent selection, primary and secondary
screening, in vivo testing, through to analysis of results and reporting
is covered by this integrated application suite.
Development and Testing
Building on productivity software, CambridgeSoft created enterprise
applications to meet the needs of an everexpanding research
and development community that relies on data sharing across scientific
disciplines, research campuses, and even oceans as globalization
has increased demands. Since the software takes advantage
of the latest web based technologies, it is deployed readily
throughout a research and development organization. Using the
integrated suite, scientific teams are well armed to solve the daily
challenges of development. These teams include scientists who
scale up and design manufacturing procedures,toxicologists who
determine the metabolic fate of drugcandidates, formulation scientists
who determine drugdosing and delivery systems, as well as
many others.
Trials
A suitable drug candidate is one that has the desired activity to
provide disease therapy while meeting drug safety requirements,
can be manufactured in a cost effective and reproducible fashion
under 21 CFR Part 11 and Good Manufacturing Processes
(GMP) guidelines, and is stable under normal formulation and
storage conditions. With a drug candidate in hand, the final challenge
is to determine safety and efficacy in a patient population.
All specifications subject to change without notice.
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WORKGROUP
and Workgroup Solutions
Trials and Manufacturing WorkflowW
Manufacturing
Manufacturing requires the transfer of data and batch process
records from the pilot plant studies using Inventory, E-Notebook,
and Registration systems under Good Laboratory and
Manufacturing Processes (GxP).
The handling of materials, including chain of custody requirements,
material documentation, material workflow, such as availability
states and recertification dates, are tracked and handled by
the system.
These systems meet the requirements and provide the basis to
manage materials and records during clinical trials. Clinicians can
design and record results from protocols, and all of these web
based software systems provide the access required by clinicians
who are removed from the sponsoring company.
Chem & Bio Office Enterprise
Chem & Bio Office Enterprise is a comprehensive knowledgemanagement
and informatics solution, covering electronic notebooks,
biological screening and chemical registration over your
intranet. ChemBioOffice Enterprise Ultra includes E-Notebook for
record keeping, BioAssay for low and high throughput screening
with integrated plate inventory, BioSAR for SAR reports,
Registration System, Inventory for reagents and biologicals, and
ChemACX database of available chemicals. Technologies include
ChemDraw ActiveX and Oracle Cartridge.
Chem & Bio Office Workgroup
Chem & Bio Office Workgroup Ultra is a comprehensive knowledge
management and informatics solution, covering electronic
notebooks, biological screening and more over your intranet.
Chem & Bio Office Workgroup Ultra includes E-Notebook
for record keeping, BioAssay for low and high-throughput screening,
BioViz for visualization, Inventory for reagents and ChemACX
database of available chemicals. Technologies also include SQL
Server for affordability and ease of administration.
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KNOWLEDGE
Overview &
E-Notebook’s Flexible Architecture
E-Notebook
Used for collaboration and knowledge sharing, regulatory compliance,
intellectual property protection, LIMS,document management,
project management, and workflow support, E-Notebook is
the leader in a new class ofapplications. Configurable, multi-purpose,
and enterprise-scalable, it provides a solution to a large set of
requirements across R&D and manufacturing. E-Notebook's foundation
layer of features includes support for 21 CFR Part 11, 37
CFR and GxP compliance, on top of which a widely configurable
design interface provides support for specific scientific and regulatory
workflows. Because this diverse portfolio of requirements is
met in a single applicationplatform, E-Notebook both lowers the
total investment required to meet these needs, and provides a substantial
increase in productivity due to a far more integratedenvironment
for scientists and technical staff.
E-Notebook Architecture
CambridgeSoft’s E-Notebook provides a comprehensive, easy-touse
interface designed to replace paper laboratorynotebooks in a
variety of settings. Underneath is a fullyconfigurable, secure system
for organizing the flow ofinformation generated by your
organization. Scientists can enter chemical reactions, Microsoft
documents (Word, Excel, PowerPoint), spectra, biological data
and images, and other types of information and documents. It also
allows you to search by text, chemical substructure, metadata tags,
organizational hierarchy, or other keys.
E-Notebook Architecture
E-Notebook Enterprise edition is a globally-deployable, Oraclebased
application designed for everyone from small research
groups to global organizations. Oracle Cartridge manages chemical
structures and reactions in a common data repository, layered with
detailed security and is 21CFR Part 11 Compliant (audit trails,
digital signatures). The enterprise edition works with procurement
databases and services including ChemACX database and Inventory
management systems to save time locating chemicals and entering
structures.
Flexible and Configurable Architecture
The E-Notebook architecture is designed to provide organizations
with an unparalleled level of flexibility. A powerful configuration
layer is provided to make it possible to modify substantially the
look and feel of the application in order to meet very diverse workflows.
Detailed workflow support in the same application is provided
for researchers in early stage discovery through early clinical
development even though the requirements for these groups are
totallydifferent. Beyond configuration, a rich API is provided for
custom development and system integration.
E-Notebook is also in production with integrated inventory systems
including CambridgeSoft’s Inventory manager, as well as
in-house systems, analytical data capturing systems, and compound
registration systems. E-Notebook supports limiting access to
certain information at the project or group level if desired, as security
is granular. Information can be shared or secured as desired
throughout the framework.
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MANAGEMENT
General R&D
IP Protection and Regulatory Compliance
General R&D
CambridgeSoft’s E-Notebook is a solution that enables
pharmaceutical and biotechnology companies to improve the
efficiency of the process from diseased target identification to product
launch. Its core Oracle database manages the workflow to be
compliant with Good Laboratory Practices (GLP), Good
Manufacturing Processes (GMP), and the FDA’s 21 CFR Part
11; while the client interface is highly configurable and flexible.
Anywhere a shared drive is used, E-Notebook can offer a better
solution.
Through the R&D process, using CambridgeSoft’s E-Notebook in
each subsequent stage adds increasing scientific and economic
value by providing workflow automation and knowledge sharing.
Research and Discovery
E-Notebook Enterprise is capable of providing knowledge management,
chemical- and biological-focused solutions in virtually all
areas of discovery. Researchers can record and share their experimental
information, while protecting intellectual property with
digital signatures and 21CFR Part 11 and 37 CFR compliance.
• Chem & Bio Draw—draw and annotate molecules,
reactions, and biological pathways
• ChemACX—find and purchase reagents
• Inventory—store and track reagents and samples
• Registration—record newly made compounds
• BioAssay—model complex protocols and record results
from biological testing
• BioSAR—generate reports linking activity with structure
• BioViz—analyze biological results
Virtually every aspect of discovery process—from synthesis
planning, library enumeration, reagent selection, primary and
secondary screening, in vivo testing, through to analysis of results
and the reporting of data—is covered by the integrated
E-Notebook solution.
• Replace Shared Drives with Oracle
• DMPK, Screening Biology, Genetics, and Microscopy
• LIMS, Method Execution, 21 CFR Part 11, GxP
Development and Testing
CambridgeSoft’s Enterprise E-Notebook meets the needs of ever
expanding research and development communities that rely on
data sharing across scientific disciplines and campuses as globalization
has increased demands.
E-Notebook allows custom integration of a large array of modules,
in-house applications, lab instruments, and back-end data storage
to provide a true end-to-end solution for development and testing.
Designing workflows and calculations is much faster and requires
far less programming using the E-Notebook than existing lab information
systems. End users include scientists and process chemists
who scale up and design manufacturing procedures, toxicologists
who determine the metabolic fate of drug candidates,
formulation scientists who determine drug dosing and
delivery systems, as well as many others.
Trials and Manufacturing
A suitable drug candidate has the desired activity to provide disease
therapy while still meeting safety requirements, can be manufactured
in a cost effective fashion under 21 CFR Part 11 and
GMP guidelines, and is stable under normal
formulation and storage conditions. The handling of
materials, including chain of custody requirements, material
documentation, material workflow, such as availability states and
recertification dates, are tracked and handled by the
E-Notebook application. CambrideSoft’s E-Notebook meets these
requirements under Good Laboratory and Manufacturing
Processes (GxP) and provides the basis to manage materials and
records during clinical trials.
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KNOWLEDGE
Chemistry &
Electronic Journal J
and Record Keeping,
Chemistry
Under the R&D value chain, chemistry can be further
divided into three separate stages: synthetic chemistry
(research/discovery), analytical chemistry (pre-clinical) and
process chemistry (development). The flexibility and configurability
of E-Notebook enables a successful data repository, analysis,
sharing, reporting, and searching efficiently and paper-free.
Synthetic Chemistry
Synthetic Chemists take advantage of many features tied into a
smooth interface within CambridgeSoft’s Enterprise E-Notebook.
Reactions are drawn with in-place editing; a stoichiometry grid
dynamically fills with the formulas, molecular weights, and chemical
names. Reagents can also be imported from other systems,
such as available chemicals from the ChemACX database or
Registration system.
CombiChem is one important aspect of library generation for
Synthetic Chemists. For some, E-Notebook serves as the complete
CombiChem solution, taking advantage of features such as the
enumeration of products from a virtual library on a flexible plate
layout, a multiple reaction site checker, and multiple step parallel
synthesis. Others simply import a list of compounds from an
external source or SDFile so that they can record and calculate
data on a library-wide stoichiometric table.
Analytical Chemistry
E-Notebook serves as a repository for analytical data, and it also
acts as a communication portal with which scientists and analysts
communicate with each other. Scientists can create and send
service requests directly to an analyst with the click of a button.
Paper is eliminated: when results are obtained, the analyst can
send the images and chromatograms directly back to the scientist's
E-Notebook.
• Chemical Synthesis, Scale-up and Analytical
• 37 CFR Electronic Signatures
• Service Requests and Discovery Workflow
Process Chemistry
The objective of process research is to identify efficient processes
for the synthesis of active pharmaceutical agents at the scale
required for clinical trials and commercial use. It is necessary to
provide precise descriptions of these processes so that they can be
executed by different groups in different locations. It is also
required that such processes be compliant with Good Laboratory
Practices (GLP), Good Manufacturing Processes (GMP) and the
FDA's 21 CFR Part 11 regulation. E-Notebook's process chemistry
modules are designed to support these dual workflow and
regulatory compliance needs of process chemists.
Reaction Properties
PowerPoint Integration
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MANAGEMENT
Biology
DMPK, Screening Biology, Microscopy
Discovery Biology
These scientists are involved at the very start of the drug
discovery process, as genomics and genetics are essential
disciplines used when identifying a disease target. This work is
methodical but unscripted, and so requires an electronic notebook
pallet that is as free form as its paper predecessor. This is
where the benefit of E-Notebook's flexibility is unmistakable.
While the system can be set up with rigid form based data entry
appropriate for later stage research and development, discovery
biology configurations are typically open and boundless. Genomic
map and DNA, RNA and protein sequence files can be draggedand-dropped
into E-Notebook, sequencing results can be sent
directly from instruments to electronic experiments, and protocols
and data can be managed with familiar tools such as Microsoft
Word and Excel.
The beauty of capturing data in E-Notebook is that
information can be compiled and viewed in a meaningful way. For
example, the creation of a new biological strain entails many steps,
potentially involving nonconsecutive workdays of various individuals.
E-Notebook can generate customized reports that meaningfully
summarize the process in real time. These reports are
navigable—clicking on each step will bring you to the
corresponding experiment.
Database Structure
• Chemical Synthesis, Scale-up and Analytical
• DMPK, Screening Biology, Genetics, and Microscopy
• LIMS, Method Execution, 21 CFR Part 11, and GxP
Assay & Screening Biology
One of E-Notebook's strengths is its ability to integrate with existing
electronic methods of data capture, including using it with
CambridgeSoft’s BioAssay module to provide full screening experimental
support. In addition to this, Microsoft Word and Excel
are also embedded directly in E-Notebook, as is image and movie
capture. Scientists benefit from the functionality of these tools
implanted in a rich, searchable environment. Biological experiments
can be managed and organized in a way that is not possible
with a traditional file system.
In vivo Experiments/Animal Management
In vivo experiments are important aspects of target discovery and
validation, and are critical paths to determine the
efficacy of selective therapeutic candidates. CambridgeSoft’s E-
Notebook becomes the centralized location to collect, store and
interpret in vivo experiment results. Again, when used with
BioAssay, the full end-to-end experimental workflow is supported,
from creation, to data analysis and quality control, to summary
and reporting. In conjunction with in vivo experiments, animal
housing and breeding can also be tracked. Traditionally, the workflow
consists of paper-based record keeping across the animal
facility, lab bench, and researchers desktop. With E-Notebook,
paper tracking and recording is eliminated. Instead, form tools can
be designed to:
• Track animal status
• Track animal pedigree
• Record Genotype
• Create mating records
• Create litter records
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KNOWLEDGE
Analytical Services &
Electronic Journal J
and Record Keeping
Formulation and Validation
E-Notebook's formulation module is designed to support the dual
workflows and regulatory compliance needs of formulation engineers.
The flexibility allows any number of formulations to be
created, and security allows only designated administrators to
create a new formulation.
Analytical & Quality Control
Analytical and Quality Control Laboratories must execute defined
procedures to test material that may be administered during preclinical
and clinical trials. This work must also be compliant with
both GxP and 21 CFR Part 11. Templates for standard analytical
tests are provided and analytical procedures are implemented as
E-Notebook forms, which are easily designed and controlled.
Equally important, E-Notebook provides workflow enforcement
that monitors data entry and ensures that the forms are completed
in sequence for proper method execution.
For example, rules can be configured such that the 'Day 3' form
of a multi-day process will not accept any entries unless all
required fields on the 'Day 2' form are first completed. The forms
can contain automatic calculations to compute totals, averages,
differences, and much more. E-Notebook can further streamline
the procedure by allowing for electronic management of solutions,
equipment, and other resources that are needed for experiments.
Drug Metabolism
E-Notebook supports the DMPK laboratories in testing the metabolism
and longevity of compounds in various in vitro and in vivo
models. DMPK data capture needs can vary significantly, and the
flexibility of the E-Notebook solution addresses this. For example,
an in vivo enzyme induction test may create relatively small
amounts of data for which scientists utilize E-Notebook integration
with Microsoft Excel. Conversely, large quantities of data,
such as those generated by in vitro enzyme inhibition studies, are
often collected and analyzed by applications such as BioAssay.
Therefore, integration with BioAssay and Excel are fundamental to
DMPK E-Notebook usage.
• Service Request Workflow
• Sample Management
• Method Execution Framework
Pharmacokinetics (DMPK)
There is a holistic approach to Drug Metabolism and
Pharmacokinetics. No single study describes the behavior of a
compound; it is the combination of data from disparate experiments
that represents the pharmacological profile for a compound.
It is here where E-Notebook reveals one of its most significant
capabilities: the reporting feature. E-Notebook reports are
flexible: any field (e.g. compound ID, study type, etc.) can be used
to query the system and any field (e.g. conclusion, dose, etc.) or
field aggregate (e.g. average radioactivity) can be displayed in the
report. Reports are dynamic and navigable: results are displayed
with links that provide quick access to experiments.
Reports are viewed directly in the E-Notebook interface, but they
can also be exported to Microsoft Word or PDF to share with
those who do not have E-Notebook access.
Inventory Enterprise
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MANAGEMENT
Sample Management
Compliance Execution and Sample TrackingT
Drug Safety / Toxicology
Paper notebooks have traditionally been considered to be the
record source for the entirety of an experiment, but they often
miss non-experimental information generated shortly after conception.
For example, toxicology studies are often initiated not
by the scientist who ultimately runs the experiment, but instead
by a manager or coordinator who assigns the study to the scientist.
Important material related to this first step in the process,
such as ideas, emails, and other communications are often left out
of traditional paper notebooks. The E-Notebook toxicology workflow
addresses this concern: studies are first created by a manager,
and subsequently assigned to the scientist for execution.
Compliance Execution
E-Notebook is also useful for capturing the Standard Operating
Procedure (SOP) corresponding to the experiment. These documents
are often stored separately from the actual data, leading to
error and confusion, thus causing risk to the validity of the data.
Storing and displaying procedures and other related documents in
concert with the data eliminates this risk and helps build perspective
on the study.
Sample Lifecycle Management
E-Notebook can manage the entire sample lifecycle through tight
integration with Inventory. Sample lifecycle management is essential
for the registration, testing, evaluation, and reporting in various
analytical and manufacturing stages. Manual tracking of samples
and test results is labor-intensive and time-consuming; and
compliance with GxP guidelines requires expensive manual
audits.
The controlled flexibility of CambridgeSoft’s E-Notebook is well
suited for these detail and compliance-oriented environments.
E-Notebook’s Sample Lifecycle Management module is compliant
with Good Laboratory Practices (GLP), Good Manufacturing
Processes (GMP) and 21 CFR Part 11.
• Track & Barcode Samples
• Create Any Report from Database
• Full Audit Trail
Sample Login
E-Notebook is able to easily configure sample logins (registration of
sample, assignment of barcode label, and initiation of sample
tracking) by incorporating CambridgeSoft’s Inventory application.
Through E-Notebook, forms can be created to keep track of newly
synthesized or acquired compounds, tracking their physical properties
and tests, and assigning unique identifiers. New compounds
are entered directly via the E-Notebook form, and chemical, along
with non-chemical, data is kept alongside the sample. When a
proprietary compound is registered, if desired, it is compared for
uniqueness via a configurable, stereoselective duplicate check and
assigned a registry number.
Sample Tracking
Tracking samples, requesting analysis and establishing chain of
custody can all be simply managed within the E-Notebook interface.
E-Notebook serves as a repository for analytical data and
experiments, linking such data directly to the sample ID, and it
acts as a communication portal with which scientists and analysts
communicate with each other during the service request lifecycle.
Scientists create and send service requests directly to an analyst
with the click of a button. Paper is eliminated: when results are
obtained, the analyst can send the images and chromatograms
directly back to the scientist's E-Notebook (which appear in the
person's E-Notebook inbox, and are then accepted into the experiment
if desired). To establish chain of custody, each step of sample
ownership is tracked, recorded and made compliant with
FDA's 21 CFR Part 11.
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LABORATORY
Workflow LIMS,
Visual LIMS, Lab Automation,
Workflow LIMS Automation
CambridgeSoft’s Workflow LIMS is a scientific data and
workflow management tool for lab automation and in silico
experimentation. Workflow LIMS eliminates the need for custom
programming by providing a visual experiment design and workflow
layout with built-in laboratory automation and analytics.
By using Workflow LIMS, researchers can connect their
laboratory processes, instruments, and decision points in a
conceptual manner that directly couples to instrumentation— for
both automation and data gathering—and provide
real-time results. The Workflow LIMS solution enables a
scientific team to design procedures, execute those procedures,
capture the results and integrate lab equipment to automate part
or all of the process. Procedures typically revolve around lab activities,
but may also draw in decision support tools on a scientist's
desktop, and queries/updates to databases.
Interactivity and Integrity
1. The modeling environment, Workshop Configuration Editor,
in which the scientific team models the capabilities of the lab - for
example, the kind of basic processes which are available in the lab,
and their inputs and outputs.
2. The design environment, Workbench, in which researchers
create workflows from these basic processes.
3. The runtime Operations Manager, which manages the assignment
of tasks to agents, tracks the progress of tasks and workflows,
and manages the storage of captured data.
4. The agent tier, made up of a number of applications that handle
specific types of task, either manually (through a user interface),
or automatically (by driving equipment through a control
interface or performing automated data processing).
5. The monitoring tier consists of a reporting tool that
provides historical utilization information, and a live activity
viewer that allows scientists to drill into individual workflows
and samples.
• Service Request Workflow allows scientists to
communicate as they work
• Direct Communication from E-Notebook to create
tasks and send results
• Method Execution Framework to enable standard
operation procedures and compliance
Applied Technologies and Benefits
Workflow management enables discovery teams to rapidly trial
new procedures, capture best practices and scale successful designs
from a manual prototype right up to a fully automated highthroughput
lab. But discovery and research, by its very nature,
demands that processes be flexible and that workflow execution
rapidly adapt to new techniques and equipment.
Conventional laboratory information workflow applications cannot
meet this requirement because of their heavyweight configuration
needs, their lack of adaptability and the cost and complexity
of integrating them with rapidly changing lab technology.
Workflow LIMS addresses these problems by providing a visual,
easy-to-use environment for describing processes and building
workflows out of those processes, enabling scientists to rapidly
trial new procedures, and by offering a rapid development tool kit
for equipment integration which supports gradual automation to
minimize up-front costs and ongoing risk.
CambridgeSoft’s Workflow LIMS simplifies even manual lab procedures
by managing the breakdown of a procedure into tasks, and
by automating the majority of data capture and transfer tasks; but
by capturing process as well as data, Pathways reduces the costs
and risks of implementing discovery techniques, and enables
companies to accelerate the entire discovery process.
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INFORMATICS
Compliant DB & Oracle Cartridge
Compliant Storage and Chemical Data Management
Compliant DB
CambridgeSoft’s Compliant DB is the industry's enterprise
content management system developed by a large pharmaceutical
company. It serves as an electronic library that collects, organizes,
warehouses, indexes and safely archives all your structured and
unstructured electronic records. From raw data and laboratory
reports to compliance records, Compliant DB also will support any
of CambridgeSoft’s workflow solutions, including E-Notebook,
BioAssay, and Inventory. As its name implies, Compliant DB is fully
compliant with the requirements of 21 CFR Part 11 for
electronic records and electronic signatures.
Compliant DB can be used directly over your company's intranet,
extranet, or over the Internet with a simple web browser.
Complaint DB gives your organization a secure, 21 CFR Part 11
compliant centralized electronic library for all electronic data files.
Not only can machine-readable instrument data files be stored,
but also images, multimedia files, presentations, human-readable
word processing and Adobe PDF documents, spreadsheets and
hundreds of other formats. This data can serve as source data
(instrument data to BioAssay), and also repository. Although
Compliant DB can operate as a stand-alone application, only
CambridgeSoft provides fully-integrated Knowledge Management
and Enterprise Informatics applications integrated with compliant
storage. Compliant DB makes this possible.
Workbench Sample
• Develop Centralized Validated Storage and
GxP Compliant Storage
• Store Documents, Machine Files & Chemical Objects
• Oracle Cartridge is compatible with Linux, Solaris,
AIX and Windows and includes structure searching,
property predictions and nomenclature
Oracle Cartridge
The CambridgeSoft Oracle Cartridge is used by all ChemOffice
Enterprise applications for storing, searching, and analyzing chemical
data. It can also be used in the development of your custom
Oracle applications. Chemical structure and reaction data is difficult
to manipulate without utilizing special software, and Oracle
data cartridges define new, recognized data types. CambridgeSoft’s
Oracle Cartridge utilizes this technology, making it possible to
manipulate chemical structure and reaction data from within
Oracle, improving portability and consistency in applications.
Since the Oracle Cartridge is accessed through native Oracle SQL,
programmers can interact with chemical structure data directly in
the database.
The CambridgeSoft Oracle Cartridge supports CDX, CDXML,
MolFile, MolFile v.3000, RXN and SMILES formats, making it
flexible enough to be included with both new and legacy data
applications, without the need for file conversion. Chemical information
can originate from either ChemDraw or ISIS Draw, E-
Notebook, Inventory, or Registration. Oracle Cartridge has extensive
support for stereochemistry, relative stereochemistry, tautomers
and structure normalization. There is also a built-in structure enumerator
(for nonspecific structures), basic property predictors,
nomenclature algorithms (name=struct), and dynamic utilities for
molecular file format conversions.
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BIOLOGICAL
BioAssay, BioViz,
Assay Screening and VisualizationV
BioAssay
For modeling complicated in vivo experiments, or
supporting an ultra-HTS platform, BioAssay has become the leading
choice for managing biological experimental data. It is the
only application of its kind to provide a best-of-breed solution for
both ultra-high volume laboratories and lower-throughput settings.
BioAssay includes support for laboratory automation, calculation,
and statistics, and also complicated low and medium
throughput assays such as animal models and in vivo experiments.
BioAssay is designed to tackle the needs of high and low throughput
screening biologists alike by providing an application flexible
enough to model any assay, regardless of complexity, through an
easy-to-use interface for importing, storing and analyzing the data.
The software supports the quick set-up of biological models, automated
calculations and curve fitting, data validation, and the creation
of customized structure activity reports.
BioAssay Extends E-Notebook
BioAssay Enterprise is a scalable, flexible biological screening solution
utilizing Oracle’s role based security and the Oracle Cartridge.
When used as part of ChemOffice Enterprise, BioAssay is integrated
with E-Notebook for experimental data, Inventory Enterprise for
plate tracking and management, Registration Enterprise for the registration
of new compounds and BioSAR Enterprise for customized
reporting.
BioAssay Ultra is designed to deliver much of the functionality of our
enterprise level applications, without a widespread roll-out.
BioAssay Ultra, coupled with BioViz, offers a user friendly interface
for importing, viewing, validating, and plotting your biological
assay data from your desktop.
• BioAssay effectively manages data from complex biological assays
involved with lead optimization.
• BioViz integrates with BioSAR for one step in-depth data
analysis from a BioSAR report.
• Effectively manage data from complex biological
assays involved with lead optimization
• Scalable HTS & HTTS
• Use BioDraw to document cellular pathways
BioDraw
Diagramming and presenting cellular pathways is made easier and
more effective with BioDraw. Formerly called Pathworks,
BioDraw does for biologists what ChemDraw has done for
chemists—saving time and producing a more professional
representation of the science.
BioDraw makes drawing and annotating biological pathways
quick and easy, adding a level of uniformity and detail which is
unmatched. Common pathway elements such as membranes,
enzymes, receptors, DNA and reaction arrows are built into the
BioDraw toolbar. BioDraw also allows the import of images in
GIF, PNG or JPEG formats. BioDraw offers many ways to share
your drawings and accompanying data. Users can export data to
Microsoft Office applications for inclusion in presentations and
grant proposals or save data as an image file for use in journal
article submission.
Draw Biological
Pathways
Plot Assay Data
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INFORMATICS
BioSAR & BioDraw
Data Mining and Pathway P
Drawing
BioSAR
BioSAR Enterprise, a strategic must for any discovery
organization interested in serious data mining, is a data dictionary
driven structure-activity analysis program. Users may choose
among assays registered in the dictionary or search for assays
of interest.
The power of BioSAR lies in the researcher’s freedom from
dependence on IT support for dynamically working with all available
scientific data. For example, once an assay is registered into
the data-dictionary, it is automatically included in the powerful
analysis framework. By reducing the time between question and
answer, BioSAR gives researchers the ability to explore new ideas
and avoids this issue by placing SAR report creation in the
researcher’s control.
BioSAR Enterprise allows the researcher to create custom reports
and views of their data. You decide what is displayed, and BioSAR
takes care of the rest.
While most SAR tools provide only a table-based interface,
BioSAR provides both a form view and table view, and connects to
BioViz for high-dimensional analysis. BioSAR merges the sophistication
of a powerful data catalog technique with knowledge
gained through years of working closely with scientist users. The
result is a SAR application that is as intuitive as it is powerful.
Security within BioSAR Enterprise is highly granular; different
roles exist for administrators, publishers, and browsers.
Administrators may add assays to the data catalog engine, publishers
may create reports and publish them, and browsers may use
data query and analysis. Most data mining tools provide a mechanism
to store queries, but the interface for creating queries is too
complex. With BioSAR, each set of assays is a complete report
with a query form, a view form, and a table view, combining the
convenience of a ChemFinder or ISIS application with the power
and flexibility of a data catalog-driven mining program.
• BioSAR is a catalog driven mining and structureactivity
analysis program
• BioSAR provides both form and table views within
a simple and powerful web interface
• BioViz provides one-step in-depth analysis of
several variables
• BioSAR is a catalog driven data-mining and structure
activity analysis program.
• BioSAR provides both form and table views within a
simple and powerful web interface.
• BioDraw makes it easy to draw and annotate
biological pathways including common elements such as membranes,
enzymes, receptors and DNA.
BioViz
BioViz with ChemFinder transforms the numbers in your database
into graphics on your screen. Retrieve or search for a set of compounds,
choose the data you want to see, whether it is biological
test results in Oracle tables, physical property values calculated
automatically or prices in a catalog, and BioViz will generate an
interactive window showing a scatterplot, histogram, or other
useful data graphic.
The Plot Window, the key to data visualization in BioViz, is able
to show two variables plotted against each other in a scatterplot
with each point representing a structure from the current hit list.
If you, for example, modify the list by performing a search, the
plot updates to show the new set of points. You can drag a rectangle
around a set of points to select them or zoom in to see
them more closely.
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CHEMICAL
Inventory, Registration,
Chemical and Biological Inventory, Freezer F
Management,
Chemicals and Biologicals
Inventory is an application designed to manage the chemical and
biological reagent tracking needs of laboratories and research centers
in multiple contexts: lab reagents, freezers/racks, plate management,
proprietary compounds and stockroom are just some of
the areas where Inventory has been deployed.
The system manages data associated with both commercially procured
and internally produced chemical substances from procurement
or initial production through depletion and disposal.
Inventory Enterprise is an Oracle-based ChemOffice Enterprise
product and can be used with other modules, such as E-Notebook,
to track batch records in manufacturing, or to look up reagents
from stockroom when planning a synthesis, BioAssay when supporting
a high throughput screening environment, Registration for
tracking proprietary compounds, DocManager for linking certificates
of analyzes, analytical reports, or other documents associated
with samples, and ChemACX available chemicals database for
sourcing new compounds.
Inventory Enterprise includes plate handling and interfaces to
liquid handlers for HTS environments, freezer/rack layout and
targeting for managing biologicals, full chain of custody, audit
trails for GxP compliance, request/disbursement workflow for use
in both manufacturing and pre-clinical settings, and features
tailored to specific material domains.
• Reagent handling and stockroom reporting
• Request/disbursement workflow for stockroom and
GxP environments
• EH&S module, and links for MSDS data sheets
• Freezer/rack layout for biological materials
• Extensive plate handling for HTS and uHTS settings
Inventory is also available in two other editions: Workgroup and
Desktop. Inventory Workgroup is a rich-client SQL Server-based
product geared at managing stockrooms and reagents. Inventory
Ultra is a desktop edition based on the Workgroup product, and
includes the ChemACX database.
• Register and Track Chemicals & Biologicals
throughout the enterprise
• Freezer/Rack/Plate Handling--Targeting, Workflow
and HTS Support
• Supports Barcoding, Report Generation & Audit Trails
Registration Enterprise
Registration Enterprise is built around robust data model for pure
compounds, batches, salt management, automatic duplicate
checking and unique ID assignments. Built on the Oracle
Cartridge, it handles stereochemistry (including advances in relative
stereochemistry), tautomerization and structure normalization
for duplicate checking. Using ChemScript, it also can enforce
drawing business rules, such as orientation around a scaffold and
functional group normalization. Compounds may be entered
individually through a user-friendly web form, through the use of
a batch loader, from Inventory, or directly from E-Notebook.
As compounds are registered, regardless of whether through the
web user interface, E-Notebook, or from a batch file, they are compared
for uniqueness via a configurable, stereoselective duplicate
check, and assigned a registry number. All information about the
compound, including its test data and other syntheses, is tracked
by the registry number, and this is used to link data throughout
ChemOffice Enterprise. Registration Enterprise is the only true
n-tiered application of its kind that is designed around thin clients
and thin servers, with interfaces directly to Inventory, batch file
registration and E-Notebook. Oracle is supported on a variety of
platforms and operating systems. Using Oracle secures your proprietary
data through the use of Oracle’s role-based security and
allows all chemical and non-chemical data to be stored directly in
the Oracle tables.
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INFORMATICS
DocManager & ChemFinder
GxP, Registration and Enterprise Infrastructure
Formulations & Mixtures
Formulation scientists face different challenges from those working
with individual molecules, yet many of the tools they are
forced to use emerge from the drug discovery world, where singlemolecule
research is the norm. Take an essential task such as compound
registration and you will find that most systems are
designed for registration of single molecules, with little thought
for the world of formulations and mixtures. CambridgeSoft has
developed a system specifically designed for this registration need
called Formulations & Mixtures.
ChemFinder Enterprise
ChemFinder Enterprise is a multiple-user system designed for sites
with comprehensive chemical and biological data needs.
ChemFinder Enterprise contains its own engine for working with
local and shared databases, and it is also delivered with the
CambridgeSoft Oracle Cartridge, the powerful Oracle-hosted
structure engine based on ChemFinder search technology. The face
of ChemFinder Enterprise is the same friendly form-oriented interface
as the desktop version, but underneath is a fast direct connection
to Oracle and the robust, scalable Oracle Cartridge running
on the server.
Manage your
Inventory
Index Documents
• DocManager parses Word, Excel and PowerPoint
documents, including free text and structures
• ChemFinder is tightly integrated with BioSAR, BioViz
and Oracle
• Support for advanced form layout and design
DocManager Enterprise
• DocManager parses Microsoft Word, Excel and PowerPoint
documents, including free text and structures.
• DocManager has a web based interface and a file drop
folder for quick submissions.
• Oracle Cartridge is compatible with Linux, Solaris, AIX
and Windows and includes structure searching, property
predictions and nomenclature.
Web browser based, DocManager Enterprise extends the capability
of standard search engines to include full free text searching and
chemically intelligent structure searching of electronic documents
including Text, Microsoft Word, Excel, PowerPoint, and Adobe
PDF. The DocManager Enterprise interface allows users to easily
submit documents through a series of simple-to-navigate web
forms. When a new document is submitted, DocManager builds a
free text index of the document, and extracts chemical information
into a chemically-aware, substructure searchable database.
Chemical information can originate from either ChemDraw or
ISIS Draw.
DocManager Enterprise includes a batch loading utility for administration
level users to load multiple documents at one time. The
system can be configured to submit a batch of documents as one
event, or as a reoccurring submission to be executed daily. The
administrator specifies a time for the submission to take place and
the location of the files. DocManager Enterprise utilizes the searching
intelligence of the ChemOffice Enterprise suite.
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MANUFACTURING
Reference Standards,
Regulated Materials Management,
Inventory Enterprise
CambridgeSoft’s Inventory Enterprise application is designed to
manage the chemical, reagent, sample and compound tracking
needs of large multi-site chemical and pharmaceutical laboratories.
Inventory Enterprise is an Oracle-based, ChemOffice Enterprise
product that is designed for multiple users with diverse container
types, racks and multi-well plate formats.
Entities in the Inventory system include locations, containers and
substances. A location is defined as any physical location where a
container, plate or another location can be stored. An inventory
container represents a container capable of storing chemical substances.
An inventory substance represents a chemical compound,
mixture, sample, etc. Inventory Enterprise manages an unlimited
number of diverse locations, containers and substances.
Containers are created to represent the actual storage vessels used
by the organization. Each container is assigned a unique barcode
identifier which can be printed, using customizable report templates,
from the Inventory interface. Updating the inventory
becomes as easy as scanning barcodes into the system and adjusting
parameters for one or multiple containers. Users are able to
order, check-in/out, move, split and merge containers at will.
Typicalcontainers include: ttles, vials, tubes, cylinders, boxes,
racks, multi-well plates, etc.
Multi-well Plates
Inventory Enterprise manages multi-well plate information. In
addition to creating, storing, moving and deleting plates, the
application allows users to create daughter plates, reformat plates
and utilize plate maps. Inventory also supports user-interfaces or
machine-interfaces for these operations (including reading files
from liquid handler robots). Inventory Enterprise has the capability
to import datafiles from other computer systems such as liquid
dispensers/handlers, Microsoft Excel spreadsheets, etc. to accommodate
automated updating of information in the Inventory
database.
• Request/Dispense/Reference Standard Materials
from Central Group to Sites
• Certification/Expiration/Certificate of Analysis of
Containers and Aliquots
• Create/Manage Container History and Genealogy
Searching
Every field in a record is searchable. The application includes a
number of specially designed inventory search forms. Search
results are returned in list form and can be exported into a document
(PDF, RTF, HTML) via the report engine.
Workflow Support
Supported user transactions include the ability to request,
dispense, modify, duplicate, dispose, etc. entities throughout the
system. These and other transactions are an integral part of
Inventory workflows.
For example: a user logs-on, finds the substance(s) they’d like to
request and makes a request entry in the system; the request is fulfilled
directly by changing the location the substance or by taking
an aliquot and creating a new container of the substance. The new
substance/container is also tracked in the system and inherits all
of the critical properties of its parent container. If a quality control
test is run on the parent, then the results are viewable in the
daughter’s properties.
The multi-select capability allows the user to select several containers
and perform a transaction on all of the selected containers
simultaneously, including check-in/out, move, retire, delete and
update. For instance, if a request is made of the system that is
fulfilled by another user (such as dispensing), the requester can
automatically receive e-mail notification of the progress. Likewise,
users can be alerted to pending requests in the system.
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INFORMATICS
Inventory & GxP
Document Storage, Batch Records
Conflict Resolution
The Conflict Resolution processes flags and corrects
duplicates in the system automatically. You may also search for
duplicates at any time. If a conflict is found, the screen
identifies the conflicting field(s) by highlighting it in red. The user
has the option to select the existing substance and edit the conflicting
substance or create a duplicate substance and resolve the
conflict later.
Printed Reports & Labels
The Inventory interface allows for printing labels and can generate
elaborate reports. Inventory Desktop and Workgroup use a report
engine that incorporates wizards that allow for the quick creation
of simple report/label templates that can be shared across an
organization. A user has the ability to design a label based on templates
for a number of commercially available label sheets (e.g.
Avery Dennison). The Inventory manager makes extensive use of
barcodes and web-based user interfaces to speed use, but substantial
gains come in the automated reporting and alerting. Examples
include notifying all users of samples derived from a single standard
of some change in status, such as different analytical results
or failure to recertify.
Inventory Enterprise
• Validated for GxP Environments with Audit Trails,
Container History
• Store Datafiles with Samples such as Batch and
Certificates of Analysis
• Allows for Flexible Reporting
Electronic Data Files
In addition to storing, moving and disposing containers, the
application allows users to reformat plates and create daughter
plates as well as integrate with liquid dispensers/ handlers for plate
reformatting from pipette log files.
Compliance
Handling FDA regulations in an organization is an area that lends
itself to automation. Thus, systems must be carefully implemented
in order to meet the letter and spirit of FDA guidelines.
Underlying the system are the controls expected by systems in regulated
environments: audit tables, security and validated development
methods. All transactions on all containers in the system are
tracked and audits are customizable for simple presentation.
Document Management
To manage the myriad of documents that get generated in research
and regulated environments, CambridgeSoft stores documents
securely in Oracle where they are indexed (by chemistry and text)
and managed by database security. Storing the associated documents
in Oracle preserves system integrity such that you can backup
to a known point, and be assured that the documents and data
are entirely in sync with each other. It also provides tight document
security, reduces IT overhead associated with file shares and
attaches directly to Inventory containers.
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DESKTOP
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SOFTWARE
Chem & Bio Office
Software Standard for Scientists
The ultimate
software suite
for scientists
Chem & Bio Office is a powerful suite of software, consisting of ChemDraw, Chem3D, ChemFinder and ChemACX
for chemists, BioDraw, BioAssay and BioViz for biologists and Inventory and E-Notebook for all types of scientists. Chem &
Bio Office is available for Microsoft Windows.
The standard
achieves the
ultimate
Computational
chemistry made easy
Desktop to
enterprise searching
Ultimate suite
for biologists
Draw pathways
Screening data
Visualize data
Handle reagent
racking
Efficient notebook
keeping
Access info
with ease
Chem & Bio Draw includes Struct=Name, ChemDraw/Excel and ChemNMR, BioDraw, a biological sequence tool,
hotlinks to 3D structures, Stoichiometry grid, live linked chemical property calculations, a TLC plate tool and more. The
ChemDraw ActiveX/Plugin adds chemical intelligence to your browser for querying databases and displaying information.
ChemBio3D provides state-of-the art visualization and display of protein structures, molecular surfaces, molecular
orbitals, electrostatic potentials, charge densities and spin densities. Chem3D provides basic computational tools such as 3D
Molecular Overlay and Dihedral Driver and utilizes MOPAC, Jaguar, Gaussian, GAMESS and extended Hückel to compute
molecular properties. ChemProp computes Connolly surface areas, molecular volumes and properties, including ClogP,
molar refractivity, critical temperature and pressure.
ChemFinder is a chemically intelligent database manager and search engine. ChemFinder provides support for a database
searching, compound profiling, R-Group Analysis, subforms, tight integration with ChemDraw/Excel and Combichem/Excel,
statistical analysis and visualization through BioViz all in a friendly form-based environment. ChemFinder/Office searches
documents, spreadsheets, and files for chemical structures and references. ChemFinder/Oracle provides enterprise solution
integration.
BioOffice is the ultimate suite for management, analysis and visualization of biological data using BioDraw for drawing
pathways and BioAssay, BioFinder and BioViz for data analysis. Includes Bio3D, Draw/Excel, CombiChem/Excel, Inventory and
E-Notebook.
BioDraw provides support for biological pathway drawing and annotation. A wide variety of customizable drawing tools
are available, including membranes, DNA, enzymes, receptors, tRNA, ribosomes, and a plasmid map tool.
BioAssay manages both high and low throughput biological screening data. Designed for complex lead optimization
experiments, the software supports the quick set-up of biological models.
BioViz offers automated statistical analysis, curve fitting, and customized structure activity reports, including a user-friendly
interface for importing, viewing, validating and plotting chemical and biological data.
Inventory manages your reagent and biological tracking needs. Using MSDE as the desktop database, you organize, store
and search over your inventory. Inventory integrates with the ChemACX database of available chemicals and ChemMSDX
safety data providing chemical sourcing and purchasing.
E-Notebook is an efficient, accurate way to write notebooks. It stores Microsoft Office documents, ChemDraw
structures and reaction drawings, and related data in a notebook searchable by text or chemical structure. Organize pages by
project, experiment or in your own style. Use CombiChem/Excel to build libraries.
Databases include ChemINDEX, including the NCI and AIDS databases. The ChemACX database contains nearly 400
catalogs from leading suppliers and ChemMSDX Database contains over 20,000 material safety data sheets for commonly
used laboratory chemicals.
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DESKTOP
ChemDraw, Chem3D,
Structure Drawing and Molecular Modeling
ChemBioDraw Ultra adds BioDraw, ChemFinder, BioViz
and E-Notebook to ChemDraw Ultra. Easily draw and annotate
publication quality biological pathway illustrations with the
BioDraw tools. The combination of the BioDraw tools with
ChemDraw and E-Notebook creates an excellent environment for
smooth communication between Chemists and Biologists.
ChemDraw Ultra adds Struct=Name, ChemDraw/ Excel,
ChemNMR, Stoichiometry Grid, CLogP, tPSA as well as the added
capabilities of Chem3D Pro and ChemFinder Std to the
ChemDraw Pro application. With rich polymer notation, generic
structure expansion, fragmentation tools, and a modern user
interface, ChemDraw is more powerful than ever before. Create
tables of structures, identify and label stereochemistry, estimate
NMR spectra from ChemDraw structures, obtain structures from
chemical names, assign names from structures, and create multipage
documents and posters.
ChemDraw Pro will boost your productivity more than ever.
Draw quality publications with structures, reactions, chemical
queries, polymers, relative stereochemistry, generic structures,
TLC plate depictions and a biological sequence tool. Publish on
the web using the ChemDraw Plug-in. Create precise database
queries by specifying atom and bond properties and stereochemistry.
Display spectra, structures and annotations on the same page
Struct=Name contains the leading comprehensive
methods for converting chemical structures into chemical names
and names to structures. It can be used for many types of compounds,
including charged compounds and salts, highly symmetric
structures and many other types of inorganic and
organometallics. Struct=Name is available in two forms: a batch
application, and an interactive version that is also available in
ChemDraw Ultra.
ChemDraw/Excel allows the user to create chemically
knowledgeable spreadsheets within the familiar Microsoft Excel
environment. You can build and manipulate chemical structures,
compute chemical properties and perform database searches.
• ChemDraw’s improved Struct=Name feature produces
names for more types of compounds
• Live ChemDraw window embedded in Chem3D application
allows simultaneous 2D and 3D editing
• Chem3D brings workstation-quality molecular graphics and
rigorous computational methods to your desktop
ChemNMR can be used to accurately estimate 13C and 1H
chemical shifts. The structure and the spectrum appear with the
chemical shifts displayed on the molecule and the spectrum is
linked to the structure so that clicking on a peak in the spectrum
highlights the corresponding fragment on the molecule.
ChemBio3D Ultra includes visualization and molecular modeling
capabilities for both small molecules and protein structures
designed for the bench chemist. Small molecule computational
methods include Molecular Overlay and Dihedral Driver. It also
includes interfaces to the MOPAC, Jaguar, Gaussian and
GAMESS semi-empirical and ab initio computational packages.
High quality Chem3D graphics can be viewed on the web using
the Chem3D ActiveX.
Chem3D Pro brings workstation quality molecular visualization
and display to your desktop. Convert ChemDraw and
ISIS/Draw sketches into 3D models. View molecular surfaces,
orbitals, electrostatic potentials, charge densities and spin densities.
Use built-in extended Hückel to compute partial atomic
charges. Use MM2 to perform rapid energy minimization and
molecular dynamics simulations. Chem3D can also be used to
estimate physical properties such as logP, boiling point, melting
point and more. Visualize Connolly surface areas and
molecular volumes.
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SOFTWARE
ChemFinder & ChemInfo
Structure Searching and Scientific Databases
ChemFinder Ultra is a chemically intelligent database management
and search system designed for chemical and biological
data. ChemFinder Ultra can be used with local (MSDE) or shared
(Oracle) databases. Either way, the face of ChemFinder is the
same friendly form-oriented interface. BioViz, included in
ChemFinder Ultra, provides data visualization features to help
the user understand relationships between biological data and
chemical structures. These features allow you to plot structural
and biological data in a variety of styles, perform statistical analysis,
filter plots based on your criteria, highlight intersecting sets on
plots, generate histograms of data distributions, and more.
BioViz, included in ChemFinder Ultra, provides statistical analysis
and visualization tools for structural and biological data. BioViz
transforms ChemFinder database information into easy to understand
graphics, allowing users to discern structure-activity relationships
more easily. With BioViz it is easy to retrieve a set of
compounds using filters or searching capabilities; and generate an
interactive window showing a wide variety of useful graphical
information.
ChemFinder Pro is a fast, chemically intelligent, relational
database search engine for the Desktop. The integration with
Microsoft Excel and Word adds chemical searching and database
capability to spreadsheets and documents. Compatibility with
MDL ISIS databases is provided by SDfile and RDfile
import/export.
Estimate Spectra
Molecular Modeling
• ChemFinder offers improved searching and hit list management,
along with new property generation
• ChemFinder is tightly integrated with CambridgeSoft's
Oracle Cartridge
• Search ChemACX and other CambridgeSoft
ChemACX Database includes over 1 million chemical
products available for purchase from 472 supplier catalogs, searchable
with a single query by structure, substructure, name, syonym,
partial name, and other text and numeric criteria.
ChemMSDX Database provides material safety datasheets
and is integrated into ChemACX, and contains over 23,000
Material Safety Data Sheets (MSDS) in PDF format.
ChemINDEX Database includes 100,000 chemicals, public
NCI compounds, AIDS data and more.
NCI Database contains over 200,000 compounds with anticancer
drug dose-response data.
AIDS Database is an NCI compiled database for AIDS antiviral
compounds.
ChemRXN Database is a collection of 30,000 fully atommapped
reactions selected and refined from chemical literature. It
also includes reactions from InfoChem’s ChemSelect database and
ISI’s ChemPrep database.
ChemBioFinder.Com is the award-winning web site within
formation and WWW links for over 100,000
chemicals. Users can search by name or partial name, view structure
drawings, or use the ChemDraw ActiveX/Plugin for structure
and substructure searches.
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DESKTOP
BioAssay, BioViz, BioDraw,
Biological Assay, Visualization V
and PathwaysP
BioAssay Ultra
BioAssay Ultra, the cornerstone of BioOffice, provides flexible
storge, retrieval and analysis of biological data. BioAssay
easily manages both high and low throughput biological screening
data.
Designed for complex lead optimization experiments, the software
supports quick set-up of biological protocols, automated
calculations and curve fitting, and the creation of customized
structure activity reports. BioAssay brings all of this functionality
to your desktop. BioAssay Ultra, compatible with the MSDE
database, offers a user-friendly interface for importing, viewing,
validating and plotting your biological assay data.
BioViz
Combining biological data with chemical structures is of the
utmost importance in any drug discovery environment. BioViz
allows you to visually analyze and perform statistical analysis on
structure-related data combined with biological data in
ChemFinder.
Users can search over structural and biological data and
construct various plots such as scatterplots or histograms. The
plots are interactive; allowing you to select subsets of your data,
perform statistical analysis, filter plots based on your criteria,
highlight lists and intersecting sets on plots, generate histograms
of data distributions and more.
BioDraw
Reporting on and presenting findings is a task familiar to every
biologist. Making this process easier and more effective benefits
everyone involved. BioDraw is doing for biologists what
ChemDraw has done for chemists for years—saving time, and
resulting in a more professional representation of the science.
BioDraw makes drawing and annotating biological pathways
quick and easy, adding a level of uniformity and detail which is
unmatched. Typical drawings of biological pathways include
• BioAssay offers flexible storage, retrieval and analysis of
biological data
• BioViz provides statistical analysis and graphical representations
of the data loaded into a ChemFinder form
• BioDraw allows for quick and easy drawing and annotation
of biological pathway depictions.
many elements that are difficult to draw with the standard presentation
and word processing software. Common pathway elements
such as membranes, enzymes, receptors, DNA, tRNA and plasmid
maps are built into the BioDraw toolbar. BioDraw is built
into the same backbone as ChemDraw, allowing users to take
advantage of the wide variety of the publishing capabilities available
in ChemDraw such as the ability to import and export images
in GIF, PNG or JPEG formats. In addition, the integration of
ChemDraw and BioDraw in Chem & Bio Draw application provides
a great communication mechanism between chemists and
biologists.
Notebook Pages
Data Visualization
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SOFTWARE
Inventory & E-Notebook
Materials Management and Electronic JournalJ
Inventory Ultra
Inventory Ultra allows users to manage the tracking needs of
chemical and non-chemical inventory data for laboratories and
research centers. The system manages data associated with both
commercially procured and internally produced chemical substances
from their procurement or initial production through
their depletion and disposal. Inventory Ultra is an MSDE based
product and includes the ChemACX database with over 450 catalogs
of chemical reagents.
The three primary entities in an Inventory system are
locations, containers and substances. Users or administrators configure
a network of locations, which represent locations within an
organization. Containers are created to represent actual containers
in your facility. Each container is assigned a unique barcode,
which can be printed using a customized template from the
Inventory interface.
Each container stores a substance. Additional text fields are available
to track other chemical contents such as the solvent. Custom
fields may also be defined. To keep track of substances the system
maintains its own internal chemical structure database containing
unique substances that can be associated with inventory containers.
Advanced duplicate checking is incorporated in the system.
Every field in a record, including the chemical structure, molecular
formula and molecular weight are searchable.
The application includes a number of specially designed inventory
search forms. Search results are returned in list form and can be
exported into a document (PDF, RTF, HTML) using the report
engine. The Inventory interface allows for printing labels as well as
generating reports. Inventory uses a report application that incorporates
wizards that allow for the quick creation of simple reports
and label templates that can be shared across an organization.
Inventory Pro
Inventory Pro contains the same features as CambridgeSoft’s
Inventory Ultra application, except without CambridgeSoft’s
ChemACX database.
• Inventory manages the chemical and reagent tracking needs
of laboratories and research centers
• Inventory maintains its own internal chemical structure database
with advanced duplicate checking
• E-Notebook stores Microsoft Office documents, ChemDraw
structures, reaction drawings and related data in a convenient,
searchable format
E-Notebook Ultra
E-Notebook Ultra is an efficient, accurate way to store lab notebook
information. It stores Microsoft Office documents,
ChemDraw structures, reaction drawings and related data in an
electronic notebook that is searchable by text or chemical structure.
You can organize pages by project, experiment or in your
own style with the MSDE database. CombiChem/Excel builds
combinatorial libraries. E-Notebook is configured exactly like a
chemist would like his or her own notebook to be. Reactions can
be easily drawn into the reaction template by either selecting from
the generous list of preloaded reagents or by entering or drawing
one’s own chemicals. Commonly used reagents can be stored in a
separate folder for easy access. Another fantastic feature is the procedural
section. This section contains pre-written procedural sentences
with the ability to easily drop in the specific names of
reagent chemicals present in the reaction. One can also easily add
other data to the notebook page such as spectra and Microsoft
Word or Excel documents.
CombiChem/Excel
CambridgeSoft provides you with the tools to effectively plan
combinatorial chemistry experiments in Excel. The
CombiChem/Excel add-in introduces additional functionality for
handling combinatorial chemistry. Users can generate products
from a reaction and lists of reagents, you can view all the products
arising from a given reagent or all the reagents of a given product,
and you can lay out reagent and reaction plates.
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SCIENTIFIC
The Merck Index, NCI, AIDS,
Scientific Reference, Chemical Reactions and PatentsP
ChemBioFinder Gateway
ChemBioFinder Gateway allows searching of the complete
CambridgeSoft reference collection of databases with a
single query. Search such databases as The Merck Index, R&D
Insight for Chemists and Traditional Chinese Medicines with only
one click of a search button. All results federate back to the specific
databases for complete information.
The Merck Index
Known for its integrity, detail, and longevity, The Merck Index
contains over 10,000 monographs on drugs, chemicals and other
biologically active molecules. Each monograph contains information
on the compound and its derivatives; common, trade, and
systematic names; trademarks and associated companies; CAS
Registry Numbers, physical and toxicity data, therapeutic and
commercial uses, literature citations, as well as chemical strucures,
formulas andmolecular weights. The electronic versions include
archived monographs from previous editions and is updated twice a year.
R&D Insight/Chemists
Information on current drug products under development is
essential for those working in research and development, licensing
and marketing at pharmaceutical and healthcare institutions.
R&D Insight for Chemists, a collaborative product from Wolters
Kluwer Health and CambridgeSoft, combines the power of chemical
structure searching with a wealth of drug development data to
give subscribers a competitive edge when making decisions relevant
to the direction of their research. Updated weekly, users can
search the collection of over 20,000 compounds by structure,
substructure, names, partial names and synonyms.
Patent Database
Researchers, chemists and patent analysts are now able to easily
search full text patents for chemical structures using
CambridgeSoft's powerful search and analysis tools. The new
CambridgeSoft Patent Database portal, co-developed by
CambridgeSoft and Reel Two, will give users access to all the
chemical compounds named in a patent, and enable them to
search by structure, keyword or chemical name.
• The Merck Index offers encyclopedic reference for over 10,000
chemicals, drugs and biological agents
• R&D Insight for Chemists has information on more than 20,000
drug products in various stages of development world-wide
from over 1,700 sources.
• All databases are updated, contain information unavailable in
print, and are searchable by structure, as well as text and
numeric range by structure, as well as text and numeric range
Traditional Chinese Medicines
Access to this wealth of knowledge is now available with the
Traditional Chinese Medicines database. The database consists of
monographs for 10,458 chemicals isolated from 4,625 natural
sources used in traditional Chinese remedies. The monographs
feature bio-activity data for many of the compounds, effects and
indications of the medicines, English, Latin, and Chinese names
for the natural sources, and over 2,000 references.
ChemINDEX, NCI AIDS & Cancer
Scientists have used the award-winning ChemFinder.Com database
since 1995. Now, the data on ChemFinder.Com is integrated into
ChemOffice as ChemINDEX. ChemINDEX contains data from
over 75,000 compounds including structures, names and
synonyms, physical properties and Internet links. Additionally,
three informative databases have been integrated into one powerful
application with the NCI and AIDS database, a collection of
over 200,000 molecules studied by the National Cancer Institute.
ChemReact and ChemSynth
These reaction database collections from InfoChem GmbH comprising
essential information on chemical reactions published in
the literature between 1974 and 2001. The largest is
ChemReact500, with almost 500,000 reactions selected with an
eye toward synthetic utility. ChemSynth is a subset of the reactions
found in ChemReact500 chosen because they have greater
than 50% yield and have been sited in leading journals more than
once. ChemReact68 has 68,000 reactions that have greater than
50% yield and have appeared in more than five example reactions.
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DATABASES
ChemACX & Sigma-Aldrich MSDS
Available Chemicals and Material Safety Data Sheets
ChemACX Database
Sifting through chemical catalogs is a poor use of time for any
researcher. ChemACX database solves this problem by offering a
complete tool for research chemical sourcing and purchasing.
With an emphasis on up-to-date information of high quality,
ChemACX allows you to purchase chemicals fast, efficiently and
without worry or cumbersome paper catalogs. The database can
be accessed from both desktop and enterprise environments and
boasts nearly 500 catalogs from major suppliers, from Alfa Aesar
and Aldrich, to TCI and Zeneca, with hundreds in between.
Sigma-Aldrich MSDS
Environmental, Heath and Safety (EH&S) is an important component
of today’s research institutions. A key document that aids
in the management of EH&S tasks is the Material Safety Data
Sheet, also commonly referred to as MSDS. In every organization,
there are several groups of personnel who require access to
MSDSs. Everyone who comes into contact with chemicals needs
• ChemACX is fully structure searchable with more than 1
million products from nearly 500 catalogs
• ChemACX and the Sigma-Aldrich MSDS are updated
semi-annually to meet the needs of scientists
• Search by name, synonym, partial name, formula, and
other criteria
to be aware of their proper handling, storage, disposal and emergency
procedures. Helping to fulfill these diverse needs is the
Sigma-Aldrich MSDS collection. The database contains over
130,000 MSDSs for the products of the Sigma-Aldrich family of
catalogs (Sigma, Aldrich, Fluka, Supelco, Riedel-de Haën) in
HTML format. With a click of a hyperlink, users will be able to
view the Sigma-Aldrich MSDS in their preferred browser. This
information is smoothly integrated with the ChemACX
database and other enterprise applications.
Drugs: Synonyms and Properties
Drugs: Synonyms and Properties from Ashgate, provides comprehensive
coverage of the 8,000 drugs currently in common use
worldwide. A key component of this reference is the extensive coverage
given to synonyms. The electronic version adds almost
70,000 synonyms and trade names that did not fit into the print
version. This information is also available as an SD file to
facilitate in silico research.
Nanogen Index
The Nanogen Index contains data on over 1,000 pesticides and
other environmental contaminants. The database is the up-to-date
and authoritative source for information on all pesticides and agricultural
chemicals in world wide use, those which are currently
under development in R&D pipelines, and compounds which
were once marketed or reached a development status. Data fields
include chemical structures and SMILES strings, names (CAS,
IUPAC, trade), the various registration codes assigned to the compounds
(RTECS, EINECS/ELINCS, CAS, US EPA, CA DPR,
Tarrifs, etc.), Hazard and Safety codes, the developing company
and use.
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PROFESSIONAL
Development, Deployment,
Custom Development and System Deployment
When processes and technologies are disjointed, organizations lose
efficiency and decision making capability. Our Professional
Services use technology to bring business processes together,
integrate systems and assist with strategic informatics planning.
Informatics Planning
Strategic and Operational Planning
A formal review of the discovery and development process and
human/system interfaces is mapped to form the basis of a
roadmap for successful technology utilization.
• Analysis of the current laboratory and technology workflows
• An analysis of the current state of the science technology
environment, including architecture/operational processes
• A view of strategic goals and the barriers to achievement
• The delivery of a phased technology transition plan
Requirements Analysis & Proof of Concept
With years of experience meeting the needs of the scientific community,
CambridgeSoft understands the user. The prototyping
process allows definition and testing of the functional and technical
feasibility of potential technology solutions. The process provides
a baseline for the future development and deployment of a
tailored solution. Users gain valuable first-hand knowledge in
experiencing how the system can help achieve individual and
workgroup goals.
Legacy System Migration
Legacy systems, with private data structures and architecture, can
be barriers for migrating systems to new technologies. Our consultants
have significant experience with these systems and can
successfully migrate chemical and biologial data, business workflow,
and other aspects of legacy informatics technologies.
21 CFR Part 11 Compliance and GxP Validation
As an integral part in creating 21 CFR Part 11 and GxP
validated applications, CambridgeSoft offers services to:
• Audit the software and process
• Create conforming systems design specifications
• Create IQ/OQ/PQ documentation
• Generate test plans and validation matrices
• Insure systems compliance with functional guidelines
With custom development, CambridgeSoft works collaboratively
with your team to create a system that meets your needs while
executing our quality driven software development process. We
deliver what you need, on time and within budget, without surprises.
Product Development
Development Consulting
With custom development, CambridgeSoft works collaboratively with
your team to create a system that meets your needs, while executing
our quality driven software development process. We meet
your needs, on time and within budget, without surprises.
Systems Integration
Process improvement often requires integrating systems designed
for focused areas of work. CambridgeSoft has integrated various
E-Notebook, registration, inventory, and biological assay systems
in a variety of settings. Whether these are CambridgeSoft, a thirdparty
product or an in-house developed solution. CambridgeSoft
has the expertise to unite these systems in order to they improve
business processes, laboratory efficiency and decision making.
Application Configuration
Your organization will see the benefit from implementing a
CambridgeSoft application, but would like to customize it for a
unique environment. Our professional services teams provide
those specific features by developing market add-ins, or other
modifications that are supported in the future.
Systems Deployment
Installation and Configuration
CambridgeSoft has a tested methodology for system
deployment that consists of an IT architectural review, a business
workflow and process review as relates to specific scientific areas,
a process integration review, and maintenance guidelines. By carefully
following this proven methodology, CambridgeSoft installs
and configures systems that are easy to maintain and have the flexibility
to accommodate variations in the science or business workflow
that come from extensive experience in these areas.
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SERVICES
Training & Support
Educational Training T
and Technical T
Support
Systems Optimization
CambridgeSoft’s systems deployment team will work with you to
make sure that your computing environment has been optimized
for high performance. Your systems,networks, applications and
databases are assessed and designed to deliver maximum achievement.
Beta and Pre-Release Programs
Committed to maximizing your productivity through the use of
our products, as well as exposing you to the newest technologies,
our beta and pre-release programs provide you with first-hand
product knowledge and allows CambridgeSoft to improve applications
with your feedback.
Pilot Software Evaluations
It makes sense to pilot an application before a major commitment
to an enterprise-wide implementation is made. CambridgeSoft
will work closely with you to plan the evaluation, deploy the
application, and gather feedback regarding systems design, API’s
and technology specifications.
Training
Effective user, administrator and help desk training is often an
afterthought in many systems deployments. However, the productivity
returns generated by an investment in systems training can
be dramatic. CambridgeSoft offers a complete array of powerful,
user-focused training services.
Managed Informatics allows your organization to focus on science,
while CambridgeSoft plans, implements and manages your
technology environment.
Systems Management
Managed Informatics
Informatics outsourcing provides the people, processes and technology
to develop a unique level of service for your organization.
For a monthly fee, CambridgeSoft will deliver the informatics
applications and the technology staff required to maximize productivity.
This service allows your organization to focus on science,
while CambridgeSoft plans, implements and manages your
technology environment.
Systems Hosting
A hosting service that allows customers to use our state-of-the-art
enterprise applications over the extranet from any location 24
hours a day, seven days a week is available. With this hosting service,
our customers can shift the responsibilities of application development
and IT infrastructure management to CambridgeSoft,
allowing more time to focus on core science, research, discovery
and development functions.
Ultra Services
The Ultra Services program is CambridgeSoft’s personalized, premium
service for supporting our customers. Organizations can
take advantage of both telephone and electronic access to
CambridgeSoft’s support scientists who can address:
• Usage and installation questions
• Product compatibility and interoperability questions
• Diagnostic review to help isolate the cause of a problem
• Configuration assistance
• Planning information for software updates and upgrades
• Assistance with problem resolution
Technical Support & Remote DBA Services
Technical Support and Remote DBA Services for Oracle and SQL
Server are also available.
US 1 800 315–7300 INT’L 1 617 588–9300 FAX 1 617 588–9390 EMAIL info@cambridgesoft.com
EU 00 800 875 20000 UK +44 1223 464900 JP 0120 146 700 WWW www.cambridgesoft.com
MAIL CambridgeSoft Corporation 100 CambridgePark Drive Cambridge, Massachusetts 02140 USA
ChemOffice, ChemDraw, BioOffice, BioDraw & ChemBioFinder are trademarks of CambridgeSoft Corporation ©2009

Chem & Bio Office
Desktop Software to Enterprise Solutions
Research, Discovery, Development, Trials T
& Manufacturing
Enterprise Solutions include Chem & Bio Office with Oracle Cartridge and Chem & Bio Office Workgroup, based on SQL Server
to help organizations from small workgroups to large enterprises collaborate and share information more effectively.
Knowledge Management with E-Notebook, including Reaction Explorer, CombiChem, E-Signatures for intellectual property
protection and 21CFR11 Compliance, streamlines daily record-keeping with rigorous security and efficient archiving.
Laboratory Informatics includes Workflow LIMs for instrumentation automation and Compliant DB for storage of your data.
Biological Informatics scientists use BioDraw, BioAssay, BioSAR and BioViz to set up biological models and visualize
information, generate spreadsheets correlating structure and activity, search by structure, and draw and annotate pathways.
Chemical Informatics, including Registration, organizes new compound information. Inventory provides complete management of
chemical and biological inventories including GxP Validation. DocManager indexes chemical structures in documents.
Manufacturing Informatics include Inventory to meet the chemical, reagent, sample and compound tracking needs of large
multi-site chemical and pharmaceutical laboratories and E-Notebook for manufacturing compliance management.
Desktop Software includes Chem & Bio Office, a powerful suite of software, consisting of ChemBioDraw, ChemBio3D,
ChemFinder and ChemACX for chemists, BioDraw, BioAssay, and BioViz and for biologists, and Inventory and E-Notebook for all.
Scientific Databases include the ChemACX Database of commercially available chemicals and Sigma-Aldrich MSDS. The Merck
Index and other scientific databases provide information about chemicals, their properties, and reactions.
Professional Services include custom development, system deployment, educational training, and technical support for
pharmaceutical, biotechnology, and chemical customers, including government and academia, by experienced staff.
Web
www.cambridgesoft.com
America 1 800 315-7300
Europe 00 800 875 20000
Japan 0120 146 700
Email
info@cambridgesoft.com
United Kingdom +44 1223 464900
Germany +49 69 2222 2280
France +33 1 70 71 98 80

Chem & Bio Office
Desktop Software to Enterprise Solutions
SDMS
Research, Discovery, Development, Trials & Manufacturing
Enterprise Solutions include Chem & Bio Office with Oracle Cartridge and Chem & Bio Office Workgroup, based on SQL Server
to help organizations from small workgroups to large enterprises collaborate and share information more effectively.
Knowledge Management with E-Notebook, including Reaction Explorer, CombiChem, E-Signatures for intellectual property
protection and 21CFR11 Compliance, streamlines daily record-keeping with rigorous security and efficient archiving.
Laboratory Informatics includes Workflow LIMs for instrumentation automation and Compliant SDMS for storage of your data.
Biological Informatics scientists use BioDraw, BioAssay, BioSAR and BioViz to set up biological models and visualize
information, generate spreadsheets correlating structure and activity, search by structure, and draw and annotate pathways.
Chemical Informatics, including Registration, organizes new compound information. Inventory provides complete management of
chemical and biological inventories including GxP Validation. DocManager indexes chemical structures in documents.
Manufacturing Informatics include Inventory to meet the chemical, reagent, sample and compound tracking needs of large
multi-site chemical and pharmaceutical laboratories and E-Notebook for manufacturing compliance management.
Desktop Software includes Chem & Bio Office, a powerful suite of software, consisting of ChemBioDraw, ChemBio3D,
ChemFinder and ChemACX for chemists, BioDraw, BioAssay, and BioViz and for biologists, and Inventory and E-Notebook for all.
Scientific Databases include the ChemACX Database of commercially available chemicals and Sigma-Aldrich MSDS. The Merck
Index and other scientific databases provide information about chemicals, their properties, and reactions.
Professional Services include custom development, system deployment, educational training, and technical support for
pharmaceutical, biotechnology, and chemical customers, including government and academia, by experienced staff.
Web
www.cambridgesoft.com
America 1 800 315-7300
Europe 00 800 875 20000
Japan 0120 146 700
MAE 09156 0902
Email
info@cambridgesoft.com
United Kingdom +44 1223 464900
Germany +49 69 2222 2280
France +33 1 70 71 98 80