Papers in PDF format

Electronic Publishing and the Web
Henryette Roth
Journal of Molecular Modeling
Computer Chemistry Centre
University of Erlangen
Germany
roth@organik.uni-erlangen.de
Timothy Clark
Computer Chemistry Centre
Department of Organic Chemistry
University of Erlangen
Germany
clark@organik.uni-erlangen.de
The real beauty of the World Wide Web is that it is a many-to-many communication medium, where the whole
world may be an extension of your mind, where some day all knowledge is accessed instantly by the electronic
pulses of your brain, where the mere act of formulating a questions prompts a global search that retrieves the
answer. The problem is that we loose the information about the quality of the published material, that no
distinction is made between tested and untested material. [ACS 1995]
The beauty of today's molecular modeling tools is that you can play with your molecules. Simply by rotating
them, zooming them in and out, looking at them from all sides, changing their shapes, it becomes easier to
understand their chemistry.
However, when it comes to scientific publishing most of the beauty is lost. Colour graphics in printed journal
are still very expensive. Molecules are constrained in 2D-structure diagrams. Stereo plots are poor solutions
that can't help the molecules come back to life.
Electronic publishing promises the way out. The idea of presenting results in the medium in which they were
created need no longer to be fantasy since the expansion of the Internet. The use of electronic media in every
step of the publication process should also lead to unprecedently short publication times. The articles of a
journal could be made accessible through FTP- and WWW-servers. The server-mode of publication, however,
does not mean that the longevity of the published material could not be provided, this could be guaranteed by
issuing CD-ROM versions. Thus the electronic journal becomes a permanent archive of science like the
classical printed ones.
The nature of the computer makes innovative new techniques necessary in electronic journals in order to make
this new medium truly user-friendly. Analysing molecules on your computer is great, but reading a longer text
on the screen is tiring. Manipulating molecules that have been investigated by others is helpful for
understanding. Changing them by accident would harm the scientific information.
Internet technology is moving fast. We can't build up today the ideal framework for electronic publishing. An
electronic journal is much more a research project. We try to apply our editorial intelligence to figuring out
what people really need in the online space. The goal is to develop tools that fit perfectly in today's world of
scientific publishing and open doors to high technology publishing projects in the future.
The Journal of Molecular Modeling is the first electronic journal in chemistry. [Clark 1995] What started as an
idea at an ACS meeting has developed into an experiment in which we are very much learning as we go along.
When the Journal of Molecular Modeling was designed, we had to rely on FTP for the data transfer and
Postscript as format for the papers. WWW, VRML and Java were still in their childhood and only used by
some few experts. When we finally started to publish, WWW could be used to published graphical abstracts
and the papers could be published in PDF (portable document format).