bioinformatics 2nd degree bologna study programme - Univerza v ...
bioinformatics 2nd degree bologna study programme - Univerza v ...
bioinformatics 2nd degree bologna study programme - Univerza v ...
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COURSE SYLLABUS<br />
Course title: Bioinformatics Algorithms and data structures<br />
Study <strong>programme</strong> and level Study field<br />
Bioinformatics 2 nd <strong>degree</strong><br />
Bologna Study <strong>programme</strong><br />
Academic<br />
year<br />
Semester<br />
Bioinformatics 1 1<br />
Course type Obligatory subject<br />
University course code:<br />
Lectures Seminar Tutorial<br />
Laboratory<br />
work<br />
Field work<br />
Individ.<br />
work<br />
ECTS<br />
30 30 90 6<br />
Lecturer: Matjaž Colnarič, PhD, Full professor<br />
David Podgorelec, PhD, Assistant professor<br />
Languages: Lectures: Slovene<br />
Tutorial: Slovene<br />
Prerequisits:<br />
- Basic programming skills.<br />
- Mathematical skills: polynomial, rational, exponential, logarithmical functions, vectors and<br />
matrices, basic knowledge of graph theory.<br />
Content (Syllabus outline):<br />
- Basic concepts: What is an algorithm? Biological and computer algorithms. Time and space<br />
complexity. Iterative and recursive algorithms.<br />
- Introduction to data structures: Object orientation of data structures. Elementary data<br />
types – arrays and connected lists. Abstract data types – stack, queue and list, trees,<br />
graphs.<br />
- Algorithm design strategies: Brute force. Greedy method. »Divide-and-conquer« strategy.<br />
Dynamic programming. Searching strategies. Stochastic algorithms (Monte Carlo<br />
algorithms, simulated annealing, genetic algorithms).<br />
- Practical algorithms of <strong>bioinformatics</strong>: Classification with respect to the algorithm design<br />
strategy. String algorithms, clustering and trees. Sequence analysis, searching for subsequences<br />
in longer sequences, sequence alignment, prediction of protein features,<br />
phylogenetic trees, physical mapping. Graph algorithms. Hidden Markov models.<br />
- Sorting algorithms: sorting by comparing the key values. Sorting in linear time.
Readings:<br />
- N. C. Jones, P. A. Pevzner: An Introduction to Bioinformatics Algorithms (Computational<br />
Molecular Biology), MIT Press, Cambridge, Massachusetts, 2004.<br />
- C. Gibas, P. Jambeck: Developing Bioinformatics Computer Skills, O'Reilly, Sebastopol,<br />
California, 2001.<br />
- T. H. Cormen, S. Clifford, C. E. Leiserson, R. L. Rivest: Introduction to Algorithms, Second<br />
Edition, MIT Press, Cambridge, Massachusetts, 2001.<br />
- I. Kononenko, M. Robnik Šikonja: Osnove algoritmov in podatkovnih struktur. Ljubljana,<br />
FRI, 2004.<br />
Objectives and competences:<br />
The objectives of this course are to represent to the students basic data structures and their<br />
implementation using static and dynamic data types, to introduce the basic algorithm strategies<br />
and to teach the students how to select among them in concrete problems, to teach the students<br />
to analyze the algorithms regarding time and space complexity, and to implement some selected<br />
problems from <strong>bioinformatics</strong>.<br />
Intended learning outcomes:<br />
Knowledge and understanding:<br />
The students will:<br />
- be aware of selecting the suitable data structures and their use at algorithms design,<br />
- understand the fundamental data structures and master their implementations,<br />
- know the fundamental strategies for algorithms design,<br />
- be able to determine the time and space complexity of the algorithms,<br />
- get the computing background for different problems of <strong>bioinformatics</strong>.<br />
- The students will be able to harmonize the usage of data structures and algorithm<br />
strategies at practical problems.<br />
- The students will skilfully use implemented data structures and algorithms during the<br />
<strong>study</strong> and later work.<br />
- At algorithm design they will reasonable search the compromises among different criteria<br />
as difficultness of implementation, time and space complexity and quality of the solution.<br />
- They will be able to use the knowledge and practical experience at different problems of<br />
<strong>bioinformatics</strong>.<br />
Learning and teaching methods:<br />
Lectures, discussions, demonstration, computer exercises.<br />
Assessment:<br />
Type (examination, oral, coursework,<br />
project):<br />
Weight (in %)<br />
coursework (practical<br />
assignments)<br />
20 %<br />
written examination (achievable 30 %<br />
also with two non obligatory<br />
colloquia),<br />
oral examination.<br />
50 %
Lecturer's references:<br />
COLNARIČ, Matjaž<br />
An example of fault detection and reconfiguration-based tolerance in distributed embedded<br />
control systems / Matjaž Colnarič. - Bibliograija: str. 286. - Abstract.V: Proceedings of COSY 2011<br />
papers / Special International Conference on Complex systems: synergy of control<br />
communications and computing, September 16-20, 2011, Ohrid, Republic of Macedonia. - Skopje :<br />
Society for Electronics, Telecommunications, Automation, and Informatics of the Republic of<br />
Macedonia, 2011. - Str. 281-286. COBISS.SI-ID 15385366<br />
COLNARIČ, Matjaž<br />
Struggle for temporal predictability of processors for real-time environments, revisited 20 years<br />
after / Matjaž Colnarič. - Abstract. - Bibliografija: str. 11-12.V: Autonomous systems / Herwig<br />
Unger, Kyandoghere Kyamaky, and Janusz Kacprzyk (Eds.). - Berlin ; Heidelberg : Springer, cop.<br />
2011. - (Studies in computational intelligence ; Vol. 391, ISSN 1860-949X). - ISBN 978-3-642-<br />
24805-4. - Str. 3-12. COBISS.SI-ID 15575830<br />
COLNARIČ, Matjaž<br />
Distributed embedded control systems : improving dependability with coherent design / Matjaž<br />
Colnarič, Domen Verber and Wolfgang A. Halang. - Berlin ; London : Springer, 2008. - XVII, 250 str.<br />
- (Advances in industrial control)ISBN 978-1-84800-051-3 ISBN 978-1-84800-052-0 (e-ISBN)<br />
COBISS.SI-ID 11970070<br />
PODGORELEC, David<br />
Dealing with redundancy and inconsistency in constructive geometric constraint solving / David<br />
Podgorelec, Borut Žalik, Vid Domiter. - . - Dostopno tudi na:<br />
http://dx.doi.org/10.1016/j.advengsoft.2007.10.003. - Abstract. - Bibliografija: str. 786.V:<br />
Advances in engineering software. - ISSN 0965-9978.. - Vol. 39, iss. 9 (Sep. 2008), Str. 770-786.<br />
. - doi: 10.1016/j.advengsoft.2007.10.003 COBISS.SI-ID 12138006, JCR, WoS, št. citatov do 6. 12.<br />
2010: 1, brez avtocitatov: 1, normirano št. citatov: 1<br />
PODGORELEC, David<br />
Cluster registration in 2D geometric constraint solving / David Podgorelec, Borut Žalik.<br />
V: 23st European Workshop on Computational Geometry / EWCG'07, march 19-21, 2007, Graz,<br />
Austria. - Graz : Technische Universität, 2007. - Str. 118-121. COBISS.SI-ID 11615254<br />
GEOMETRIC data preparation for GIS applications / David Podgorelec ... [et al.]. - Soavtorji: Gregor<br />
Klajnšek, Sebastian Krivograd, Borut Žalik. - Bibliografija: str. 124-127. - Abstract.<br />
V: Geoinformation technologies for geocultural landscapes / editors Oliver Bender ... [et al.]. -<br />
Boca Raton [etc.] : CRC Press/Balkema, cop. 2009. - ISBN 978-0-415-46859-6. - Str. 107-127.<br />
COBISS.SI-ID 13051670
COURSE SYLLABUS<br />
Course title: Informarion and communication technologies for <strong>bioinformatics</strong><br />
Study <strong>programme</strong> and level Study field<br />
Bioinformatics 2 nd <strong>degree</strong><br />
Bologna Study <strong>programme</strong><br />
Academic<br />
year<br />
Semester<br />
Bioinformatics 1 1<br />
Course type Obligatory subject<br />
University course code:<br />
Lectures Seminar Tutorial<br />
Laboratory<br />
work<br />
Field work<br />
Individ.<br />
work<br />
ECTS<br />
18 42 90 6<br />
Lecturer: Milan Zorman, PhD, Full professor<br />
Domen Verber, PhD, Assistant professor<br />
Languages: Lectures: slovene<br />
Tutorial: slovene<br />
Prerequisits:<br />
This subject can be selected by all regularly registered students of Master's <strong>degree</strong> <strong>study</strong><br />
<strong>programme</strong> Bioinformatics with the background in health or natural sciences<br />
Content (Syllabus outline):<br />
1. History of computing<br />
2. Von Neumans Arhitecture, personal computer<br />
3. Input/output units, central processing unit<br />
4. Software and hardware<br />
5. Data bases,<br />
6. Networks and world wide web<br />
7. Computers in biology<br />
8. Computer tools in <strong>bioinformatics</strong><br />
9. Visualisation
Readings:<br />
E. Turban, R. K. Rainer Jr., R. E. Potter: Introduction to Information Technology. 3rd ed., Wiley,<br />
2004.<br />
P. Kokol: Računalništvo v zdravstvu I. Maribor: NICE textbooks from the Phare Tempus program.<br />
Visoka zdravstvena šola, 1998.<br />
C. Gibas, P. Jambeck. Developing Bioinformatics Computer Skills: OReily and Associates, 2001<br />
Objectives and competences:<br />
Student will learn the advanced contents of computer science and methods, used in the field of<br />
<strong>bioinformatics</strong>.<br />
Intended learning outcomes:<br />
Knowledge and understanding:<br />
Student:<br />
Learns the computer architecture and its working principles<br />
Understands the role of the computer in the health systems related to informatics<br />
Learns about software and hardware<br />
Learns the basics of management of databases<br />
Understands the role of information technology in biology<br />
Learns the basics of visualisation<br />
Learning and teaching methods:<br />
Lectures, seminar work.<br />
Assessment:<br />
Type (examination, oral, coursework,<br />
project):<br />
Written exam,<br />
project.<br />
Weight (in %)<br />
50<br />
50<br />
Lecturer's references:<br />
ZORMAN, Milan<br />
Classification of follicular lymphoma images : a holistic approach with symbol-based machine<br />
learning methods / Milan Zorman, José Luis Sánches de la Rosa, Dejan Dinevski. - Graf. prikazi. -<br />
Abstract ; Zusammenfassung. - Bibliografija: str. 708-709. V: Wiener Klinische Wochenschrift. -<br />
ISSN 0043-5325.. - Jg. 123, Heft 23/24 (2011), str. 700-709. COBISS.SI-ID 15706134, JCR<br />
ZORMAN, Milan<br />
Opening the knowledge tombs - web based text mining as approach for re-evaluation of machine<br />
learning rules / Milan Zorman, Sandi Pohorec and Boštjan Brumen. - Abstract. - Bibliografija: str.<br />
542. V: Lecture notes in computer science. - ISSN 0302-9743. - Vol. 6295 (2010), str. 533-542.<br />
COBISS.SI-ID 14444310<br />
ZORMAN, Milan<br />
Explanatory approach for evaluation of machine learning-induced knowledge / M. Zorman and M.<br />
Verlič. - Abstract. - Bibliografija: str. 1550-1551.V: Journal of international medical research. - ISSN
0300-0605.. - Letn. 37, št. 5 (2009), str. 1543-1551. COBISS.SI-ID 13645334, JCR<br />
VERBER, Domen<br />
Implementation of non-intrusive fault detection in embedded control systems / Domen Verber,<br />
Matej Šprogar, Matjaž Colnarič. - Bibliografija: str. 30. V: Informacije MIDEM. - ISSN 0352-9045.. -<br />
Letn. 37, št. 1(121) (mar. 2007), str. 23-30. COBISS.SI-ID 11552534, JCR<br />
VERBER, Domen<br />
Utilization of high performance computing in everyday business applications / Domen Verber. -<br />
Ilustr. - Bibliografija: str. [5]. - Abstract. V: The proceedings of the <strong>2nd</strong> International Conference on<br />
Information Society and Information Technologies - ISIT 2010, [Dolenjske Toplice, 10-12<br />
November 2010] / edited by Matej Mertik. - Novo mesto : Faculty of Information Studies, 2010. -<br />
ISBN 978-961-92509-5-2. - [5] str. COBISS.SI-ID 14700054<br />
VERBER, Domen<br />
Decentralized fault and resource management for distributed control systems / Domen Verber.<br />
V: Applications of systems science / editors Adam Grzech, Paweł Świątek, Krysztof Brzostowski. -<br />
Warsaw : EXIT, cop. 2010. - ISBN 978-83-60434-78-9. - Str. 237-243. COBISS.SI-ID 14487574
COURSE SYLLABUS<br />
Course title: Selected topics in Biophysics<br />
Study <strong>programme</strong> and level Study field<br />
Bioinformatics 2 nd <strong>degree</strong><br />
Bologna Study <strong>programme</strong><br />
Academic<br />
year<br />
Semester<br />
Bioinformatics 1 1<br />
Course type Optional subject<br />
University course code:<br />
Lectures Seminar Tutorial<br />
Laboratory<br />
work<br />
Field work<br />
Individ.<br />
work<br />
ECTS<br />
30 30 90 6<br />
Lecturer: Aleš Fajmut, PhD, Assistant professor<br />
Languages: Lectures: slovene<br />
Tutorial: slovene<br />
Prerequisits:<br />
No special prerequisites required.<br />
However, for all students that have not gained the knowledge of fundamental physics in the 1.<br />
level of university <strong>degree</strong> this subject is compulsory.<br />
Content (Syllabus outline):<br />
Mechanics: force, pressure, torque, work, energy, power; deformations; hydrostatics and<br />
hydrodynamics. Electricity and magnetism; electric and magnetic fields. Thermodynamics:<br />
thermodynamic laws and potentials, heat and mass flow. Oscillations and waves: sound, light;<br />
properties of waves, geometric optics. Experiments essential in modern physics. Structure and<br />
models of atoms, atomic and intermolecular interactions. Structure and stability of atomic<br />
nucleus, radioactivity.<br />
Selected illustrative examples from biology:<br />
1. Biomechanics: forces in bones and muscles; flow of blood in the circulatory system;<br />
transport of respiratory gases; mechanical properties of biological membranes, cell shape<br />
and its transformation.<br />
2. Thermodynamics: the first law of thermodynamics, metabolism, heat, work and power of<br />
human and animals; the second law of thermodynamics, conditions of minimal free energy<br />
and maximal entropy in biological systems; regulatory systems and mechanisms, body<br />
temperature regulation, cell volume regulation.<br />
3. Electromagnetism: diffusion of ions, the Donnan equilibrium, membrane potential; action
potential and nerve impulses; magnetic fields and orientation of organisms, weak<br />
magnetic fields in biology<br />
4. Vibrational and wave motion: biochemical and cellular oscillators; sound and an ear,<br />
ultrasound; light, an eye.<br />
5. Molecular biophysics: atomic and molecular interactions and chemical bonds. Biological<br />
effects of ionizing radiation.<br />
Students perform 10 laboratory experiments from mechanics, thermodynamics, electricity and<br />
magnetism, wave nature of light and geometric optics, atomic physics and radioactivity. The<br />
content of labor work is applied to biological systems.<br />
Readings:<br />
R. Kladnik: Visokošolska fizika, 1. del: Mehanika in toplotni pojavi, 2. del: Elektrika, Atomika, 3. del:<br />
Valovni pojavi, Akustika in optika, Državna založba Slovenije, Ljubljana 1989<br />
R. Glaser: Biophysics, Springer, Berlin 2001<br />
G. B: Benedek, F. M. H. Villars: Physics with Illustrative Examples from Medicine and Biology:<br />
Mechanics, Statistical Physics, Electricity and Magnetism, Springer, New York 2000<br />
P. R. Bergethon: The Physical Basis of Biochemistry. The Foundations of Molecular Biophysics,<br />
Springer, New York 1998<br />
Interna navodila za izvedbo eksperimentalnih vaj/ Guidelines for labor work.<br />
Objectives and competences:<br />
The main objective is to gain the knowledge of physical concepts and laws which are essential for<br />
understanding the biological processes.<br />
Intended learning outcomes:<br />
Knowledge and Understanding:<br />
Students get knowledge of structure and function of selected biological systems based on the<br />
fundamental principles and concepts of physics.<br />
Transferable/Key Skills and other attributes:<br />
Students are able to use simple mathematical models for quantitative studies of structure and<br />
function of biological systems.<br />
Learning and teaching methods:<br />
Lectures<br />
Labor work with concomitant mathematical exercises in problem solving<br />
Assessment:<br />
Type (examination, oral, course work,<br />
project):<br />
Written test on labor work<br />
Written exam.<br />
Oral exam.<br />
Weight (in %)<br />
30%<br />
30%<br />
40%
Lecturer's references:<br />
FAJMUT, Aleš<br />
MLC-kinase/phosphatase control of Ca[sup]2+ signal transduction in airway smooth muscles /<br />
Aleš Fajmut, Milan Brumen. - . - Dostopno tudi na: http://dx.doi.org/10.1016/j.jtbi.2007.10.005. -<br />
Available online Oct. 11 2007. - Bibliografija: str. 481. V: Journal of theoretical biology. - ISSN<br />
0022-5193.. - Vol. 252, no. 3 (2008), str. 474-481.<br />
. - doi: 10.1016/j.jtbi.2007.10.005 COBISS.SI-ID 15856392, JCR, WoS, št. citatov do 6. 5. 2011: 5,<br />
brez avtocitatov: 4, normirano št. citatov: 2<br />
CONTRIBUTION of Rho kinase to the early phase of the calcium-contraction coupling in airway<br />
smooth muscle / Prisca Mbikou ... [et al.]. - Ilustr. - Nasl. z nasl. zaslona. - Opis vira z dne 7. 12.<br />
2010. - Soavtorji: Ales Fajmut, Milan Brumen, Etienne Roux. - Bibliografija: str. 257-258. - Abstract.<br />
V: Experimental physiology. - ISSN 0958-0670.. - Vol. 96, issue 2 (2011), str. 240-258.<br />
. - doi: 10.1113/expphysiol.2010.054635 COBISS.SI-ID 18009864, JCR, WoS, št. citatov do 10. 4.<br />
2012: 2, brez avtocitatov: 2, normirano št. citatov: 1<br />
DOBOVIŠEK, Andrej<br />
Role of expression of prostaglandin synthases 1 and 2 and leukotriene C [sub] 4 synthase in<br />
aspirin-intolerant asthma: a theoretical <strong>study</strong> / A. Dobovišek, A. Fajmut, M. Brumen. -<br />
Bibliografija: str. 277-278. - Abstract.V: Journal of pharmacokinetics and pharmacodynamics. -<br />
ISSN 1567-567X.. - Vol. 38, no. 2 (2011), str. 261-278. . - doi: 10.1007/s10928-011-9192-6<br />
COBISS.SI-ID 18203144, JCR, WoS, št. citatov do 6. 4. 2012: 1, brez avtocitatov: 0, normirano št.<br />
citatov: 0
COURSE SYLLABUS<br />
Course title: Selected topics in biochemistry<br />
Study <strong>programme</strong> and level Study field<br />
Bioinformatics 2 nd <strong>degree</strong><br />
Bologna Study <strong>programme</strong><br />
Academic<br />
year<br />
Semester<br />
Bioinformatics 1 1<br />
Course type Optional subject<br />
University course code:<br />
Lectures Seminar Tutorial<br />
Laboratory<br />
work<br />
Field work<br />
Individ.<br />
work<br />
ECTS<br />
30 30 90 6<br />
Lecturer:<br />
Languages: Lectures: slovene<br />
Tutorial: slovene<br />
Prerequisits:<br />
Understanding basics of molecular biology and biochemistry.<br />
Content (Syllabus outline):<br />
Biochemistry: From Atoms to Molecules to Cells, Biomolecules in Water<br />
Proteins: Amino Acids, Peptides, and Proteins, : Protein Architecture and Biological Function<br />
Enzymes: Reactions, Kinetics, Inhibition, Coenzymes, Regulation, Abzymes, and Ribozymes.<br />
Carbohydrates: Structure and Biological Function.<br />
Lipids: Structure and Biological Function, Biological Membranes and Cellular Transport.<br />
Nucleid acids; DNA and RNA: Structure and Function.<br />
Vitamines; Hormones.<br />
Basic Concepts of Cellular Metabolism and Bioenergetics.<br />
Metabolism of Carbohydrates.<br />
Production of NADH and NADPH: The Citric Acid Cycle.<br />
ATP Formation by Electron-Transport Chains.<br />
Metabolism of Fatty Acids and Lipids.<br />
Metabolism of Amino Acids and Other Nitrogenous Compounds.<br />
Integration, Specialization, and Hormonal Control of Metabolism.
Readings:<br />
Boyer, Rodney F.: Concepts in biochemistry, 3rd ed., J. Wiley & Sons, Hoboken , 2006<br />
L. STRAYER et al.: Biochemistry, 4th ed, W.H. Freeman and Company, New York, 1995<br />
Voet,Donald: Fundamentals of biochemistry : life at the molecular level, <strong>2nd</strong> ed., J. Wiley<br />
& sons, Hoboken (New Jersey), 2006.<br />
Nelson DL, Cox MM.; Lehninger Principles of Biochemistry, 4th ed, W.H. Freeman and<br />
Company, New York, 2004<br />
Objectives and competences:<br />
Students will be provided with structural characteristics of major groups of biomolecules and their<br />
role in cell metabolism and other important biological processes.<br />
Intended learning outcomes:<br />
Knowledge and Understanding:<br />
structural characteristics of biomoleculs<br />
the role of biomolecules in cell function<br />
Learning and teaching methods:<br />
Lectures<br />
Tutorial<br />
Assessment:<br />
Type (examination, oral, coursework,<br />
project):<br />
writen and<br />
oral exemination<br />
Lecturer's references:<br />
Weight (in %)<br />
60<br />
40
Course title: Chemistry<br />
COURSE SYLLABUS<br />
Study <strong>programme</strong> and level Study field<br />
Bioinformatics 2 nd <strong>degree</strong><br />
Bologna Study <strong>programme</strong><br />
Academic<br />
year<br />
Semester<br />
Bioinformatics 1 1<br />
Course type Optional subject<br />
University course code:<br />
Lectures Seminar Tutorial<br />
Laboratory<br />
work<br />
Field work<br />
Individ.<br />
work<br />
ECTS<br />
30 30 90 6<br />
Lecturer: Željko Knez, PhD, Full professor<br />
Languages: Lectures: slovene<br />
Tutorial: slovene<br />
Prerequisits:<br />
None.<br />
Content (Syllabus outline):<br />
Chemical bonds, forces between molecules<br />
Water: structure, characteristics, H bond, water as dissolvent<br />
pH, water ionization, Kw, pH, weak and strong electrolyte, acids and bases (titration<br />
curves, Ka, Kb, pKa, pKb), pufer, pufer systems in organism, biological meaning of pH<br />
Solutions: gas dissolving in water (Henry law) koligativno characteristics of solutions (Rault<br />
law, decreasing of freezing point, increasing of boiling point, osmotic pressure), osmotic<br />
phenomenon in cell (Donnans balance, passive transport – Fickos law)<br />
Oxidation – reduction : definitions, quantitative characterization redox reactions<br />
Redox potential and free reaction enthalpy,<br />
Velocity of chemical reactions: definitions,<br />
Basics of transportability phenomenon,<br />
Molecular basics of life: biological important elements, ions and molecules,<br />
Organics molecules: isomerism, mutual influence of functional groups (inductive and<br />
resonant effect),<br />
Short overview of organic compound by functional groups.<br />
Short review of chemistry:<br />
- carbon hydrates (monosaccharide, disaccharide, polysaccharide)
- lipid and steroids (steroids, steroli, gall acid, steroids hormones,- structure)<br />
- aminoacid,<br />
- nucleotides and nucleic acid.<br />
Readings:<br />
- Lazarini F., Brencic J.: Splošna in anorganska kemija, 3. izd. Ljubljana : Državna založba<br />
Slovenije, 1992<br />
- Lehninger A.L., Nelson D.L., Cox M.M., Waites J.: Principles of biochemistry : with an<br />
extended discussion of oxygen-binding proteins, <strong>2nd</strong> ed., 9th printing, New York : Worth,<br />
2000.<br />
- Ebbing D.D., Gammon S.D.: General chemistry, 6th ed.,Boston, New York : Houghton<br />
Mifflin, cop. 1999.<br />
- Hunt, Harold R., Block, Toby F., McKelvy, George M.: Laboratory experiments for general<br />
chemistry, 4th ed., Australia, United States : Brooks/Cole-Thomson Learning, 2002.<br />
- Strauss S.H.: Guide to solutions for Inorganic chemistry: 3rd ed. Oxford University Press,<br />
1999.<br />
Objectives and competences:<br />
Student will gain knowledge of general chemistry, get familiar with chemical structure of organic<br />
molecules and reactions between them to better understand the reactions in organism.<br />
Intended learning outcomes:<br />
Knowledge and understanding:<br />
Student will be able to understand selected chemical concepts.<br />
Learning and teaching methods:<br />
Lectures, seminar work, workshops.<br />
Assessment:<br />
Type (examination, oral, coursework,<br />
project):<br />
Seminar<br />
Oral exam<br />
Written exam<br />
Weight (in %)<br />
40<br />
30<br />
30<br />
Lecturer's references:<br />
KNEZ, Željko, ŠKERGET, Mojca, KNEZ HRNČIČ, Maša. Principles of supercritical fluid extraction and<br />
applications in the food, beverage and nutraceutical industries. V: RIZVI, Syed S. H. (ur.).<br />
Separation, extraction and concentration processes in the food, beverage and nutraceutical<br />
industries. Oxford [etc.]: Woodhead Publishing Limited, 2010.<br />
KNEZ, Željko, ŠKERGET, Mojca, MANDŽUKA, Zoran. Determination of S-L phase transitions under<br />
gas pressure. J. supercrit. fluids. [Print ed.], Dec. 2010, vol. 55, iss. 2, str. 648-652.<br />
KNEZ, Željko, AIONICESEI, Elena, NOVAK, Zoran, KNEZ HRNČIČ, Maša. Processing polymeric<br />
biomaterials using supercritical CO[sub]2. Chemieingenieurtech., 2011, vol. 83, no. 9, str. 1371-<br />
1380.
COURSE SYLLABUS<br />
Course title: Molecular biophysics<br />
Study <strong>programme</strong> and level Study field<br />
Bioinformatics 2 nd <strong>degree</strong><br />
Bologna Study <strong>programme</strong><br />
Academic<br />
year<br />
Semester<br />
Bioinformatics 1 1<br />
Course type Obligatory subject<br />
University course code:<br />
Lectures Seminar Tutorial<br />
Laboratory<br />
work<br />
Field work<br />
Individ.<br />
work<br />
ECTS<br />
30 30 90 6<br />
Lecturer: Milan Brumen, PhD, Full professor<br />
Languages: Lectures: slovene<br />
Tutorial: slovene<br />
Prerequisits:<br />
Knowledge of physics on the level of a general university course in physics or biophysics given to<br />
students of studies others than physics.<br />
Content (Syllabus outline):<br />
1. Chemical bonds, intra- and intermolecular forces. Structure of biological macromolecules<br />
(proteins, nucleic acids, polysaccharides). and Cooperative ligand binding to macromolecules.<br />
Dynamics of conformational changes of macromolecules. Structure of supramolecular complexes<br />
(lipoproteins, biological membrane). Relation between structure and function of macromolecular<br />
and supramolecular systems, regulation of biological activity. Water, its structure and meaning for<br />
biological systems.<br />
2. Biophysics of cytoskeleton and molecular machines of subcellular scales. Microtubules,<br />
microfilaments. Motor proteins: myosins, kinesins, dyneins; muscle contraction, mitosis, transport<br />
of organelles, cilia and flagella movement. protein motors<br />
3. Cell and cell membrane biophysics. Structure of biological cell. Transport across the cell<br />
membrane. Intra and intercellular signalisation and communications.<br />
4. Outline of selected experimental methods in molecular biophysics: X-ray crystallography,
absorption and fluorescence spectroscopy, spectroscopic methods NMR and EPR.<br />
Readings:<br />
J.A. Tuszynski, M. Kurzynski: Introduction to Molecular Biophysics, CRC Press 20<br />
R. Glaser: Biophysics, Springer, New York 2004<br />
P. R. Bergethon: The Physical Basis of Biochemistry. The Foundations of Molecular<br />
Biophysics, Springer, New York 1998<br />
D. Voet, J.G. Voet: Biochemistry, John Wiley & Sons, New York 1995<br />
Objectives and competences:<br />
Students get knowledge of structure and function of biological systems with respect to different<br />
levels of organisation and complexity, from molecules, macromolecules and supramolecular<br />
structures to the cell and tissue. The approach is based on concepts and methods of theoretical<br />
biophysics.<br />
Knowledge of biological systems on molecular level that is essential to deal with the data and data<br />
bases in <strong>bioinformatics</strong>.<br />
Intended learning outcomes:<br />
Knowledge and understanding:<br />
Students get knowledge and understanding of structure and function of selected biological<br />
systems based on principles and concepts of physics.<br />
Learning and teaching methods:<br />
Lectures<br />
Coursework from selected field in biophysics<br />
Tutorials<br />
Assessment:<br />
Type (examination, oral, coursework,<br />
project):<br />
Written exam<br />
Oral exam<br />
Course work<br />
Weight (in %)<br />
35%<br />
35%<br />
30%
Lecturer's references:<br />
POISSON-Helmholtz-Boltzmann model of the electric double layer : analysis of monovalent ionic<br />
mixtures / Klemen Bohinc ... [et al.]. - Bibliografija: str. 031130-11-031130-12. V: Physical review.<br />
E, Statistical, nonlinear, and soft matter physics. - ISSN 1539-3755.. - Vol. 85, no. 3 (2012), str.<br />
031130-1-031130-12. . - doi: 10.1103/PhysRevE.85.031130 COBISS.SI-ID 4353131, JCR, WoS, št.<br />
citatov do 6. 5. 2012: 0, brez avtocitatov: 0, normirano št. citatov: 0<br />
ENZYME kinetics and the maximum entropy production principle / Andrej Dobovišek ... [et al.]. -<br />
Soavtorji: Paško Županović, Milan Brumen, Željana Bonačić-Lošić, Domagoj Kuić, Davor Juretić. -<br />
Bibliografija: str. 55. - Abstract.V: Biophysical chemistry. - ISSN 0301-4622.. - Vol. 154, iss. 2/3<br />
(2011), str. 49-55. . - doi: 10.1016/j.bpc.2010.12.009 COBISS.SI-ID 18206984, JCR, WoS, št. citatov<br />
do 6. 5. 2011: 0, brez avtocitatov: 0, normirano št. citatov: 0<br />
CONTRIBUTION of Rho kinase to the early phase of the calcium-contraction coupling in airway<br />
smooth muscle / Prisca Mbikou ... [et al.]. - Ilustr. - Nasl. z nasl. zaslona. - Opis vira z dne 7. 12.<br />
2010. - Soavtorji: Ales Fajmut, Milan Brumen, Etienne Roux. - Bibliografija: str. 257-258. - Abstract.<br />
V: Experimental physiology. - ISSN 0958-0670.. - Vol. 96, issue 2 (2011), str. 240-258. . - doi:<br />
10.1113/expphysiol.2010.054635COBISS.SI-ID 18009864, JCR, WoS, št. citatov do 10. 4. 2012: 2,<br />
brez avtocitatov: 2, normirano št. citatov: 1
COURSE SYLLABUS<br />
Course title: Multivariate statistical methods<br />
Study <strong>programme</strong> and level Study field<br />
Bioinformatics 2 nd <strong>degree</strong><br />
Bologna Study <strong>programme</strong><br />
Academic<br />
year<br />
Semester<br />
Bioinformatics 1 2<br />
Course type Obligatory subject<br />
University course code:<br />
Lectures Seminar Tutorial<br />
Laboratory<br />
work<br />
Field work<br />
Individ.<br />
work<br />
ECTS<br />
30 30 90 6<br />
Lecturer: Petra Povalej Bržan, PhD, Assistant professor<br />
Languages: Lectures: slovene<br />
Tutorial: slovene<br />
Prerequisits:<br />
Basics of statistics,<br />
basics of databases,<br />
basics of software package SPSS.<br />
Content (Syllabus outline):<br />
Basics:<br />
• Data<br />
• Identifiers<br />
• Hypothesis<br />
• Distribution<br />
• Data types<br />
Introduction to statistical data analysis:<br />
• Data preprocessing<br />
• Descriptive data analysis<br />
• Normal distribution<br />
• Other distributions<br />
• Generating hypotheses
• Correlations<br />
• Univariate analysis<br />
Graphical representation of data for multivariate analysis:<br />
• Scattered plot<br />
• Radar plot<br />
• Polar plot<br />
• Multidimensional scaling<br />
Introduction to multivariate analysis:<br />
• Data preprocessing<br />
• Multinormal distribution<br />
• Normalisation<br />
• Generating hypotheses<br />
Overview of multivariate analysis methods:<br />
• MANOVA<br />
• Covariance<br />
• Factor analysis<br />
• Cluster analysis<br />
• Time series analysis<br />
• Loglinear models<br />
Practical examples:<br />
• Genom analysis example<br />
• • Molecular biology example<br />
Readings:<br />
1. Warren J. Ewens, Gregory R. Grant: Statistical Methods in Bioinformatics: An Introduction,<br />
Second Edition. Springer Verlag, New York 2005.<br />
2. Johnson, R.A. & Wichern, D.W.: Applied Multivariate Statistical Analysis. New Jersey:<br />
PrenticeHall, 2002.<br />
3. Marija Norusis: SPSS 14.0 Statistical Procedures Companion, Prentice Hall, 2005. ISBN: 0-<br />
13-199527-8.<br />
4. Marija Norusis: SPSS 14.0 Advanced Statistical Procedures Companion, Prentice Hall, 2005.<br />
5. Joseph F. Hair, Bill Black, Barry Babin, Rolph E. Anderson, Ronald L. Tatham: Multivariate<br />
Data Analysis. Prentice Hall, 2005.<br />
6. Alexander Isaev: Introduction to Mathematical Methods in Bioinformatics. Springer, 2004.<br />
Objectives and competences:<br />
Refresh knowledge of basic statistical methods,<br />
Show different data representations for multivariate analysis,<br />
Give overview of multivariate methods,<br />
Teach students which statistical analysis method to choose,<br />
Demonstrate usage of some methods on microbiology cases.<br />
Students should know which multivariate statistical method to use in a given case.<br />
Gained knowledge will be routinely used in their future work.<br />
Experience gathered here will be aplicable to actual real world cases from the field of<br />
<strong>bioinformatics</strong>.
Intended learning outcomes:<br />
Knowledge and understanding:<br />
Students:<br />
Should know how to preprocess and analyse data and how to determine an appropriate<br />
method according to hypothesis set<br />
will find out about different graphical data representations<br />
will find out about different distributions and common normalisation approaches,<br />
will gain knowledge about most widely used multivariate analysis methods,<br />
should know how to practically use gained knowledge for solving problems in the field of<br />
<strong>bioinformatics</strong>.<br />
Learning and teaching methods:<br />
Lectures, discussion, demonstration, theoretical exercises, computer exercises<br />
Assessment:<br />
Type (examination, oral, coursework,<br />
project):<br />
coursework (practical<br />
assignments)<br />
written examination (can be<br />
achieved also with two non<br />
obligatory colloquia)<br />
oral examination.<br />
Lecturer's references:<br />
Weight (in %)<br />
20<br />
30<br />
50
COURSE SYLLABUS<br />
Course title: Basics of molecular and cell biology<br />
Study <strong>programme</strong> and level Study field<br />
Bioinformatics 2 nd <strong>degree</strong><br />
Bologna Study <strong>programme</strong><br />
Academic<br />
year<br />
Semester<br />
Bioinformatics 1 1<br />
Course type Optional subject<br />
University course code:<br />
Lectures Seminar Tutorial<br />
Laboratory<br />
work<br />
Field work<br />
Individ.<br />
work<br />
ECTS<br />
30 30 90 6<br />
Lecturer: Saška Lipovšek Delakorda, PhD, Assistant professor<br />
Languages: Lectures: slovene<br />
Tutorial: slovene<br />
Prerequisits:<br />
Content (Syllabus outline):<br />
DNA structure and characteristics, replication (prokaryotes, eukaryotes), recombination, repair<br />
and mutations,, structure and function of genes and chromosomes.<br />
RNA structure characteristics: role of different types of RNA, transcription (prokaryotes,<br />
eukaryotes), post transcription modification.<br />
Protein structures, synthesis of proteins, translation, posttranslational modifications, protein<br />
folding, protein trafficking.<br />
Regulation of protein synthesis: transcriptional regulation of gene expression,, regulation of<br />
translation, posttranslational regulation .<br />
Embryonic development.<br />
Cell division (meiosis, mitosis).<br />
Cell cycle: proliferation, differentiation, apoptosis.<br />
Integration of cells into tissues, communication between cells, signal transduction, receptors,<br />
hormone signaling.<br />
Immune system.<br />
Viruses :HIV, SARS, Avian influence, DNA diagnostics and infection diseases.
Readings:<br />
1. B. ALBERTS et al.: Molecular biology of the cell., 4th Ed., Gerland Publish, Inc., New York, 2002<br />
2. LODISH H., Baltimore D., Berk A., Zipursky S.L., Matsudaira P., Darnell J.: Molecular Cell<br />
Biology, 5th Ed., Scientific American Books, Freeman and Co., New York, 2004<br />
3. Bruce Alberts, Dennis Bray, Karen Hopkin, Alexander Johnson, Julian Lewis, Martin Raff, Keith<br />
Roberts, Peter Walter: Essential cell biology, <strong>2nd</strong> Ed., Gerland Publish, Inc., New York, 2003<br />
Objectives and competences:<br />
Students will understand basic molecular mechanisms in the cell, how cells are organized in<br />
tissues, organs and whole organisms. The focus will be on transfer of genomic information to<br />
synthesis of proteins.<br />
Intended learning outcomes:<br />
Knowledge and understanding:<br />
basic molecular processes in the cell<br />
Learning and teaching methods:<br />
Lectures<br />
Tutorial<br />
Assessment:<br />
Type (examination, oral, coursework,<br />
project):<br />
writen and<br />
oral exemination<br />
Weight (in %)<br />
60<br />
40<br />
Lecturer's references:<br />
The EVIDENCE on the degradation processes in the midgut epithelial cells of the larval antlion<br />
Euroleon nostras (Geoffroy in Fourcroy, 1785) (Myrmeleontidae, Neuroptera) [Elektronski vir] /<br />
Saška Lipovšek ... [et al.]. - Ilustr. - Nasl. z nasl. zaslona. - Opis vira z dne 27. 3. 2012. - Soavtorji:<br />
Ilse Letofsky-Papst, Ferdinand Hofer, Gerd Leitinger, Dušan Devetak. - Bibliografija: str. 664-665. -<br />
Abstract. V: Micron. - ISSN 0968-4328.. - Vol. 43, iss. 5 (2012), str. 651-665. . - doi:<br />
10.1016/j.micron.2011.11.012 COBISS.SI-ID 18855176, JCR, WoS, št. citatov do 6. 5. 2012: 0, brez<br />
avtocitatov: 0, normirano št. citatov: 0<br />
APPLICATION of analytical electron microscopic methods to investigate the function of spherites<br />
in the midgut of the larval antlion Euroleon nostras (Neuroptera: Myrmeleontidae) [Elektronski<br />
vir] / Saška Lipovšek ... [et al.]. - Ilustr. - Nasl. z nasl. zaslona. - Opis vira z dne 27. 3. 2012. -<br />
Soavtorji: Ilse Letofsky-Papst, Ferdinand Hofer, Maria Anna Pabst, and Dušan Devetak. -<br />
Bibliografija: str. 406-407. - Abstract. V: Microscopy research and technique. - ISSN 1059-910X.. -<br />
Vol. 75, iss. 4 (2012), str. 397-407. . - doi: 10.1002/jemt.21069 COBISS.SI-ID 18638856, JCR, WoS,<br />
št. citatov do 8. 5. 2012: 1, brez avtocitatov: 0, normirano št. citatov: 0<br />
DUALITY of terrestrial subterranean fauna / Tone Novak ... [et al.]. - Soavtorji: Matjaž Perc, Saška<br />
Lipovšek and Franc Janžekovič. - Bibliografija: str. 62-64. - Abstract. V: International journal of<br />
speleology. - ISSN 0392-6672.. - Vol. 41, no. 2 (2012), str. 181-188. . - doi: 10.5038/1827-<br />
806X.41.2.5 COBISS.SI-ID 19061512, JCR
COURSE SYLLABUS<br />
Course title: Data mining and knowledge discovery<br />
Study <strong>programme</strong> and level Study field<br />
Bioinformatics 2 nd <strong>degree</strong><br />
Bologna Study <strong>programme</strong><br />
Academic<br />
year<br />
Semester<br />
Bioinformatics 1 2<br />
Course type Obligatory subject<br />
University course code:<br />
Lectures Seminar Tutorial<br />
Laboratory<br />
work<br />
Field work<br />
Individ.<br />
work<br />
ECTS<br />
30 30 90 6<br />
Lecturer: Milan Zorman, PhD, Full professor, Vili Podgorelec, PhD,<br />
Associate professor, Boštjan Brumen, PhD, Assistant professor<br />
Languages: Lectures: slovene<br />
Tutorial: slovene<br />
Prerequisits:<br />
Basic computer user skills: working with mouse, keyboard, MS Windows operating system,<br />
spreadsheets (MS Excel)<br />
Computer Science for Bioinformatics<br />
Content (Syllabus outline):<br />
Introduction to inteligent systems<br />
Basics of data sets<br />
Data preprocessing<br />
Working with missing data<br />
Methods for supervised machine learning:<br />
o Decision trees<br />
o Neural networks<br />
o Rough sets<br />
o Hybrid methods<br />
Evaluation of acquired knowledge
Readings:<br />
- Zorman Milan, Podgorelec Vili, Lenič Mitja, Povalej Petra, Kokol Peter in Tapajner Alojz:<br />
Inteligentni sistemi in profesionalni vsakdan, <strong>Univerza</strong> v Mariboru, Center za<br />
Interdisciplinarne in multidisciplinarne raziskave in študije UM, Maribor, 2003<br />
- Toshinori Munakata: Fundamentals of the New Artificial Intelligence: Beyond Traditional<br />
Paradigms. Springer Verlag New York, 1998.<br />
- internet sources<br />
Objectives and competences:<br />
To introduce students to knowledge acquisition from data sets.<br />
To teach students about intelligent methods for automatic acquisition and evaluation of<br />
knowledge.<br />
Intended learning outcomes:<br />
Knowledge and understanding:<br />
Data acquisition<br />
Storing data.<br />
Data preprocessing for analysis with intelligent methods.<br />
Basics and usage of intelligent methods.<br />
Evaluation of results of intelligent methods.<br />
Usage of acquired knowledge.<br />
Capability to more efficiently acquire, store and use data.<br />
Knowledge about data mining and knowledge acquisition in various areas.<br />
Familiarity with intelligent methods.<br />
Learning and teaching methods:<br />
Lectures, discussion, demonstration, computer exercises<br />
Assessment:<br />
Type (examination, oral, coursework,<br />
project):<br />
- coursework (practical<br />
assignments)<br />
- written examination (can be<br />
achieved also with two non<br />
obligatory colloquia),<br />
- oral examination.<br />
Weight (in %)<br />
20<br />
30<br />
50<br />
Lecturer's references:<br />
ZORMAN, Milan<br />
Classification of follicular lymphoma images : a holistic approach with symbol-based machine<br />
learning methods / Milan Zorman, José Luis Sánches de la Rosa, Dejan Dinevski. - Graf. prikazi. -<br />
Abstract ; Zusammenfassung. - Bibliografija: str. 708-709. V: Wiener Klinische Wochenschrift. -<br />
ISSN 0043-5325.. - Jg. 123, Heft 23/24 (2011), str. 700-709. COBISS.SI-ID 15706134, JCR
ZORMAN, Milan<br />
Opening the knowledge tombs - web based text mining as approach for re-evaluation of machine<br />
learning rules / Milan Zorman, Sandi Pohorec and Boštjan Brumen. - Abstract. - Bibliografija: str.<br />
542. V: Lecture notes in computer science. - ISSN 0302-9743. - Vol. 6295 (2010), str. 533-542.<br />
COBISS.SI-ID 14444310<br />
ZORMAN, Milan<br />
Explanatory approach for evaluation of machine learning-induced knowledge / M. Zorman and M.<br />
Verlič. - Abstract. - Bibliografija: str. 1550-1551.V: Journal of international medical research. - ISSN<br />
0300-0605.. - Letn. 37, št. 5 (2009), str. 1543-1551. COBISS.SI-ID 13645334, JCR<br />
PODGORELEC, Vili, 1972-<br />
Taking advantage of education data : advanced data analysis and reporting in virtual learning<br />
environments / V. Podgorelec, S. Kuhar. - Bibliografija: str. 116. - Abstract. V: Elektronika ir<br />
elektrotechnika. - ISSN 1392-1215.. - Nr. 8 (2011), str. 111-116. COBISS.SI-ID 15441174, JCR, WoS,<br />
št. citatov do 6. 5. 2012: 0, brez avtocitatov: 0, normirano št. citatov: 0<br />
PODGORELEC, Vili, 1972-<br />
Supporting the <strong>study</strong> process using semantic web technologies / V. Podgorelec, M. Gresak. - . -<br />
Dostopno tudi na: http://www.ee.ktu.lt/journal/2011/10/23__ISSN_1392-<br />
1215_Supporting%20the%20Study%20Process%20using%20Semantic%20Web%20Technologies.p<br />
df. - Bibliografija: str. 108. - Abstract.V: Elektronika ir elektrotechnika. - ISSN 1392-1215.. - No. 10<br />
(2011), str. 105-108. COBISS.SI-ID 15625238, JCR, WoS, št. citatov do 11. 4. 2012: 0, brez<br />
avtocitatov: 0, normirano št. citatov: 0<br />
PODGORELEC, Vili, 1972-<br />
Expert-assisted classification rules extraction algorithm / Vili Podgorelec. - Abstract. - Bibliografija:<br />
str. 462.V: Lecture notes in computer science. - ISSN 0302-9743. - Vol. 6295 (2010), str. 450-462.<br />
COBISS.SI-ID 14444566<br />
ASSESSMENT of classification models with small amounts of data / Boštjan Brumen ... [et al.]. -<br />
Soavtorji: Matjaž B. Jurič, Tatjana Welzer, Ivan Rozman, Hannu Jaakkola, Apostolos Papadopoulos.<br />
V: Informatica. - ISSN 0868-4952.. - Vol. 18, no. 3 (2007), str. 343-362. COBISS.SI-ID 11983638,<br />
JCR, WoS, št. citatov do 10. 2. 2010: 3, brez avtocitatov: 3, normirano št. citatov: 3<br />
ZORMAN, Milan<br />
Opening the knowledge tombs - web based text mining as approach for re-evaluation of machine<br />
learning rules / Milan Zorman, Sandi Pohorec and Boštjan Brumen. - Abstract. - Bibliografija: str.<br />
542.V: Lecture notes in computer science. - ISSN 0302-9743. - Vol. 6295 (2010), str. 533-542.<br />
COBISS.SI-ID 14444310<br />
JEREB, Borut, 1962-<br />
Upravljanje IT tveganj s pomočjo Risk IT [Elektronski vir] / Borut Jereb, Boštjan Brumen. - ilustr. -<br />
Sekcija UI: Upravljanje informatike / IT governance. - Nasl. pri prispevku. - Bibliografija: str. 14.<br />
V: Uravnotežite naložbe, tveganja in razvoj za uspeh [Elektronski vir] / Dnevi slovenske<br />
informatike 2010 - DSI, Portorož, Slovenija, 14.-16. april 2010. - Ljubljana : Slovensko društvo<br />
Informatika, 2010. - ISBN 978-961-6165-32-7. - 14 str. COBISS.SI-ID 512183357
COURSE SYLLABUS<br />
Course title: Computational geometry for <strong>bioinformatics</strong><br />
Study <strong>programme</strong> and level Study field<br />
Bioinformatics 2 nd <strong>degree</strong><br />
Bologna Study <strong>programme</strong><br />
Academic<br />
year<br />
Semester<br />
Bioinformatics 1 2<br />
Course type Obligatory subject<br />
University course code:<br />
Lectures Seminar Tutorial<br />
Laboratory<br />
work<br />
Field work<br />
Individ.<br />
work<br />
ECTS<br />
30 30 90 6<br />
Lecturer: Borut Žalik, PhD, Full professor<br />
Languages: Lectures: slovene<br />
Tutorial: slovene<br />
Prerequisits:<br />
Basic programming skills are required.<br />
In addition, the basic understanding of <strong>bioinformatics</strong>, analytical geometry and linear algebra are<br />
recommended (distances, surfaces, volume, scalar and vector product).
Content (Syllabus outline):<br />
Introduction (Importance of geometric structures in <strong>bioinformatics</strong>)<br />
Convex hulls<br />
o Algorithms for the convex hull construction (brute force, Jarvish’s approach,<br />
Graham’s scan, incremental method, sweep-line-based approach, quickhull)<br />
o Use of convex hull in PSIMAP algorithms<br />
The closest point problem<br />
o uniform plane subdivision,<br />
o spiral algorithm<br />
o static and dynamical problem<br />
o Frenet distance (protein backbone construction)<br />
o closest k-pair search in large sets of imprecise points - proteins<br />
Triangulation (definition, characteristics, MWT, Hammilton triangulation, Delaunay<br />
triangulation)<br />
o Algorithms for Delaunay triangulation construction (random incremental<br />
algorithms, sweep-line algorithms)<br />
o Delaunay tetrahedronisation<br />
o Application of Delaunay tetrahedronisation for shape in position transformations<br />
of proteins.<br />
Voronoi diagram (definition, properties)<br />
o Algorithms for Voronoi diagram construction (brute force, Fortune’s approach)<br />
o Molecular surface determination from the Voronoi diagrams<br />
o Determination of proteins’ volume<br />
Minkowski’s sum<br />
o Minkowski’ sum construction on points and line segments<br />
o Application of Minkowski’ sum: van der Waals’ hull<br />
Collision detection<br />
o Method with hierarchically organised bounding boxes and spheres; method with<br />
dimension reduction<br />
o Collision detection among moving elementary particles<br />
Readings:<br />
1. M. de Berg, M. van Kreveld, M.Overmars, O. Schwarzkopf, Computational Geometry -<br />
Algorithms and Applications, Springer 1997.<br />
2. F. P. Preparata, M. I. Shamos, Computational Geometry: An Introduction, Springer Verlag,<br />
1985.<br />
3. J. O'Rourke, Computational Geometry in C, Cambridge University Press, 1998.<br />
4. N. C. Jones, P. A. Pevzner, An Introduction to Bioinformatics Algorithms, The MIT Press,<br />
2004.<br />
Objectives and competences:<br />
A student gets the knowledge about the importance of computational geometry and its<br />
applicability in <strong>bioinformatics</strong>. He/she recognises key problems in processing large amounts of<br />
geometric data, and acceleration techniques, dealing efficiently with these problems. He/she<br />
knows to link existing knowledge of computational geometry and apply it to the problems in<br />
<strong>bioinformatics</strong>. He knows efficient and stable algorithms of computational geometry, solving tasks<br />
from the field of <strong>bioinformatics</strong>.
Intended learning outcomes:<br />
Knowledge and understanding:<br />
Students:<br />
o get knowledge to find the convex hull for a set of points, and to use it in PSIMAP<br />
algorithms,<br />
o they recognize the closests point problem and existing solutions. They know how construct<br />
the protein backbone by using Frenet’s distance<br />
o they know different kinds of triangulation<br />
o they know algorithms for Delaunay triangulation construction,<br />
o they know applications of Delaunay triangulation in <strong>bioinformatics</strong><br />
o they know Voronoi diagrams<br />
o they are able to determine the surface and the volume of molecules, organised in Voronoi<br />
structures<br />
o they know Mikowski’s sum and the algorithms for its construction<br />
o they know how to generalise the Mikowski’s sum,<br />
o to Van der Waals’ hulls<br />
Key skills:<br />
o they know how to translate problems from the <strong>bioinformatics</strong> into already solved<br />
problems of computational geometry,<br />
o they know to select appropriate algorithm for geometrical problems in <strong>bioinformatics</strong>,<br />
o they get skills for implementing geometric algorithms (rounding error, error propagation).<br />
Learning and teaching methods:<br />
Explanation, discussion, demonstration, computer exercises<br />
Assessment:<br />
Weight (in %)<br />
Type (examination, oral, coursework,<br />
project):<br />
oral examination,<br />
50 %<br />
homework,<br />
20 %<br />
computer exercises.<br />
30 %<br />
Reference nosilca / Lecturer's references:<br />
1. ŠPELIČ, Denis, ŽALIK, Borut. Lossless compression of threshold-segmented medical images.<br />
Journal of medical systems, Published online: 15 April 2011, doi: 10.1007/s10916-011-9702-5.<br />
2. ZADRAVEC, Mirko, BRODNIK, Andrej, MANNILA, Markus, WANNE, Merja, ŽALIK, Borut. A<br />
practical approach to the 2D incremental nearest-point problem suitable for different point<br />
distributions. Pattern recognition, Vol. 41, No. 2, 2008, pp. 646-653.<br />
3. KLAJNŠEK, Gregor, ŽALIK, Borut. Progressive lossless compression of volumetric data using<br />
small memory load. Computerized medical imaging and graphics, Vol. 29, No. 4, 2005, pp. 305-<br />
312.
COURSE SYLLABUS<br />
Course title: Applied computer science in <strong>bioinformatics</strong><br />
Study <strong>programme</strong> and level Study field<br />
Bioinformatics 2 nd <strong>degree</strong><br />
Bologna Study <strong>programme</strong><br />
Academic<br />
year<br />
Semester<br />
Bioinformatics 1 2<br />
Course type Obligatory subject<br />
University course code:<br />
Lectures Seminar Tutorial<br />
Laboratory<br />
work<br />
Field work<br />
Individ.<br />
work<br />
ECTS<br />
30 30 90 6<br />
Lecturer: Milan Zorman, PhD, Full professor<br />
Languages: Lectures: slovene<br />
Tutorial: slovene<br />
Prerequisits:<br />
Basic computer user skills: working with mouse, keyboard, MS Windows operating system.<br />
Content (Syllabus outline):<br />
Word processors, advanced – MS Word<br />
Spreadsheets, advanced – MS Excel<br />
Working with data bases - MS Access<br />
o Relational model<br />
o Entry forms<br />
o Querying<br />
o Creating reports<br />
Internet searchers<br />
Bibliographic data bases<br />
Readings:<br />
Dan Gookin: Word 2003 for Dummies, Wiley publishing, 2003.<br />
Greg Harvey: Excel 2003 for Dummies, Wiley publishing, 2003.<br />
John Kaufeld: Access 2003 for Dummies, Wiley publishing, 2003.
Objectives and competences:<br />
- introduce students to applied computer science<br />
- to teach students how to use word processors<br />
- to teach students how to use spreadsheets<br />
- to teach students usage of databases<br />
- introduce students to internet searchers<br />
- to teach students how to use bibliographic data bases<br />
Intended learning outcomes:<br />
Knowledge and understanding:<br />
- of basics of applied computer science,<br />
- of word processors,<br />
- of spreadsheets,<br />
- of database basics,<br />
- of internet searchers,<br />
- basics of bibliographic data bases<br />
- using computer for solving problems in everday professional situations<br />
- improved efficiency<br />
Learning and teaching methods:<br />
Lectures, discussion, demonstration, theoretical exercises, computer exercises<br />
Assessment:<br />
Type (examination, oral, coursework,<br />
project):<br />
- coursework (practical assignments)<br />
- written examination (can be achieved<br />
also with two non obligatory colloquia),<br />
- oral examination.<br />
Weight (in %)<br />
30%<br />
50%<br />
20%<br />
Lecturer's references:<br />
ZORMAN, Milan<br />
Classification of follicular lymphoma images : a holistic approach with symbol-based machine<br />
learning methods / Milan Zorman, José Luis Sánches de la Rosa, Dejan Dinevski. - Graf. prikazi. -<br />
Abstract ; Zusammenfassung. - Bibliografija: str. 708-709. V: Wiener Klinische Wochenschrift. -<br />
ISSN 0043-5325.. - Jg. 123, Heft 23/24 (2011), str. 700-709. COBISS.SI-ID 15706134, JCR<br />
ZORMAN, Milan<br />
Opening the knowledge tombs - web based text mining as approach for re-evaluation of machine<br />
learning rules / Milan Zorman, Sandi Pohorec and Boštjan Brumen. - Abstract. - Bibliografija: str.<br />
542. V: Lecture notes in computer science. - ISSN 0302-9743. - Vol. 6295 (2010), str. 533-542.<br />
COBISS.SI-ID 14444310<br />
ZORMAN, Milan<br />
Explanatory approach for evaluation of machine learning-induced knowledge / M. Zorman and M.<br />
Verlič. - Abstract. - Bibliografija: str. 1550-1551.V: Journal of international medical research. - ISSN<br />
0300-0605.. - Letn. 37, št. 5 (2009), str. 1543-1551. COBISS.SI-ID 13645334, JCR
COURSE SYLLABUS<br />
Course title: Introduction to <strong>bioinformatics</strong><br />
Study <strong>programme</strong> and level Study field<br />
Bioinformatics 2 nd <strong>degree</strong><br />
Bologna Study <strong>programme</strong><br />
Academic<br />
year<br />
Semester<br />
Bioinformatics 1 2<br />
Course type Obligatory subject<br />
University course code:<br />
Lectures Seminar Tutorial<br />
Laboratory<br />
work<br />
Field work<br />
Individ.<br />
work<br />
ECTS<br />
30 30 90 6<br />
Lecturer: Uroš Potočnik, PhD, Associate professor<br />
Languages: Lectures: slovene<br />
Tutorial: slovene<br />
Prerequisits:<br />
Understanding basics of molecular biology, biochemistry and molecular genetics.<br />
Content (Syllabus outline):<br />
Databases in molecular biology and genomics:<br />
- database indexing and search profiles<br />
- bibliographic databases (PubMed)<br />
- text databases (OMIM)<br />
- surveys of molecular biology databases and servers: nucleotide acid sequence databases<br />
(GenBank), genome databases, protein sequence databases (Swiss Prot), databases of<br />
structures, expression databases, databases of metabolic pathways<br />
- Integrated systems for data retrieving: ENTREZ (NCBI), ExPASy, Ensembl<br />
Sequence alignments and phylogenetic trees: measures of similarity, computing the alignment of<br />
two sequences, multiple sequence alignments (profiles, PSI-BLAST, Hidden Markov Models),<br />
phylogenetic trees (clustering methods, cladistic method, the problem of varying rates of<br />
evolution)<br />
Protein structure and drug discovery: protein stability and folding, superposition of structures and<br />
structural alignments, evolution of protein structures, classification of protein structures, protein<br />
prediction and modeling, assignment of protein structures to genomes, drug discovery and<br />
development, computer-assisted drug design
Readings:<br />
1. Lesk A: (2005) Introduction to Bioinformatics. 2 nd Ed, Oxford University Press, Oxford, UK<br />
2. Barnes MR, Gray IC: Bioinformatics for geneticist. John Wiley&Sons, R.J.M , West Sussex,<br />
2003.<br />
3. Attwood TK, Parry-Smith DJ (1999) Introduction to Bioinformatics. Prentice Hall, Harlow,<br />
England.<br />
4. Baxevanis AD, Francis Ouellette BF (1998) Bioinformatics A Practical Guide to the Analysis<br />
of Genes and Proteins. Wiley-Interscience, A John Wiley & Sons Inc., Publication, New<br />
York, USA.<br />
5. Higgins D, Taylor W (2000) Bioinformatics. Sequence, Structure and Databanks. Oxford<br />
University Press, Oxford, UK.<br />
6. Kanehisa M (2002) Post-genome Informatics. Oxford University Press, Oxford, United<br />
Kingdom<br />
Objectives and competences:<br />
Students will be provided with comprehensive review of the most relevant databases and<br />
bioinformatic tools in the fields of biochemistry, molecular biology and genomics.<br />
Students will be able to access and retrieve most relevant data from available databases in the<br />
field of molecular biology and genomics.<br />
Intended learning outcomes:<br />
Knowledge and understanding:<br />
type and structure of databases<br />
meaning and interpretation of molecular biology and genomic data<br />
Learning and teaching methods:<br />
Lectures<br />
Tutorial<br />
Assessment:<br />
Type (examination, oral, coursework,<br />
project):<br />
Weight (in %)<br />
writen and<br />
60<br />
oral exemination<br />
40
Lecturer's references:<br />
POTOČNIK, Uroš, 1969-<br />
Trenutna komercializacija osebne genetske analize-zanesljiva napoved tveganja za pogoste<br />
kompleksne bolezni ali zavajanje potrošnikov? [Elektronski vir] = Current commercialization of<br />
personal genetic analysis-reliable prediction of susceptibility to common complex diseases or<br />
misleading of the consumers? / Uroš Potočnik. - Povzetek ; Abstract. - Bibliografija: str. 4-5.<br />
V: Slovenski kemijski dnevi 2011, Portorož, 14-16 september 2011 [Elektronski vir] / [organizirala]<br />
Fakulteta za kemijo in kemijsko tehnologijo, <strong>Univerza</strong> v Mariboru [v sodelovanju s Slovenskim<br />
kemijskim društvom ... et al.]. - Maribor : FKKT, 2011. - ISBN 978-961-248-289-3. - 5 str.<br />
COBISS.SI-ID 15319318<br />
ŠIMENC, Janez, 1973-<br />
Rapid differentiation of bacterial species by high resolution melting curve analysis / J. Šimenc and<br />
U. Potočnik. - Abstract. - Bibliografija: str. 262-263.V: Applied biochemistry and microbiology. -<br />
ISSN 0003-6838.. - Vol. 47, no. 3 (2011), str. 256-263. . - doi: 10.1134/S0003683811030136<br />
COBISS.SI-ID 14937622, JCR, WoS, št. citatov do 11. 4. 2012: 1, brez avtocitatov: 1, normirano št.<br />
citatov: 0<br />
A CYP17A1 gene polymorphism in association with multiple uterine leimyomas; a meta-analysis /<br />
Maja Pakiz ... [et al.]. - Soavtorji: Uros Potocnik, Igor But, Faris Mujezinovic. - Bibliografija: str. 33-<br />
34. – Abstract V: Disease markers. Section A, Cancer biomarkers. - ISSN 1574-0153.. - Vol. 8, no. 1<br />
(2010/2011), str. 29-34. . - doi: 10.3233/DMA-2011-0817 COBISS.SI-ID 4033599, JCR, WoS, št.<br />
citatov do 6. 10. 2011: 0, brez avtocitatov: 0, normirano št. citatov: 0
COURSE SYLLABUS<br />
Course title: Bioinformatics in genetic research<br />
Study <strong>programme</strong> and level Study field<br />
Bioinformatics 2 nd <strong>degree</strong><br />
Bologna Study <strong>programme</strong><br />
Academic<br />
year<br />
Semester<br />
Bioinformatics 2 3<br />
Course type Obligatory subject<br />
University course code:<br />
Lectures Seminar Tutorial<br />
Laboratory<br />
work<br />
Field work<br />
Individ.<br />
work<br />
ECTS<br />
30 30 90 6<br />
Lecturer: Uroš Potočnik, PhD, Associate professor<br />
Languages: Lectures: slovene<br />
Tutorial: slovene<br />
Prerequisits:<br />
Understanding basics of molecular biology, biochemistry, human genetics and <strong>bioinformatics</strong><br />
Content (Syllabus outline):<br />
Principles and strategies in identifying human disease genes:<br />
-patients and families enrolled in the <strong>study</strong><br />
-positional cloning and definition of candidate region<br />
-linkage analysis: selection of microsatellite markers, recombination fraction, LOD score, twopoint<br />
mapping, multipoint mapping, program tools (GENHUNTER)<br />
-sib.pair analysis<br />
-transmission disequilibrium test (TDT)<br />
-association studies (case:controls),<br />
-genetic studies from genome sequence: locus definition, identification and extraction of<br />
sequence between two markers, evaluating genome sequence integrity between two markers,<br />
definition of known and new genes in the candidate region, candidate gene selection: molecular<br />
and physiological function, expression; using new markers for fine mapping of candidate region,<br />
design of panel markers for genotyping<br />
Identification on Single nucleotide polymorphisms (SNPs) and genotyping protocol, functional and<br />
biological significant SNPs, PC primer design,validation of genotyping data<br />
Technology for mutation detection and polymorphism genotyping
Statistical analysis of genotype and allele frequency in patients and controls (Hi2, Fischer exact)<br />
Haplotype estimation (Expectation maximization algorithm), linkage disequilibrium,<br />
Mapping quantitative locus traits (QTL)<br />
Examples of successful identification of disease genes in monogenic (Mendel) and complex traits<br />
Design, application and interpretation of genetic tests, genetic counseling<br />
Molecular targets for drug design<br />
Readings:<br />
1. Barnes MR, Gray IC: Bioinformatics for geneticist. John Wiley&Sons, R.J.M , West Sussex,<br />
2003.<br />
2. STRACHAN T and READ AP: Human Molecular genetics, Gerland Publish, Inc., New York,<br />
3rd ed., 2004<br />
3. David J. Balding (Editor), M. Bishop (Editor), C. Cannings (Editor): Handbook of Statistical<br />
Genetics, Second Edition, John Wiley&Sons, , 2003<br />
4. Tekoča periodika<br />
Objectives and competences:<br />
Students will be trained to use available resources, databases and <strong>bioinformatics</strong> tools for<br />
research in the field of molecular genetics and genomics. The aim of this course is to keep the<br />
students up to date with the most important discoveries with highest impact in the field of human<br />
molecular genetics. The course will address the possibilities of transfer of new discoveries and<br />
achievements in the field of genomics, molecular genetics and biomedicine into clinical practice<br />
including improved disease prevention and diagnosis, design and application of molecular drugs<br />
and personalized medicine.<br />
The focus will be on identification and mapping of human disease genes and potential molecular<br />
targets for drug design.<br />
Intended learning outcomes:<br />
Knowledge and understanding:<br />
approaches for identification and mapping of disease gene<br />
gene function and their role in pathogenesis<br />
Learning and teaching methods:<br />
Lectures<br />
Tutorial<br />
Assessment:<br />
Type (examination, oral, coursework,<br />
project):<br />
Weight (in %)<br />
writen and<br />
60<br />
oral exemination<br />
40
Lecturer's references:<br />
POTOČNIK, Uroš, 1969-<br />
Trenutna komercializacija osebne genetske analize-zanesljiva napoved tveganja za pogoste<br />
kompleksne bolezni ali zavajanje potrošnikov? [Elektronski vir] = Current commercialization of<br />
personal genetic analysis-reliable prediction of susceptibility to common complex diseases or<br />
misleading of the consumers? / Uroš Potočnik. - Povzetek ; Abstract. - Bibliografija: str. 4-5.<br />
V: Slovenski kemijski dnevi 2011, Portorož, 14-16 september 2011 [Elektronski vir] / [organizirala]<br />
Fakulteta za kemijo in kemijsko tehnologijo, <strong>Univerza</strong> v Mariboru [v sodelovanju s Slovenskim<br />
kemijskim društvom ... et al.]. - Maribor : FKKT, 2011. - ISBN 978-961-248-289-3. - 5 str.<br />
COBISS.SI-ID 15319318<br />
ŠIMENC, Janez, 1973-<br />
Rapid differentiation of bacterial species by high resolution melting curve analysis / J. Šimenc and<br />
U. Potočnik. - Abstract. - Bibliografija: str. 262-263.V: Applied biochemistry and microbiology. -<br />
ISSN 0003-6838.. - Vol. 47, no. 3 (2011), str. 256-263. . - doi: 10.1134/S0003683811030136<br />
COBISS.SI-ID 14937622, JCR, WoS, št. citatov do 11. 4. 2012: 1, brez avtocitatov: 1, normirano št.<br />
citatov: 0<br />
A CYP17A1 gene polymorphism in association with multiple uterine leimyomas; a meta-analysis /<br />
Maja Pakiz ... [et al.]. - Soavtorji: Uros Potocnik, Igor But, Faris Mujezinovic. - Bibliografija: str. 33-<br />
34. – Abstract V: Disease markers. Section A, Cancer biomarkers. - ISSN 1574-0153.. - Vol. 8, no. 1<br />
(2010/2011), str. 29-34. . - doi: 10.3233/DMA-2011-0817 COBISS.SI-ID 4033599, JCR, WoS, št.<br />
citatov do 6. 10. 2011: 0, brez avtocitatov: 0, normirano št. citatov: 0
COURSE SYLLABUS<br />
Course title: DNA micro nets and analyze of expressions of genes<br />
Study <strong>programme</strong> and level Study field<br />
Bioinformatics 2 nd <strong>degree</strong><br />
Bologna Study <strong>programme</strong><br />
Academic<br />
year<br />
Semester<br />
Bioinformatics 2 3<br />
Course type Obligatory subject<br />
University course code:<br />
Lectures Seminar Tutorial<br />
Laboratory<br />
work<br />
Field work<br />
Individ.<br />
work<br />
ECTS<br />
15 45 90 6<br />
Lecturer: Uroš Potočnik, PhD, Associate professor<br />
Languages: Lectures: slovene<br />
Tutorial: slovene<br />
Prerequisits:<br />
Understanding basics of molecular biology, biochemistry, human genetics and <strong>bioinformatics</strong><br />
Content (Syllabus outline):<br />
Regulation of gene expression: binding of trans-acting proteins to cis elements, modification of<br />
histones, chromatine remodeling<br />
Alternative transcription and gene processing<br />
Allele specific expression: DNA methylation, imprinting, SNPs in regulatory regions<br />
Transcriptomics<br />
Chemistry of binding to surface, preparation of microarrays (cDNA and oligo probes)<br />
Statistical analysis of microarray data: experimental design, normalization issues, Two-sample<br />
statistics for differential expression (DE) and multiple testing issues, linear models and its<br />
application in analyzing complex gene expression experiments with two or more treatment<br />
comparisons, clustering algorithms, cross –validation, functional annotation using Gene Ontology<br />
and sequence information<br />
Protein microarrays<br />
Application of microarray technology in diagnostics and in drug design and development
Readings:<br />
1. Statistical Analysis of Gene Expression Microarray Data edited by T.P. Speed. 2003. Chapman<br />
& Hall/CRC.<br />
2. Mark Schena: Microarray Analysis, John Willey&Sons, 2003<br />
3. Steen Knudsen: Guide to Analysis of DNA Microarray Data, <strong>2nd</strong> Edition, John Willey&Sons<br />
2004<br />
Objectives and competences:<br />
This course will introduce, illustrate and evaluate a variety of statistical methods employed in the<br />
context of microarray data analysis. Techniques covered correspond to commonly encountered<br />
research questions and <strong>study</strong> designs and include preprocessing/normalization, linear models,<br />
multiple hypothesis testing, clustering, discrimination, prediction and annotation with gene<br />
ontology and sequence information.<br />
Intended learning outcomes:<br />
Knowledge and understanding:<br />
Perform microarray data analyses.<br />
Identify and use relevant resources (genomic data and tools) for their own research.<br />
Assess microarray data analyses performed by others.<br />
Design studies using microarray technology.<br />
Learning and teaching methods:<br />
Lectures<br />
Tutorial<br />
Assessment:<br />
Type (examination, oral, coursework,<br />
project):<br />
Weight (in %)<br />
writen and<br />
60<br />
oral exemination<br />
40<br />
Lecturer's references:<br />
POTOČNIK, Uroš, 1969-<br />
Trenutna komercializacija osebne genetske analize-zanesljiva napoved tveganja za pogoste<br />
kompleksne bolezni ali zavajanje potrošnikov? [Elektronski vir] = Current commercialization of<br />
personal genetic analysis-reliable prediction of susceptibility to common complex diseases or<br />
misleading of the consumers? / Uroš Potočnik. - Povzetek ; Abstract. - Bibliografija: str. 4-5.<br />
V: Slovenski kemijski dnevi 2011, Portorož, 14-16 september 2011 [Elektronski vir] / [organizirala]<br />
Fakulteta za kemijo in kemijsko tehnologijo, <strong>Univerza</strong> v Mariboru [v sodelovanju s Slovenskim<br />
kemijskim društvom ... et al.]. - Maribor : FKKT, 2011. - ISBN 978-961-248-289-3. - 5 str.<br />
COBISS.SI-ID 15319318<br />
ŠIMENC, Janez, 1973-<br />
Rapid differentiation of bacterial species by high resolution melting curve analysis / J. Šimenc and
U. Potočnik. - Abstract. - Bibliografija: str. 262-263.V: Applied biochemistry and microbiology. -<br />
ISSN 0003-6838.. - Vol. 47, no. 3 (2011), str. 256-263.. - doi:<br />
10.1134/S0003683811030136COBISS.SI-ID 14937622, JCR, WoS, št. citatov do 11. 4. 2012: 1, brez<br />
avtocitatov: 1, normirano št. citatov: 0<br />
A CYP17A1 gene polymorphism in association with multiple uterine leimyomas; a meta-analysis /<br />
Maja Pakiz ... [et al.]. - Soavtorji: Uros Potocnik, Igor But, Faris Mujezinovic. - Bibliografija: str. 33-<br />
34. – Abstract V: Disease markers. Section A, Cancer biomarkers. - ISSN 1574-0153.. - Vol. 8, no. 1<br />
(2010/2011), str. 29-34. . - doi: 10.3233/DMA-2011-0817 COBISS.SI-ID 4033599, JCR, WoS, št.<br />
citatov do 6. 10. 2011: 0, brez avtocitatov: 0, normirano št. citatov: 0
COURSE SYLLABUS<br />
Course title: Pharmacogenomics<br />
Study <strong>programme</strong> and level Study field<br />
Bioinformatics 2 nd <strong>degree</strong><br />
Bologna Study <strong>programme</strong><br />
Academic<br />
year<br />
Semester<br />
Bioinformatics 2 3<br />
Course type Optional subject<br />
University course code:<br />
Lectures Seminar Tutorial<br />
Laboratory<br />
work<br />
Field work<br />
Individ.<br />
work<br />
ECTS<br />
15 30 105 6<br />
Lecturer: Uroš Potočnik, PhD, Associate professor<br />
Languages: Lectures: slovene<br />
Tutorial: slovene<br />
Prerequisits:<br />
Understanding basics of molecular biology, biochemistry, human genetics and <strong>bioinformatics</strong><br />
Content (Syllabus outline):<br />
The students will be provided with information about the state of art technology and<br />
bioinformatic tools in pharmacogenomic research including high-throughput genotyping,<br />
microarrays and mass spectroscopy. The pharmacogenomic markers such as single nucleotide<br />
polymorphisms (SNPs), alleles, haplotypes, gene expression profiles and proteomes and their role<br />
in drug discovery and therapy will be discussed. Basics of statistical genetics relevant for<br />
pharmaogenomics will be explained. Molecular mechanisms and genes involved in drug<br />
metabolism (Cyp450), drug transport (ABCB1/MDR1) and drug receptors will be described.<br />
Already known associations between genes and drug response will be comprehensively reviewed.<br />
Ethic and social economic issues in pharmacogenomic research and application will be discussed.
Readings:<br />
1. Kalow W. (ed.): Pharmacogenomics, Marcel Dekker; 1st edition 2001<br />
2. Liciano J. (ed.): Pharmacogenomics, The Search for Individualized Therapies, John<br />
Wiley&Sons, 2002R.J.M.<br />
3. Potočnik U, Ferkolj I, Glavač D, Dean M: Polymorphisms in multidrug resistance 1 (MDR1)<br />
gene are associated with refractory Crohn disease and ulcerative colitis. Genes Immun.<br />
2004 Nov;5(7):530-9.<br />
Objectives and competences:<br />
The aim of this course is to provide student with understanding of molecular genetic and<br />
biochemical mechanisms underlaying different response to drug terapy. Student will be able to<br />
collaborate with medical doctors doing presonalized medicine and will be able to design and<br />
conduct research for discovery of molecular markers in pharmacogenomic.<br />
Intended learning outcomes:<br />
Knowledge and understanding:<br />
students will understant molecular genetic and biochemical mechanisms underlying variation in<br />
drug response among different individuals<br />
Learning and teaching methods:<br />
Lectures<br />
Tutorial<br />
Assessment:<br />
Type (examination, oral, coursework,<br />
project):<br />
Weight (in %)<br />
writen and<br />
60<br />
oral exemination<br />
40<br />
Lecturer's references:<br />
POTOČNIK, Uroš, 1969-<br />
Trenutna komercializacija osebne genetske analize-zanesljiva napoved tveganja za pogoste<br />
kompleksne bolezni ali zavajanje potrošnikov? [Elektronski vir] = Current commercialization of<br />
personal genetic analysis-reliable prediction of susceptibility to common complex diseases or<br />
misleading of the consumers? / Uroš Potočnik. - Povzetek ; Abstract. - Bibliografija: str. 4-5.<br />
V: Slovenski kemijski dnevi 2011, Portorož, 14-16 september 2011 [Elektronski vir] / [organizirala]<br />
Fakulteta za kemijo in kemijsko tehnologijo, <strong>Univerza</strong> v Mariboru [v sodelovanju s Slovenskim<br />
kemijskim društvom ... et al.]. - Maribor : FKKT, 2011. - ISBN 978-961-248-289-3. - 5 str.<br />
COBISS.SI-ID 15319318<br />
ŠIMENC, Janez, 1973-<br />
Rapid differentiation of bacterial species by high resolution melting curve analysis / J. Šimenc and<br />
U. Potočnik. - Abstract. - Bibliografija: str. 262-263.V: Applied biochemistry and microbiology. -<br />
ISSN 0003-6838.. - Vol. 47, no. 3 (2011), str. 256-263. . - doi: 10.1134/S0003683811030136<br />
COBISS.SI-ID 14937622, JCR, WoS, št. citatov do 11. 4. 2012: 1, brez avtocitatov: 1, normirano št.<br />
citatov: 0<br />
A CYP17A1 gene polymorphism in association with multiple uterine leimyomas; a meta-analysis /
Maja Pakiz ... [et al.]. - Soavtorji: Uros Potocnik, Igor But, Faris Mujezinovic. - Bibliografija: str. 33-<br />
34. – Abstract V: Disease markers. Section A, Cancer biomarkers. - ISSN 1574-0153.. - Vol. 8, no. 1<br />
(2010/2011), str. 29-34. . - doi: 10.3233/DMA-2011-0817 COBISS.SI-ID 4033599, JCR, WoS, št.<br />
citatov do 6. 10. 2011: 0, brez avtocitatov: 0, normirano št. citatov: 0
COURSE SYLLABUS<br />
Course title: Human moleclar genetics-selcted topics<br />
Study <strong>programme</strong> and level Study field<br />
Bioinformatics 2 nd <strong>degree</strong><br />
Bologna Study <strong>programme</strong><br />
Academic<br />
year<br />
Semester<br />
Bioinformatics 2 3<br />
Course type Optional subject<br />
University course code:<br />
Lectures Seminar Tutorial<br />
Laboratory<br />
work<br />
Field work<br />
Individ.<br />
work<br />
ECTS<br />
15 15 15 105 6<br />
Lecturer: Damjan Glavač, PhD, Full professor<br />
Languages: Lectures: slovene<br />
Tutorial: slovene<br />
Prerequisits:<br />
Graduate <strong>degree</strong> 40 ECTS.<br />
Content (Syllabus outline):<br />
Advances in functional genomics<br />
New approaches to treating disease: Gene therapy, embryonic stem cell research and therapeutic<br />
cloning for tissue repair and regeneration<br />
Molecular cancer genetics: oncogenes, tumors suppressor genes, hereditary cancer, molecular<br />
diagnostic and treatment, screening<br />
Molecular genetics and aging-can we reverse aging?<br />
Molecular evolution of genomes-what make us human?<br />
Behavioral genetics and neurobiology<br />
Readings:<br />
1. STRACHAN T and READ AP: Human Molecular genetics, Gerland Publish, Inc., New York, 3rd<br />
ed., 2004<br />
2. Tekoča periodika
Objectives and competences:<br />
The aim of this course is to inform students about most important and atractive up to date topics<br />
in the field of human molecular genetics. Students will get deep inside into heredity, structures of<br />
genes and genomes, comparative genomics, genomic diversity and mutations associated with<br />
diseases. The possibilities, advantages, risk, limitations and ethical issues of molecular genetic and<br />
genomic based medicine will be discussed. The interpretation of genetic tests and genetic<br />
counseling in rare monogenic and common complex multifactorial diseases will be discussed.<br />
Intended learning outcomes:<br />
Knowledge and understanding:<br />
corellations genotype-complex phenotype; heredity of complex phenotypes<br />
aplication of molecular genetics in medicine<br />
reading current scientific literature and discussing future developments in the field<br />
Learning and teaching methods:<br />
Lectures<br />
Tutorial<br />
Assessment:<br />
Type (examination, oral, coursework,<br />
project):<br />
Weight (in %)<br />
writen and<br />
60<br />
oral exemination<br />
40<br />
Lecturer's references:<br />
ASSESSMENT of the tumourigenic and metastatic properties of SK-MEL28 melanoma cells<br />
surviving electrochemotherapy with bleomycin = Določitev tumorigenih in metastatskih lastnosti<br />
melanomskih celic SK-MEL28 po preživetju elektrokemoterapije z bleomicinom / Vesna Todorović<br />
... [et al.]. - . - Dostopno tudi na:<br />
http://versita.metapress.com/content/24337t420311w012/fulltext.pdf. - Soavtorji: Gregor Serša,<br />
Vid Mlakar, Damjan Glavač, Maja Čemažar. - Izvleček v angl. in slov. - Bibliografija str. 44-45.<br />
V: Radiology and oncology. - ISSN 1318-2099.. - Vol. 46, no. 1 (2012), str. 32-45.<br />
. - doi: 10.2478/v10019-012-0010-6 COBISS.SI-ID 3203441, JCR, WoS, št. citatov do 11. 4. 2012: 0,<br />
brez avtocitatov: 0, normirano št. citatov: 0<br />
2.MICRORNAS, innate immunity and ventricular rupture in human myocardial infarction / Nina<br />
Zidar ... [et al.]. - Soavtorji: Emanuela Boštjančič, Damjan Glavač, Dušan Štajer. - Abstract. -<br />
Bibliografija na koncu prispevka. V: Disease markers. - ISSN 0278-0240.. - Vol. 31, issue 5 (2011),<br />
str. 259-265 . - doi: 10.3233/DMA-2011-0827 COBISS.SI-ID 29193689, JCR, WoS, št. citatov do 11.<br />
4. 2012: 0, brez avtocitatov: 0, normirano št. citatov: 0<br />
DOWN-regulation of microRNAs of the miR-200 family and miR-205, and an altered expression of<br />
classic and desmosomal cadherins in spindle cell carcinoma of the head and neck-hallmark of<br />
epithelial-mesenchymal transition / Nina Zidar ... [et al.]. - Ilustr. - Soavtorji: Emanuela Boštjančič,
Nina Gale, Nika Kojc, Mario Poljak, Damjan Glavač, Antonio Cardesa. - Summary. - Bibliografija na<br />
koncu prispevka. V: Human pathology. - ISSN 0046-8177.. - Vol. 42, issue 4 (2011), str. 482-488.<br />
. - doi: 10.1016/j.humpath.2010.07.020 COBISS.SI-ID 28112089, JCR, WoS, št. citatov do 6. 2.<br />
2012: 1, brez avtocitatov: 1, normirano št. citatov: 0
COURSE SYLLABUS<br />
Course title: Mathematical modeling and simulations in health science<br />
Study <strong>programme</strong> and level Study field<br />
Academic<br />
year<br />
Semester<br />
Bioinformatics <strong>2nd</strong> <strong>degree</strong><br />
Bologna Study <strong>programme</strong><br />
Bioinformatics 2 3<br />
Course type Optional subject<br />
University course code:<br />
Lectures Seminar Tutorial<br />
Laboratory<br />
work<br />
Field work<br />
Individ.<br />
work<br />
ECTS<br />
15 30 105 6<br />
Lecturer: Aleš Fajmut, PhD, Assistant professor<br />
Languages: Lectures: Slovenian<br />
Tutorial: Slovenian<br />
Prerequisits:<br />
Formal or informal knowledge of subjects Introduction to Biophysics and Molecular Biophysics is<br />
required.<br />
Content (Syllabus outline):<br />
Lectures outline:<br />
The subject introduces selected examples of mathematical modeling biological processes from<br />
the health care point of view with emphasis on:<br />
- blood circulation<br />
- mechanics of breathing<br />
- gas exchange in lungs and blood<br />
- control of cell volume<br />
- muscle mechanics<br />
- intracellular and intercellular signaling<br />
- biological rhythms<br />
- biomechanics<br />
- population dynamics<br />
Laboratory work outline:
- mathematical modeling and computer simulation of selected processes<br />
- computer simulation and visualization of results with computer tools<br />
Readings:<br />
Hoppensteadt F. C., Peskin C. S. Modeling and Simulation in Medicine and the Life Sciences,<br />
Springer-Verlag, New York 2004.<br />
Keener J., Sneyd J. Mathematical Physiology, Springer-Verlag, New York 1998<br />
Goldbeter A. Biochemical Oscillations and Cellular Rhythms, Cambridge University Press,<br />
Cambridge 1996<br />
Hobbie R. K. Intermediate Physics for Medicine and Biology, John Wiley & Sons, New York 1988<br />
Objectives and competences:<br />
The subject is focused on the biological processes on the level of human organism as well as on<br />
the level of population from the point of view of modeling and simulation. The major aim is to<br />
<strong>study</strong> selected processes and its application in health science with methods of mathematical<br />
modeling and computer simulations.<br />
Intended learning outcomes:<br />
Knowledge and Understanding:<br />
Student gets:<br />
- knowledge and understanding of selected physiological processes on the level of<br />
mathematical model;<br />
- knowledge of the selected processes studied in details. This enables her/him further<br />
research in this field.<br />
Learning and teaching methods:<br />
Lectures<br />
Laboratory work<br />
Assessment:<br />
Type (examination, oral, coursework,<br />
project):<br />
• Oral<br />
• Practical work in laboratory<br />
and Homework<br />
Weight (in %)<br />
50<br />
50<br />
Lecturer's references:<br />
FAJMUT, Aleš<br />
MLC-kinase/phosphatase control of Ca[sup]2+ signal transduction in airway smooth muscles /<br />
Aleš Fajmut, Milan Brumen. - . - Dostopno tudi na: http://dx.doi.org/10.1016/j.jtbi.2007.10.005. -<br />
Available online Oct. 11 2007. - Bibliografija: str. 481. V: Journal of theoretical biology. - ISSN<br />
0022-5193.. - Vol. 252, no. 3 (2008), str. 474-481.<br />
. - doi: 10.1016/j.jtbi.2007.10.005 COBISS.SI-ID 15856392, JCR, WoS, št. citatov do 6. 5. 2011: 5,<br />
brez avtocitatov: 4, normirano št. citatov: 2<br />
CONTRIBUTION of Rho kinase to the early phase of the calcium-contraction coupling in airway
smooth muscle / Prisca Mbikou ... [et al.]. - Ilustr. - Nasl. z nasl. zaslona. - Opis vira z dne 7. 12.<br />
2010. - Soavtorji: Ales Fajmut, Milan Brumen, Etienne Roux. - Bibliografija: str. 257-258. - Abstract.<br />
V: Experimental physiology. - ISSN 0958-0670.. - Vol. 96, issue 2 (2011), str. 240-258.<br />
. - doi: 10.1113/expphysiol.2010.054635 COBISS.SI-ID 18009864, JCR, WoS, št. citatov do 10. 4.<br />
2012: 2, brez avtocitatov: 2, normirano št. citatov: 1<br />
DOBOVIŠEK, Andrej<br />
Role of expression of prostaglandin synthases 1 and 2 and leukotriene C [sub] 4 synthase in<br />
aspirin-intolerant asthma: a theoretical <strong>study</strong> / A. Dobovišek, A. Fajmut, M. Brumen. -<br />
Bibliografija: str. 277-278. - Abstract.V: Journal of pharmacokinetics and pharmacodynamics. -<br />
ISSN 1567-567X.. - Vol. 38, no. 2 (2011), str. 261-278. . - doi: 10.1007/s10928-011-9192-6<br />
COBISS.SI-ID 18203144, JCR, WoS, št. citatov do 6. 4. 2012: 1, brez avtocitatov: 0, normirano št.<br />
citatov: 0
COURSE SYLLABUS<br />
Course title: Advanced research methodology in <strong>bioinformatics</strong><br />
Study <strong>programme</strong> and level Study field<br />
Bioinformatics 2 nd <strong>degree</strong><br />
Bologna Study <strong>programme</strong><br />
Academic<br />
year<br />
Semester<br />
Bioinformatics 2 4<br />
Course type Obligatory subject<br />
University course code:<br />
Lectures Seminar Tutorial<br />
Laboratory<br />
work<br />
Field work<br />
Individ.<br />
work<br />
ECTS<br />
15 30 105 6<br />
Lecturer: Peter Kokol, PhD, Full professor<br />
Languages: Lectures: slovene<br />
Tutorial: slovene<br />
Prerequisits:<br />
None.<br />
Content (Syllabus outline):<br />
The student gets familiar with methodological issues and process of scientific research expecially<br />
qualitative and quantitative research.<br />
This subject aims to prepare students for the practice of undertaking high quality research<br />
methodology, quantitative and qualitative research in <strong>bioinformatics</strong>.<br />
They will upgrade their knowledge about principles of research ethics and became aware of<br />
specific research questions which appears on the field of <strong>bioinformatics</strong>.<br />
Readings:<br />
1. Trends in Bioinformatics Research. Peter V. Yan. Nova publishers. 2005.<br />
2. Bioinformatics: New Research. Peter V. Yan. Nova publishers. 2005.<br />
3. Researching health care consumers : critical approaches / edited by Jennifer Burr and<br />
Paula Nicolson. - Basingstoke ; New York, N.Y. : Palgrave Macmillan, 2005.<br />
4. Nursing research : a qualitative perspective / [edited by] Patricia L. Munhall. - 3rd ed. -<br />
Sudbury, Mass. : Jones and Bartlett Publishers, cop. 2001.
5. The student's guide to research ethics / Paul Oliver. - Maidenhead ;Philadelphia : Open<br />
University Press, 2003.<br />
Objectives and competences:<br />
Student:<br />
- Is acquainted with research paradigms and research approaches which form<br />
<strong>bioinformatics</strong>;<br />
- and recognizes significance and characteristics of research in <strong>bioinformatics</strong>;<br />
On successful completion of this subject students should be able to:<br />
Develop an expertise in qualitative and quantitative advanced research design, with particular<br />
reference to issues of sampling, access, ethics and rigour.<br />
Become skilled in the use of a range of techniques for the collection and analysis of qualitative<br />
and quantitative data.<br />
Develop the knowledge and skills essential for the effective dissemination and evaluation of<br />
qualitative and quantitative research.<br />
Intended learning outcomes:<br />
Knowledge and understanding:<br />
Knowledge of advanced research methodology and different research approaches;<br />
Qualified for independent quantitative and qualitative research;<br />
Student will be able to independently form and report their observations and results and actively<br />
comprehend in publishing of research contributions on the field of <strong>bioinformatics</strong>.<br />
Learning and teaching methods:<br />
Lectures, seminars.<br />
Assessment:<br />
Weight (in %)<br />
Type (examination, oral, coursework,<br />
project):<br />
Written exam,<br />
70<br />
seminary work.<br />
30<br />
Lecturer's references:<br />
EVOLUTIONARY design of decision trees for medical application [Elektronski vir] / Peter Kokol ...<br />
[et al.]. - Soavtorji: Sandi Pohorec, Gregor Štiglic, Vili Podgorelec. - Bibliografija: str. 252-254.<br />
V: Wiley interdisciplinary reviews. Data mining and knowledge discovery [Elektronski vir]. - ISSN<br />
1942-4795. - Vol. 2, iss. 3 (May 2012), str. 237-254. . - doi: 10.1002/widm.1056 COBISS.SI-ID<br />
15997462<br />
KOKOL, Peter, 1957-<br />
Intelligent system supported evidence based management [Elektronski vir] / Peter Kokol, Gregor<br />
Štiglic. - ilustr. - Bibliografija: str. 198. - Abstract. V: CAINE-2011 [Elektronski vir] / 24th<br />
International Conference on Computers and Their Applications in Industry and Engineering<br />
November 16-18, 2011, Honolulu, HI USA. - Cary, NC : ISCA, 2011. - ISBN 978-1-880843-83-3. - Str.<br />
195-198.COBISS.SI-ID 1764516
COMPUTATIONAL complexity : theory, techniques, and applications / editor-in-chief, Robert A.<br />
Meyers. - New York : Springer, cop. 2012. - 6 zv. (XLIV, 3492 str.) ISBN 1-4614-1799-6 (hbk)<br />
ISBN 978-1-4614-1799-6 (hbk.) COBISS.SI-ID 1780644
COURSE SYLLABUS<br />
Course title: Basics of molecular and population genetics<br />
Study <strong>programme</strong> and level Study field<br />
Bioinformatics 2 nd <strong>degree</strong><br />
Bologna Study <strong>programme</strong><br />
Academic<br />
year<br />
Semester<br />
Bioinformatics 2 3<br />
Course type Optional subject<br />
University course code:<br />
Lectures Seminar Tutorial<br />
Laboratory<br />
work<br />
Field work<br />
Individ.<br />
work<br />
ECTS<br />
15 30 90 6<br />
Lecturer: Uroš Potočnik, PhD, Associate professor<br />
Languages: Lectures: slovene<br />
Tutorial: slovene<br />
Prerequisits:<br />
Understanding basics of molecular biology<br />
Content (Syllabus outline):<br />
Basic molecular genetics: DNA structure and characteristics, replication (prokaryotes,<br />
eukaryotes), recombination, repair and mutations, organization, structure and function of<br />
genes and chromosomes, genome structure (plant, animal, human) transcription<br />
(prokaryotes, eukaryotes), translation, regulation of gene expression<br />
Chromosomal basis of heredity, Mendelian inheritance, polygenic inheritance<br />
Gene mapping, mitochondrial genome<br />
Mutations, polymorphisms, phenotype, genotype, allele frequency, haplotypes, haplotype<br />
blocks (HapMap project), the Hardy-Weinberg law, linkage analysis, linkage disequilibrium.<br />
Size and structure of population<br />
Natural selection, mutations, genetic drift, gene flow, inbreeding<br />
Molecular evolution, molecular clocks, how genomes evolve, conservation genetics<br />
Quantitative traits<br />
Gene testing in individuals and populations: mutation detection and genotyping methods,<br />
genetic testing in medicine (genetic diseases with classical Mendelian and complex<br />
inheritance), DNA analysis in forensics and bone marrow transplantation typing<br />
Molecular and population genetic and society: ethical, social and economical issues
Readings:<br />
HEDRICK PW: Genetics of Populations, Jones & Bartlett Publishers, Sudbury, Inc., 3rd ed,<br />
2004<br />
STRACHAN T and READ AP: Human Molecular genetics, Gerland Publish, Inc., New York, 3rd<br />
ed., 2004<br />
KLUG M and CUMMINGS MR.: Genetics: A Molecular Perspective. Pearson Education, Inc.<br />
New Jersey, 2003<br />
Objectives and competences:<br />
Students will be provided with basic population genetics principles. The focus will be on new<br />
molecular data including genome projects that compare population samples to identify patterns<br />
of genetic diversity and genes that have been under selection which helps to understand<br />
molecular evolution.<br />
Intended learning outcomes:<br />
Knowledge and understanding:<br />
principals of heredity and transfer of genetic information between generations<br />
correlations genotype-phenotype<br />
factors that influence frequency of DNA polymorphisms and genetic diversity in different<br />
populations<br />
the role of mutations and genetic diversity in evolution<br />
Learning and teaching methods:<br />
Lectures<br />
Tutorial<br />
Assessment:<br />
Type (examination, oral, coursework,<br />
project):<br />
Weight (in %)<br />
writen and<br />
60<br />
oral exemination<br />
40<br />
Lecturer's references:<br />
POTOČNIK, Uroš, 1969-<br />
Trenutna komercializacija osebne genetske analize-zanesljiva napoved tveganja za pogoste<br />
kompleksne bolezni ali zavajanje potrošnikov? [Elektronski vir] = Current commercialization of<br />
personal genetic analysis-reliable prediction of susceptibility to common complex diseases or<br />
misleading of the consumers? / Uroš Potočnik. - Povzetek ; Abstract. - Bibliografija: str. 4-5.<br />
V: Slovenski kemijski dnevi 2011, Portorož, 14-16 september 2011 [Elektronski vir] / [organizirala]<br />
Fakulteta za kemijo in kemijsko tehnologijo, <strong>Univerza</strong> v Mariboru [v sodelovanju s Slovenskim<br />
kemijskim društvom ... et al.]. - Maribor : FKKT, 2011. - ISBN 978-961-248-289-3. - 5 str.<br />
COBISS.SI-ID 15319318<br />
ŠIMENC, Janez, 1973-<br />
Rapid differentiation of bacterial species by high resolution melting curve analysis / J. Šimenc and
U. Potočnik. - Abstract. - Bibliografija: str. 262-263.V: Applied biochemistry and microbiology. -<br />
ISSN 0003-6838.. - Vol. 47, no. 3 (2011), str. 256-263. . - doi: 10.1134/S0003683811030136<br />
COBISS.SI-ID 14937622, JCR, WoS, št. citatov do 11. 4. 2012: 1, brez avtocitatov: 1, normirano št.<br />
citatov: 0<br />
A CYP17A1 gene polymorphism in association with multiple uterine leimyomas; a meta-analysis /<br />
Maja Pakiz ... [et al.]. - Soavtorji: Uros Potocnik, Igor But, Faris Mujezinovic. - Bibliografija: str. 33-<br />
34. – Abstract V: Disease markers. Section A, Cancer biomarkers. - ISSN 1574-0153.. - Vol. 8, no. 1<br />
(2010/2011), str. 29-34. . - doi: 10.3233/DMA-2011-0817 COBISS.SI-ID 4033599, JCR, WoS, št.<br />
citatov do 6. 10. 2011: 0, brez avtocitatov: 0, normirano št. citatov: 0
COURSE SYLLABUS<br />
Course title: Proteine structures and proteomics<br />
Study <strong>programme</strong> and level Study field<br />
Bioinformatics 2 nd <strong>degree</strong><br />
Bologna Study <strong>programme</strong><br />
Academic<br />
year<br />
Semester<br />
Bioinformatics 2 3<br />
Course type Optional subject<br />
University course code:<br />
Lectures Seminar Tutorial Laboratory<br />
work<br />
Field work<br />
Individ.<br />
work<br />
ECTS<br />
15 30 30 6<br />
Lecturer: Damjan Glavač, PhD, Full professor<br />
Languages: Lectures: slovene<br />
Tutorial: slovene<br />
Prerequisits:<br />
Understanding basics of molecular biology, biochemistry, molecular genetics and <strong>bioinformatics</strong><br />
Content (Syllabus outline):<br />
Proteomics basics: definitions, separation of proteins, chromatographic methods, protein<br />
identification and characterization, elecrophoresis, image analysis, mass spectrometry,<br />
protein sequence analysis, proteomics databases<br />
Basics of protein structure: properties of, amino acids, peptide bond, building blocks of<br />
protein structures, overview of molecular forces, protein geometry<br />
Secondary structures, motifs of protein structure, alpha, beta and alpha-beta motifs in<br />
protein structures<br />
Basics of protein folding<br />
Structure- function relationship: DNA binding proteins, examples of enzyme catalysis,<br />
membrane proteins, signal transduction, fibrous proteins, structures of the immune<br />
response molecules, virus structures<br />
Interaction proteomics, protein complexes<br />
Protein structure determination: X-ray crystallography, protein crystallization, NMR,<br />
electron microscopy<br />
Structural genomics: basic principles and methods
Structural based drug design, in silico screening, protein modelling<br />
Protein data bank (PDB) and its use<br />
Readings:<br />
1. Carl-Ivar Branden and John Tooze. Introduction to Protein Structure, <strong>2nd</strong> edition, 1999,<br />
Garland Publishing<br />
2. Donald Voet & Judith Voet, Biochemistry, J.Wiley&Sons, 2004, 3rd ed.<br />
3. Gale Rhodes, Crystallography Made Crystal Clear- A Guide for Users of Macromolecular<br />
Models, Third Edition, February 2006, Elsevier/Academic Press<br />
4. Twyman, R. M. 2004. Principles of proteomics. BIOS Scientific Publishers, New York.<br />
5. Liebler, D. C. 2002. Introduction to proteomics: tools for the new biology. Humana Press,<br />
Totowa, NJ.<br />
6. Mechanisms of Protein Folding, <strong>2nd</strong> edn., (2000) R.H. Pain (ed.), Oxford University Press<br />
7. A. Skoog, F. J. Holler and T. A. Nieman, Principles of Instrumental Analysis, 5th Edition,<br />
Saunders College Publishing, Philadelphia, 1998.<br />
Objectives and competences:<br />
The overall course objective is to provide the student with a broad understanding of the main<br />
fundamentals of the protein structure, proteomics and methods that are used in that field.<br />
Intended learning outcomes:<br />
Knowledge and understanding:<br />
On successful completion of this course, student should be able to:<br />
Describe basic principles of protein structure, protein structure motifs, secondary<br />
structure properties and protein folding.<br />
Explain structure function relationship.<br />
Describe methodologies used for protein characterization and structure determination<br />
and how these techniques can be applied to industry objectives and outcomes<br />
Use computer sotware to visualise, compare, analyse and interpret protein structures<br />
Learning and teaching methods:<br />
Lectures<br />
Tutorials<br />
Seminar<br />
Assessment:<br />
Type (examination, oral, coursework,<br />
project):<br />
Weight (in %)<br />
writen and oral exemination 70<br />
seminar<br />
30<br />
Lecturer's references:<br />
ASSESSMENT of the tumourigenic and metastatic properties of SK-MEL28 melanoma cells<br />
surviving electrochemotherapy with bleomycin = Določitev tumorigenih in metastatskih lastnosti<br />
melanomskih celic SK-MEL28 po preživetju elektrokemoterapije z bleomicinom / Vesna Todorović<br />
... [et al.]. - . - Dostopno tudi na:<br />
http://versita.metapress.com/content/24337t420311w012/fulltext.pdf. - Soavtorji: Gregor Serša,
Vid Mlakar, Damjan Glavač, Maja Čemažar. - Izvleček v angl. in slov. - Bibliografija str. 44-45.<br />
V: Radiology and oncology. - ISSN 1318-2099.. - Vol. 46, no. 1 (2012), str. 32-45.<br />
. - doi: 10.2478/v10019-012-0010-6 COBISS.SI-ID 3203441, JCR, WoS, št. citatov do 11. 4. 2012: 0,<br />
brez avtocitatov: 0, normirano št. citatov: 0<br />
2.MICRORNAS, innate immunity and ventricular rupture in human myocardial infarction / Nina<br />
Zidar ... [et al.]. - Soavtorji: Emanuela Boštjančič, Damjan Glavač, Dušan Štajer. - Abstract. -<br />
Bibliografija na koncu prispevka. V: Disease markers. - ISSN 0278-0240.. - Vol. 31, issue 5 (2011),<br />
str. 259-265 . - doi: 10.3233/DMA-2011-0827 COBISS.SI-ID 29193689, JCR, WoS, št. citatov do 11.<br />
4. 2012: 0, brez avtocitatov: 0, normirano št. citatov: 0<br />
DOWN-regulation of microRNAs of the miR-200 family and miR-205, and an altered expression of<br />
classic and desmosomal cadherins in spindle cell carcinoma of the head and neck-hallmark of<br />
epithelial-mesenchymal transition / Nina Zidar ... [et al.]. - Ilustr. - Soavtorji: Emanuela Boštjančič,<br />
Nina Gale, Nika Kojc, Mario Poljak, Damjan Glavač, Antonio Cardesa. - Summary. - Bibliografija na<br />
koncu prispevka. V: Human pathology. - ISSN 0046-8177.. - Vol. 42, issue 4 (2011), str. 482-488.<br />
. - doi: 10.1016/j.humpath.2010.07.020 COBISS.SI-ID 28112089, JCR, WoS, št. citatov do 6. 2.<br />
2012: 1, brez avtocitatov: 1, normirano št. citatov: 0
COURSE SYLLABUS<br />
Course title: Recombinant DNA technology<br />
Study <strong>programme</strong> and level Study field<br />
Bioinformatics 2 nd <strong>degree</strong><br />
Bologna Study <strong>programme</strong><br />
Academic<br />
year<br />
Semester<br />
Bioinformatics 2 3<br />
Course type Optional subject<br />
University course code:<br />
Lectures Seminar Tutorial<br />
Laboratory<br />
work<br />
Field work<br />
Individ.<br />
work<br />
ECTS<br />
15 30 105 6<br />
Lecturer: Uroš Potočnik, PhD, Associate professor<br />
Languages: Lectures: slovene<br />
Tutorial: slovene<br />
Prerequisits:<br />
Understanding basics of molecular biology and molecular genetics<br />
Content (Syllabus outline):<br />
Cloning: Host organisms, DNA cloning vectors, cloning strategy in eukaryotes and<br />
prokaryotes, transformation and transfect ion, expression of recombinant proteins<br />
preparation of genomic and cDNA libraries<br />
Hybridization of nucleic acids, DNA micro arrays<br />
Polymerase DNA reaction (PCR), DNA sequencing<br />
Yeast two-hybrid system for identification of protein-protein interaction<br />
Site directed mutagenesis, knock-out technology and animal models-the role in functional<br />
genomics and animal disease models<br />
Silencing gene expression: RNAi, antisense RNA technology<br />
Cloning human genes, reproductive cloning of mammalians, therapeutic cloning<br />
Transgenic plants and animals<br />
DNA fingerprinting in forensics<br />
Gene technology in drug production and diagnostics<br />
Low regulations and safety precautions for research and applications of genetic modified<br />
organisms<br />
Recombinant DNA technology and society: ethic and social economic issues
Readings:<br />
1. Bernard R. Glick, Jack J. Pasternak: Principles and applications of recombinant DNA, 3rd<br />
edition, ASM Press, Washington, 2003<br />
2. Sandy Primrose, Richard Twyman, Bob Old: Principles of Gene Manipulation, 6th edition,<br />
Blackwell Science, Oxford, 2001<br />
Objectives and competences:<br />
Students will be provided with basic techniques and applications of recombinant DNA technology<br />
in research and industry.<br />
Intended learning outcomes:<br />
Knowledge and understanding:<br />
techiques and principals of DNA cloning and other recombinant DNA technology<br />
applications of recombinant DNA technology in research and industry<br />
Learning and teaching methods:<br />
Lectures<br />
Tutorial<br />
Assessment:<br />
Type (examination, oral, coursework,<br />
project):<br />
Weight (in %)<br />
writen and<br />
60<br />
oral exemination<br />
40<br />
Lecturer's references:<br />
POTOČNIK, Uroš, 1969-<br />
Trenutna komercializacija osebne genetske analize-zanesljiva napoved tveganja za pogoste<br />
kompleksne bolezni ali zavajanje potrošnikov? [Elektronski vir] = Current commercialization of<br />
personal genetic analysis-reliable prediction of susceptibility to common complex diseases or<br />
misleading of the consumers? / Uroš Potočnik. - Povzetek ; Abstract. - Bibliografija: str. 4-5.<br />
V: Slovenski kemijski dnevi 2011, Portorož, 14-16 september 2011 [Elektronski vir] / [organizirala]<br />
Fakulteta za kemijo in kemijsko tehnologijo, <strong>Univerza</strong> v Mariboru [v sodelovanju s Slovenskim<br />
kemijskim društvom ... et al.]. - Maribor : FKKT, 2011. - ISBN 978-961-248-289-3. - 5 str.<br />
COBISS.SI-ID 15319318<br />
ŠIMENC, Janez, 1973-<br />
Rapid differentiation of bacterial species by high resolution melting curve analysis / J. Šimenc and<br />
U. Potočnik. - Abstract. - Bibliografija: str. 262-263.V: Applied biochemistry and microbiology. -<br />
ISSN 0003-6838.. - Vol. 47, no. 3 (2011), str. 256-263. . - doi: 10.1134/S0003683811030136<br />
COBISS.SI-ID 14937622, JCR, WoS, št. citatov do 11. 4. 2012: 1, brez avtocitatov: 1, normirano št.<br />
citatov: 0<br />
A CYP17A1 gene polymorphism in association with multiple uterine leimyomas; a meta-analysis /<br />
Maja Pakiz ... [et al.]. - Soavtorji: Uros Potocnik, Igor But, Faris Mujezinovic. - Bibliografija: str. 33-<br />
34. – Abstract V: Disease markers. Section A, Cancer biomarkers. - ISSN 1574-0153.. - Vol. 8, no. 1
(2010/2011), str. 29-34. . - doi: 10.3233/DMA-2011-0817 COBISS.SI-ID 4033599, JCR, WoS, št.<br />
citatov do 6. 10. 2011: 0, brez avtocitatov: 0, normirano št. citatov: 0
COURSE SYLLABUS<br />
Course title: Theoretical Biophysics<br />
Study <strong>programme</strong> and level Study field<br />
Bioinformatics 2 nd <strong>degree</strong><br />
Bologna Study <strong>programme</strong><br />
Academic<br />
year<br />
Semester<br />
Bioinformatics 2 3<br />
Course type Obligatory subject<br />
University course code:<br />
Lectures Seminar Tutorial<br />
Laboratory<br />
work<br />
Field work<br />
Individ.<br />
work<br />
ECTS<br />
30 15 15 90 6<br />
Lecturer: Aleš Fajmut, PhD, Assistant professor<br />
Languages: Lectures: slovene<br />
Tutorial: slovene<br />
Prerequisits:<br />
Formal or informal knowledge of subjects Introduction to Biophysics and Molecular Biophysics is<br />
required.<br />
Content (Syllabus outline):<br />
General description of the subject:<br />
The subject introduces theoretical and computational tools and cutting edge research approaches<br />
from physics, chemistry, mathematics and computer science in the context of biological problems<br />
and situations. Functioning of different complex biological systems such as metabolic system,<br />
signaling networks, organelles, cells, organs, organisms and populations will be discussed from<br />
the point of view of <strong>study</strong>ing their integral parts. On the basis of understanding the interactions<br />
and relationships between the systems subunits it will be possible to deduce to the functioning of<br />
the system as integrity.<br />
Lectures outline:<br />
- INTRODUCTION: (principles from physics and mathematics in systems biology, principles of<br />
working with computer tools for mathematical modeling and working with databases)<br />
- STANDARD APPROACHES IN MODELING BIOLOGICAL SYSTEMS: (biochemical and enzyme<br />
kinetics, metabolic networks, control analysis, signal transduction pathways)<br />
- SELECTED EXAMPLES OF MODELING BIOLOGICAL SYSTEMS: (oscillations in biological
systems, signal transduction, muscle contraction, whole cell modeling, cell cycle, aging,<br />
gene expression, evolution and self-organization)<br />
Seminar outline:<br />
Student chooses one of the themes offered by the lecturer. Project has a form of short scientific<br />
contribution. After the review of the final version student presents his project for the colleagues.<br />
Laboratory work outline:<br />
- work with computer tools like Mathematica, MatLab, Madonna, Gepasi, PLAS, Model<br />
Maker, Virtual Cell…<br />
- work with computer databases from the internet like BRENDA, Swiss-Prot, TrEMBL,<br />
UniProt…<br />
- modeling of selected problems from systems biology<br />
- solving of mathematical models and visualization of the results with help of computer<br />
tools<br />
Readings:<br />
1. Klipp E., Herwig R., Kowald A., Wierling C., Lehrach H. Systems Biology in Practice, Wiley-<br />
VCH, Weinheim 2005<br />
2. Kitano H. Foundations of Systems Biology, MIT Press, Cambridge 2001<br />
3. Voit E.O. Computational Analysis of Biochemical Systems: A Practical Guide for<br />
Biochemists<br />
and Molecular Biologists, Cambridge University Press, New York 2000<br />
4. Vodovnik L., Miklavčič D., Kotnik T. Biološki sistemi, <strong>Univerza</strong> v Ljubljani, Fakulteta za<br />
elektrotehniko, Ljubljana 1998<br />
Objectives and competences:<br />
- To develop an understanding of how and why theoretical approaches can drive new<br />
experiments.<br />
- To show students how theoretical results can deliver novel insight into the functioning of<br />
biosystems.<br />
- To get an insight into the current theoretical research approaches in bio-sciences.<br />
To get an insight how to test the hypotheses resulting from molecular biology, physiology or<br />
biochemistry with mathematical modeling.<br />
Students should leave the subject better able to identify important unsolved problems in biology<br />
and with an appreciation of how to select and solve problems for which quantitative and<br />
theoretical approaches will be productive.<br />
Intended learning outcomes:<br />
Knowledge and understanding:<br />
Student gets:<br />
- knowledge and understanding of physical, chemical, mathematical and computational<br />
methods in theoretical approach to <strong>study</strong> biological systems;<br />
- ability of working with presented computational tools and having acquaintance with<br />
others;<br />
- understanding of presented theoretical examples, knowledge of their advantages and<br />
disadvantages, as well as having acquaintance with other similar examples.
Learning and teaching methods:<br />
Lectures<br />
Seminar<br />
Laboratory work<br />
Assessment:<br />
Type (examination, oral, coursework,<br />
project):<br />
Oral<br />
Written<br />
Project<br />
Weight (in %)<br />
40<br />
30<br />
30<br />
Lecturer's references:<br />
FAJMUT, Aleš<br />
MLC-kinase/phosphatase control of Ca[sup]2+ signal transduction in airway smooth muscles /<br />
Aleš Fajmut, Milan Brumen. - . - Dostopno tudi na: http://dx.doi.org/10.1016/j.jtbi.2007.10.005. -<br />
Available online Oct. 11 2007. - Bibliografija: str. 481. V: Journal of theoretical biology. - ISSN<br />
0022-5193.. - Vol. 252, no. 3 (2008), str. 474-481.<br />
. - doi: 10.1016/j.jtbi.2007.10.005 COBISS.SI-ID 15856392, JCR, WoS, št. citatov do 6. 5. 2011: 5,<br />
brez avtocitatov: 4, normirano št. citatov: 2<br />
CONTRIBUTION of Rho kinase to the early phase of the calcium-contraction coupling in airway<br />
smooth muscle / Prisca Mbikou ... [et al.]. - Ilustr. - Nasl. z nasl. zaslona. - Opis vira z dne 7. 12.<br />
2010. - Soavtorji: Ales Fajmut, Milan Brumen, Etienne Roux. - Bibliografija: str. 257-258. - Abstract.<br />
V: Experimental physiology. - ISSN 0958-0670.. - Vol. 96, issue 2 (2011), str. 240-258.<br />
. - doi: 10.1113/expphysiol.2010.054635 COBISS.SI-ID 18009864, JCR, WoS, št. citatov do 10. 4.<br />
2012: 2, brez avtocitatov: 2, normirano št. citatov: 1<br />
DOBOVIŠEK, Andrej<br />
Role of expression of prostaglandin synthases 1 and 2 and leukotriene C [sub] 4 synthase in<br />
aspirin-intolerant asthma: a theoretical <strong>study</strong> / A. Dobovišek, A. Fajmut, M. Brumen. -<br />
Bibliografija: str. 277-278. - Abstract.V: Journal of pharmacokinetics and pharmacodynamics. -<br />
ISSN 1567-567X.. - Vol. 38, no. 2 (2011), str. 261-278. . - doi: 10.1007/s10928-011-9192-6<br />
COBISS.SI-ID 18203144, JCR, WoS, št. citatov do 6. 4. 2012: 1, brez avtocitatov: 0, normirano št.<br />
citatov:
COURSE SYLLABUS<br />
Course title: Complexity theory and chaos<br />
Study <strong>programme</strong> and level Study field<br />
Bioinformatics 2 nd <strong>degree</strong><br />
Bologna Study <strong>programme</strong><br />
Academic<br />
year<br />
Semester<br />
Bioinformatics 2 3<br />
Course type Optional subject<br />
University course code:<br />
Lectures Seminar Tutorial<br />
Laboratory<br />
work<br />
Field work<br />
Individ.<br />
work<br />
ECTS<br />
15 30 105 6<br />
Lecturer: Peter Kokol, PhD, Full professor<br />
Languages: Lectures: slovene<br />
Tutorial: slovene<br />
Prerequisits:<br />
None.<br />
Content (Syllabus outline):<br />
History<br />
The concepts of system theory<br />
Definition of complexity<br />
Theory of complexity<br />
Theory of chaos<br />
Complex systems and chaos theory in computer science<br />
Complex systems and chaos theory in biology<br />
Complex systems and chaos theory in economy<br />
Application of complex systems and chaos theory in bionformatics<br />
Soft system theory<br />
Soft system theory and decision making, problem solving in conflicts situations and<br />
planning
Readings:<br />
1. P. Checkland: Systems Thinking Practice, John Wiley & Sons, Chichester, 1981.<br />
2. P. Checkland, J. Scholes: Soft Systems Methodology in Action, John Wiley & Sons,<br />
Chichester, 1990.<br />
3. R. L. Flood, M. C. Jackson: Creative problem Solving: Total System Intervention, John Wiley<br />
& Sons, 1991.<br />
4. R. Peitgen: Chaos and Fractals – New Frontiers of Science, Springer Verlag, 1993<br />
5. K. Frenken: Innovation, Evolution and Complexity Theory, EE Press, 2006)<br />
Objectives and competences:<br />
The first goal is to teach students to understand the differences between scientific approach and<br />
system theory and the concepts of system theory, complexity theory and the chaos theory.<br />
The other more pragmatic goal is to teach the students how to use the above theories in<br />
<strong>bioinformatics</strong>. The students should be able to understand the Aristotle’s rule that the whole is<br />
more then the sum of its parts.<br />
Intended learning outcomes:<br />
Knowledge and understanding:<br />
Student:<br />
Understands the difference between scientific and system approach<br />
The student understands the Aristotels rule<br />
The student has the competencies in system theory, soft system theory, theory of<br />
complexity and chaos theory<br />
Students is able to use the above theories in practical applications in <strong>bioinformatics</strong><br />
Learning and teaching methods:<br />
Lectures, seminar work, workshops.<br />
Assessment:<br />
Type (examination, oral, coursework,<br />
project):<br />
Weight (in %)<br />
Kolokviji<br />
30<br />
Pisni izpit<br />
20<br />
Projekt.<br />
50<br />
Lecturer's references:<br />
EVOLUTIONARY design of decision trees for medical application [Elektronski vir] / Peter Kokol ...<br />
[et al.]. - Soavtorji: Sandi Pohorec, Gregor Štiglic, Vili Podgorelec. - Bibliografija: str. 252-254.<br />
V: Wiley interdisciplinary reviews. Data mining and knowledge discovery [Elektronski vir]. - ISSN<br />
1942-4795. - Vol. 2, iss. 3 (May 2012), str. 237-254. . - doi: 10.1002/widm.1056 COBISS.SI-ID<br />
15997462<br />
KOKOL, Peter, 1957-<br />
Intelligent system supported evidence based management [Elektronski vir] / Peter Kokol, Gregor<br />
Štiglic. - ilustr. - Bibliografija: str. 198. - Abstract. V: CAINE-2011 [Elektronski vir] / 24th
International Conference on Computers and Their Applications in Industry and Engineering<br />
November 16-18, 2011, Honolulu, HI USA. - Cary, NC : ISCA, 2011. - ISBN 978-1-880843-83-3. - Str.<br />
195-198.COBISS.SI-ID 1764516<br />
COMPUTATIONAL complexity : theory, techniques, and applications / editor-in-chief, Robert A.<br />
Meyers. - New York : Springer, cop. 2012. - 6 zv. (XLIV, 3492 str.) ISBN 1-4614-1799-6 (hbk)<br />
ISBN 978-1-4614-1799-6 (hbk.) COBISS.SI-ID 1780644
COURSE SYLLABUS<br />
Course title: Scientific Visualisation<br />
Study <strong>programme</strong> and level Study field<br />
Bioinformatics 2 nd <strong>degree</strong><br />
Bologna Study <strong>programme</strong><br />
Academic<br />
year<br />
Semester<br />
Bioinformatics 2 3<br />
Course type Optional subject<br />
University course code:<br />
Lectures Seminar Tutorial<br />
Laboratory<br />
work<br />
Field work<br />
Individ.<br />
work<br />
ECTS<br />
15 30 105 6<br />
Lecturer: Sebastian Krivograd, PhD, Assistant professor<br />
Languages: Lectures: slovene<br />
Tutorial: slovene<br />
Prerequisits:<br />
Basic programming skills and basic knowledge of algorithms and data structures.<br />
Content (Syllabus outline):<br />
Introduction: why scientific visualisation, historical overview, models for scientific<br />
visualization, simulation, animation and virtual reality.<br />
Fundamentals of computer graphics and geometric modelling: different representations of<br />
geometric objects, geometric transformations, projections, basic principles of rendering.<br />
Information visualisation: 1D, 2D, 3D and 4D data, plotting trees, grids, and graphs, graphs and<br />
trees interactions, scalar and vector fields, non-photorealistic rendering.<br />
Surface visualisation and visualization of volumetric data: surface rendering, direct<br />
visualisation of voxel data, indirect visualization of sampled objects by surface reconstruction.<br />
Applications of scientific visualisation: visualisation of chemical structures in biology,<br />
chemistry and physics, fluid visualisation, geographic, geological and meteorological<br />
visualization, medical visualisation.<br />
Bioinformatics visualization: molecular modelling, anatomic visualization, visualization of DNA<br />
sequences.<br />
Software for <strong>bioinformatics</strong> visualization: a survey and use of software packages for structure<br />
visualization in <strong>bioinformatics</strong> (Cn3D, Rasmol, Protein Explorer, Chime), analysis and<br />
comparison of packages.
Readings:<br />
1. Chaomei Chen: Information Visualization. Springer; 2 edition, 2004. ISBN: 1852337893.<br />
2. Michael Jünger (Editor), Petra Mutzel (Editor): Graph Drawing Software. Springer, 2003.<br />
ISBN: 3540008810.<br />
3. Isaac Bankman: Handbook of Medical Imaging: Processing and Analysis. Academic Press;<br />
2000. ISBN: 0120777908.<br />
4. Wen Jei Yang: Handbook of Flow Visualization. Taylor & Francis, <strong>2nd</strong> edition, 2001. ISBN:<br />
1560324171.<br />
Objectives and competences:<br />
The objective of this course is to enrich student’s experience in using visualisation, to organize, to<br />
formalize and to widen his knowledge of visualisation by learning the theoretical background,<br />
data types and algorithms and, consequently, to qualify him for more efficient use, development<br />
and implementation of scientific visualisation systems.<br />
Communication skills: oral manner of expression at oral exemination and lab work defense,<br />
writing report about completed project.<br />
Use of information technology: use of present software for <strong>bioinformatics</strong> visualisation,<br />
present software development tools and special visualisation libraries.<br />
Problem solving: individual project work.<br />
Intended learning outcomes:<br />
Knowledge and understanding:<br />
On completion of this course the student will be able to:<br />
- demonstrate broad knowledge of visualisation principles, data types and algorithms,<br />
- select a proper representation and visualisation technique for soliving real scientific and<br />
engineering problems,<br />
- use theoretical knowledge and practical experience for eficient use of visualisation<br />
software in <strong>bioinformatics</strong>,<br />
- evaluate applicability of existing software in a given practical situation and, as necessary,<br />
design and implement own system,<br />
- list and illustrate use of scientific visualisation in some other fields (medicine, geography,<br />
geology, meteorology...).<br />
Learning and teaching methods:<br />
Lectures, discussions, demonstration, computer exercises.<br />
Assessment:<br />
Type (examination, oral, coursework,<br />
project):<br />
Weight (in %)<br />
- coursework (computer exercises ) 30<br />
- projects (seminary work)<br />
20<br />
- oral examination.<br />
50<br />
Lecturer's references:<br />
KRIVOGRAD, Sebastian<br />
A hexahedral mesh connectivity compression with vertex <strong>degree</strong>s / Sebastian Krivograd, Mladen
Trlep, Borut Žalik. - . - Dostopno tudi na: http://dx.doi.org/doi:10.1016/j.cad.2008.10.013. -<br />
Abstract. - Bibliografija: str. 1112. V: Computer Aided Design. - ISSN 0010-4485.. - Vol. 40, iss. 12<br />
(Dec. 2008), str. 1105-1112. . - doi: 10.1016/j.cad.2008.10.013 COBISS.SI-ID 12964630, JCR, WoS,<br />
št. citatov do 10. 3. 2009: 0, brez avtocitatov: 0, normirano št. citatov: 0<br />
GEOMETRIC data preparation for GIS applications / David Podgorelec ... [et al.]. - Soavtorji: Gregor<br />
Klajnšek, Sebastian Krivograd, Borut Žalik. - Bibliografija: str. 124-127. - Abstract. V:<br />
Geoinformation technologies for geocultural landscapes / editors Oliver Bender ... [et al.]. - Boca<br />
Raton [etc.] : CRC Press/Balkema, cop. 2009. - ISBN 978-0-415-46859-6. - Str. 107-127. COBISS.SI-<br />
ID 13051670
Course title: Health informatics<br />
COURSE SYLLABUS<br />
Study <strong>programme</strong> and level Study field<br />
Bioinformatics 2 nd <strong>degree</strong><br />
Bologna Study <strong>programme</strong><br />
Academic<br />
year<br />
Semester<br />
Bioinformatics 2 3<br />
Course type Optional subject<br />
University course code:<br />
Lectures Seminar Tutorial<br />
Laboratory<br />
work<br />
Field work<br />
Individ.<br />
work<br />
ECTS<br />
15 30 105 6<br />
Lecturer: Kokol Peter, PhD, Full professor,<br />
Tatjana Welzer Družovec, PhD, Full professor<br />
Languages: Lectures: slovene<br />
Tutorial: slovene<br />
Prerequisits:<br />
Knowledge in computer science and informatics.<br />
Content (Syllabus outline):<br />
- Health and nursing informatics<br />
- Requirements engineering, information system development, implementation.<br />
- Databases in <strong>bioinformatics</strong> and health<br />
- Quality assurance of hospital information systems for health and nursing<br />
- Intelligent systems<br />
- Decision trees in health and nursing<br />
- Telemedicine<br />
- Informatics in organization and working processes in health systems
Readings:<br />
1. M.J. Ball et all. Nursing Informatics: Where carring and Technology Meet. 3rd ed./ New<br />
York: Springer-Verlag, 2000.<br />
2. L. Burke, B. Weill. Information Technology for the Health Professions. <strong>2nd</strong> ed./ Prentice<br />
Hall, 2004.<br />
3. E. Turban et all. Introduction to Information Technology. 3rd ed./ Wiley, 2004<br />
4. Kokol P. Računalništvo v zdravstvo I. Maribor: Visoka zdravstvena šola, 1998 NICE<br />
textbooks from the Phare Tempus program.<br />
5. Saba VK, McCormick A. Essentials of Nursing Informatics, IOS Press, 2005.<br />
Objectives and competences:<br />
Student:<br />
- will be capable to take an active part in hospital information systems development.<br />
Intended learning outcomes:<br />
Knowledge and understanding:<br />
- understands the importance of information, information systems and information<br />
technology in health and nursing care;<br />
- understands the importance of nursing leaders in process of nursing information systems<br />
development;<br />
- is able to use theory and practice of information systems development<br />
Learning and teaching methods:<br />
Lectures, seminar work, workshops.<br />
Assessment:<br />
Weight (in %)<br />
Type (examination, oral, coursework,<br />
project):<br />
Written exam,<br />
40<br />
project.<br />
60<br />
Lecturer's references:<br />
EVOLUTIONARY design of decision trees for medical application [Elektronski vir] / Peter Kokol ...<br />
[et al.]. - Soavtorji: Sandi Pohorec, Gregor Štiglic, Vili Podgorelec. - Bibliografija: str. 252-254.<br />
V: Wiley interdisciplinary reviews. Data mining and knowledge discovery [Elektronski vir]. - ISSN<br />
1942-4795. - Vol. 2, iss. 3 (May 2012), str. 237-254. . - doi: 10.1002/widm.1056 COBISS.SI-ID<br />
15997462<br />
KOKOL, Peter, 1957-<br />
Intelligent system supported evidence based management [Elektronski vir] / Peter Kokol, Gregor<br />
Štiglic. - ilustr. - Bibliografija: str. 198. - Abstract. V: CAINE-2011 [Elektronski vir] / 24th<br />
International Conference on Computers and Their Applications in Industry and Engineering<br />
November 16-18, 2011, Honolulu, HI USA. - Cary, NC : ISCA, 2011. - ISBN 978-1-880843-83-3. - Str.<br />
195-198.COBISS.SI-ID 1764516
COMPUTATIONAL complexity : theory, techniques, and applications / editor-in-chief, Robert A.<br />
Meyers. - New York : Springer, cop. 2012. - 6 zv. (XLIV, 3492 str.) ISBN 1-4614-1799-6 (hbk)<br />
ISBN 978-1-4614-1799-6 (hbk.) COBISS.SI-ID 1780644<br />
VIRTUAL education centre for the development of expert skills and competencies [Elektronski vir]<br />
/ Tatjana Welzer ... [et al.]. - Nasl. z nasl. zaslona. - Opis vira z dne 21. 11. 2011. - Bibliografija: str.<br />
54. - Abstract. V: International journal of advanced corporate learning [Elektronski vir]. - ISSN<br />
Y505-6985. - Vol. 4, no. 4 (2011), str. 51-54. - doi: ijac.v4i4.1747 COBISS.SI-ID 15528726<br />
HÖLBL, Marko<br />
Two improved two-party identity-based authenticated key agreement protocols / Marko Hölbl,<br />
Tatjana Welzer. V: Computer standards & interfaces. - ISSN 0920-5489.. - Vol. 31, iss. 6 (Nov.<br />
2009), str. 1056-1060. . - doi: 10.1016/j.csi.2008.09.024 COBISS.SI-ID 13379606, JCR, WoS, št.<br />
citatov do 6. 6. 2012: 3, brez avtocitatov: 3, normirano št. citatov: 2<br />
WELZER-Družovec, Tatjana<br />
Culture sensitive aspects in informatics education [Elektronski vir] / Tatjana Welzer, Marjan<br />
Družovec, Hannu Jaakkola. - Ilustr. - Bibliografija na koncu prispevka. - Abstract. V: EAEEIE2012<br />
[Elektronski vir] / 23rd EAEEIE annual conference, Cagliary, Italy, February 26-27, 2012. - [S. l. : s.<br />
n.], cop. 2012. - Str. 1-3. COBISS.SI-ID 15829270