FEKT-MPC-SYSAcad. year: 2020/2021
The course is oriented to gain knowledge of methods used in systems biology, creating models of cellular organisms and possibilities of their usage. It aims on computational methods used to describe behavior of living organisms on molecular level that are utilizable in cellular biology, biochemistry, and biotechnology.
Studied models are represented by extensive network graphs. Special attention is paid to both methodologies of model analysis, static as well as dynamic, especially using quantitative ODE models. The concept of hierarchy is followed and all functional layers, from gene regulatory network to signaling pathways and metabolic networks, are presented. Examples of models are given on systems of particular, especially unicellular, organisms.
Learning outcomes of the course unit
Students will be able to:
- mathematically describe the main components of gene expression
- mathematically describe the main components of signal transduction pathways
- mathematically describe the main components of neuronal pathways
- analyze network graphs using network motifs
- name the main network motifs of transcription, signal-transduction and neuronal-system networks
- explain principles of the main network motifs of transcription, signal-transduction and neuronal-system networks
- describe experimental mathods in systems biology
Students enrolled in this subject should be able to describe cellular systems, its main components regarding structure and function; analyze systems of ordinary differential equations and apply basic knowledge of probability distribution and combinatorics. In general, knowledge on the Bachelor's degree level is requested.
Recommended optional programme components
Recommended or required reading
Konopka, A.K. Systems Biology: Principles, Methods, and Concepts. CRC, 2006, ISBN: 978-0824725204 (EN)
Klipp, E., Liebermeister, W., Wierling, C., Kowald, A., Lehrach, H., Herwig, R. Systems Biology: A Textbook. Wiley, 2009. ISBN: 978-3-527-31874-2 (EN)
Alon, U: An Introduction to Systems Biology, Design Principles of Biological Circuits. CRC, 2007, ISBN: 1-58488-642-0 (EN)
Maly, Ivan V. Systems biology. Humana Press, New York 2009. ISBN 978-1-934115-64-0. (CS)
Rosypal, S. Nový přehled biologie. Scientia, Praha 2003. ISBN 80-7183-268-5 (CS)
Dubitzky, W., Wolkenhauer, O., Cho, K.-H., Yokota, H., Encyclopedia of systems biology. Springer, New York 2013. ISBN 978-144-1998-644. (CS)
Planned learning activities and teaching methods
Techning methods include lectures and computer laboratories. Course is taking advantage of e-learning (Moodle) system.
Assesment methods and criteria linked to learning outcomes
upto 30 points from laboratories
upto 70 points from examination.
Examination has a written form.
Language of instruction
1. Introduction to systems biology
2. Laboratory techniques for systems biology
3. Model organisms, biological networks and pathways
4. Basics of dynamic analysis of continuous models
5. Enzyme kinetics
6. Regulation of transcription
7. Prediction of network motifs, autoregulation motif
8. FFL motif
9. Additional network motifs
10. Gene ontology
11. Qualitative Boolean models
12. Gene regulatory network inference and parameter estimation
13. Project presentations
The aim of the subject is to provide students with basic knowledge of computational models in cellular biology and way of their use, knowledge of analysis methods applied to models in systems biology.
Specification of controlled education, way of implementation and compensation for absences
Laboratory tutorials are compulsory, properly justified absence can be compensated based on agreement of the tutor (usually in the last semester week).
Classification of course in study plans