FEKT-FSYSAcad. year: 2017/2018
The course is oriented to knowledge of methods of systems biology, design of models of cellular organisms and possibilites of their use. It is aimed at computational methods for description of living organisms on the molecular level applicable in cellular biology and biochemistry. The considered models are represented by networks. Methodology of analysis of these models by means of network motifs is emphasised. The theory of network analysis is applied to models of sensory and developmental transcription networks, models of signal transduction networks and neural networks. These models are illustrated on specific organisms, 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
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)
Konopka, A.K. Systems Biology: Principles, Methods, and Concepts. CRC, 2006, ISBN: 978-0824725204 (EN)
Alon, U: An Introduction to Systems Biology, Design Principles of Biological Circuits. CRC, 2007, ISBN: 1-58488-642-0 (EN)
Rosypal, S. Nový přehled biologie. Scientia, Praha 2003. ISBN 80-7183-268-5 (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 78 points from examination.
Examination has a written form.
Language of instruction
1. Definition of Systems biology, related fields
2. Biological introduction, model organisms
3. Kinetics of chemical reactions
4. Transkription networks
5. Network motifs of negative autoregulation
6. Network motifs FFL
7. Network motifs SIM, generalized motifs FFL, DOR
8. Developmental transcription networks, signal-transduction network motifs
9. Model of chemotaxis of escherichia coli
10. Multi-layer network motifs, network motifs of neural networks
11. Principles of proofreading of gene expression
12. Experimental methods in systems biology - optical methods
13. Experimental methods in systems biology - NMR and ultrasonography methods
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).