Course detail
System Biology
FEKT-FSYSAcad. year: 2018/2019
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.
Language of instruction
Number of ECTS credits
Mode of study
Learning outcomes of the course unit
- 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
Prerequisites
Co-requisites
Planned learning activities and teaching methods
Assesment methods and criteria linked to learning outcomes
upto 78 points from examination.
Examination has a written form.
Course curriculum
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
Work placements
Aims
Specification of controlled education, way of implementation and compensation for absences
Recommended optional programme components
Prerequisites and corequisites
Basic literature
Rosypal, S. Nový přehled biologie. Scientia, Praha 2003. ISBN 80-7183-268-5 (CS)
Recommended reading
Classification of course in study plans
Type of course unit
Lecture
Teacher / Lecturer
Syllabus
2. Modeling of biochemical systems - mathematical and computational models to describe processes in living organisms
3. Specific biochemical systems - mathematical modelling of biological and chemical processes in examples
4. Model fitting - design and verification of correct models, comparison to real living systems
5. Analysis of high-throughput data - recent methods used in bioinfnormatics and their implications to systems biology
6. Gene expression models - mathematical modelling of gene expression
7. Stochastic systems and variability - from deterministic to stochastic description of nearly chaotic biochemical processes
8. Network structures, dynamics, and function - networks of models and their use
9. Optimality and evolution - extended dynamic and adaptive models for evolving processes
10. Experimental techniques in molecular biology
11. Linear control systems in modelling
12. Computer modeling tools in practice
13. Systems biology for future
Exercise in computer lab
Teacher / Lecturer
Syllabus
2. Gene expression models - mathematical modelling of gene expression
3. Stochastic systems and variability - from deterministic to stochastic description of nearly chaotic biochemical processes
4. Optimality and evolution - extended dynamic and adaptive models for evolving processes
5. Selected computer modeling tools
6. Individual projects