Course details
System Biology
FSYS FEKT FSYS Acad. year 2018/2019 Summer semester 5 credits
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.
Guarantor
Language of instruction
Completion
Time span
- 26 hrs lectures
- 26 hrs pc labs
Department
Lecturer
Instructor
Subject specific learning outcomes and competences
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
Learning objectives
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.
Prerequisite knowledge and skills
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.
Study literature
- Klipp, E., Liebermeister, W., Wierling, C., Kowald, A., Lehrach, H., Herwig, R. Systems Biology: A Textbook. Wiley, 2009. ISBN: 978-3-527-31874-2
- Konopka, A.K. Systems Biology: Principles, Methods, and Concepts. CRC, 2006, ISBN: 978-0824725204
Fundamental literature
- Alon, U: An Introduction to Systems Biology, Design Principles of Biological Circuits. CRC, 2007, ISBN: 1-58488-642-0
Syllabus of lectures
1. Introduction to systems biology - from molecular biology of cell to computational models
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
Syllabus of computer exercises
1. Specific biochemical systems - mathematical modelling of biological and chemical processes in examples
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
Progress assessment
upto 30 points from laboratories
upto 78 points from examination.
Examination has a written form.
Teaching methods and criteria
Techning methods include lectures and computer laboratories. Course is taking advantage of e-learning (Moodle) system.
Controlled instruction
Laboratory tutorials are compulsory, properly justified absence can be compensated based on agreement of the tutor (usually in the last semester week).
Course inclusion in study plans