Course detail
Systems Biology
FEKT-MPA-SYSAcad. year: 2022/2023
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.
Language of instruction
Number of ECTS credits
Mode of study
Guarantor
Offered to foreign students
Learning outcomes of the course unit
- mathematically describe the main components of gene expression
- mathematically describe the main components of signal transduction pathways
- analyze network graphs using network motifs
- name the main network motifs of transcriptional networks and signal-transduction pathways
- explain function of the main motifs of transcriptional networks and signal-transduction pathways
- describe experimental mathods in systems biology
Prerequisites
Co-requisites
Planned learning activities and teaching methods
Assesment methods and criteria linked to learning outcomes
up to 14 points for completion and presentation of the semestral project
up to 70 points for exam.
Examination has an oral form.
Course curriculum
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
Work placements
Aims
Specification of controlled education, way of implementation and compensation for absences
Recommended optional programme components
Prerequisites and corequisites
Basic literature
Dubitzky, W., Wolkenhauer, O., Cho, K.-H., Yokota, H., Encyclopedia of systems biology. Springer, New York 2013. ISBN 978-144-1998-644. (EN)
Konopka, A.K. Systems Biology: Principles, Methods, and Concepts. CRC, 2006, ISBN: 978-0824725204 (EN)
Maly, Ivan V. Systems biology. Humana Press, New York 2009. ISBN 978-1-934115-64-0. (EN)
Recommended reading
Elearning
Classification of course in study plans
- Programme MPC-BTB Master's 1 year of study, summer semester, compulsory
- Programme MITAI Master's
specialization NADE , 0 year of study, summer semester, elective
specialization NBIO , 0 year of study, summer semester, elective
specialization NCPS , 0 year of study, summer semester, elective
specialization NEMB , 0 year of study, summer semester, elective
specialization NGRI , 0 year of study, summer semester, elective
specialization NHPC , 0 year of study, summer semester, elective
specialization NIDE , 0 year of study, summer semester, elective
specialization NISD , 0 year of study, summer semester, elective
specialization NISY up to 2020/21 , 0 year of study, summer semester, elective
specialization NMAL , 0 year of study, summer semester, elective
specialization NMAT , 0 year of study, summer semester, elective
specialization NNET , 0 year of study, summer semester, elective
specialization NSEC , 0 year of study, summer semester, elective
specialization NSEN , 0 year of study, summer semester, elective
specialization NSPE , 0 year of study, summer semester, elective
specialization NVER , 0 year of study, summer semester, elective
specialization NVIZ , 0 year of study, summer semester, elective - Programme IT-MSC-2 Master's
branch MBI , 0 year of study, summer semester, elective
- Programme MITAI Master's
specialization NISY , 0 year of study, summer semester, elective
specialization NEMB up to 2021/22 , 0 year of study, summer semester, elective
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
Elearning