Course details
Systems Biology
MPA-SYS FEKT MPA-SYS Acad. year 2026/2027 Summer semester 5 credits
The course is oriented towards acquiring knowledge about the methods of systems biology, inferring models of cellular organisms and possibilities of their use. It focuses on the study of computational methods for describing the behavior of living organisms at the molecular level, usable in cell biology, biochemistry and biotechnology.
The studied models are represented by extensive network graphs. Emphasis is placed on the methods for analyzing these models, using both static and dynamic analyses. From dynamic analyses, the focus is on both quantitative analysis using ODE models and qualitative analysis using Boolean models. The concept of hierarchy of functional layers in the cell is followed, presenting all layers from gene regulatory networks, through signaling pathways to metabolic networks. These models are illustrated on systems of specific, mainly unicellular, organisms.
Guarantor
Language of instruction
Completion
Time span
- 26 hrs lectures
- 26 hrs pc labs
- 40 hrs projects
Department
Learning objectives
The aim of the course is to provide students with a basic orientation in the use of computer models in cell biology and how to use them and master the methods of model analysis for systems biology.
The graduate of the course is able to:
- mathematically describe the main components of gene expression
- mathematically describe the main components of signaling pathways
- analyze network graphs using network motifs
- list the main network motifs of transcriptional networks and signaling pathways
- explain the function of the main network motifs in transcriptional networks and signaling pathways
- describe experimental methods in systems biology and the main model organisms
- infer a model and estimate its parameters from experimental data
- use gene ontology for functional annotation
Prerequisite knowledge and skills
Basic knowledge of biology (especially the description of the cell, the central dogma of molecular biology) and mathematics (especially differential equations, probability distributions of random variables, combinatorics) is required.
Fundamental literature
- ALON, Uri. An introduction to systems biology: design principles of biological circuits. Second edition. CRC Press, 2019. ISBN 978-1439837177.
- KLIPP, Edda, Wolfram LIEBERMEISTER, Christoph WIERLING a Axel KOWALD. Systems biology: a textbook. 2nd edition. Weinheim: Wiley-VCH, 2016. ISBN 978-3-527-33636-4.
Syllabus of lectures
1. An Introduction to Systems Biology
2. Laboratory Techniques
3. Model Organisms, Biological Networks and Pathways
4. Basics of Dynamic Analysis of Continuous Models
5. Enzyme Kinetics
6. Transcriptional Regulation
7. Prediction of Network Motifs, Autoregulation Motif
8. Network Motif FFL
9. Other Network Motifs
10. Gene Regulatory Network Inference
11. Parameter Estimation
12. Gene Ontology
13. Project Presentation
Syllabus of computer exercises
1. An Introduction to Systems Biology
2. Databases for Systems Biology
3. Graph Theory, Data Formats, Cytoscape
4. Dynamic analysis (Copasi)
5. Enzyme Kinetics, Michaelis-Menten
6. Transcriptional Regulation
7. Prediction of Network Motifs
8. Static and Dynamic Analysis of FFL Motif
9. Cell Collective I, project assignments
10. Cell Collective II, project briefing and consultation
11. Cell Collective III, project briefing and consultation
12. Cell Collective IV, project briefing and consultation
13. Consultations, compensation for missed exercises
Syllabus - others, projects and individual work of students
Work on a group project (1-3 member groups).
Progress assessment
Criteria for obtaining credit:
- to obtain at least 20 points in total from all scoring activities of the semester
- to complete at least 7 out of 8 continuous scoring activities, i.e., reports of computer exercises) (max. 16 points)
- to complete and defend a project (max. 24 points)
Exercises are obligatory, one absence is allowed. Other absences are only possible for medical reasons, immediately excused (by a doctor's certificate). Compensation for uncompleted exercise is possible in the last week of semester. Only students with a credit can take the final oral exam.
To successfully complete the course, it is necessary to obtain at least 30 points from the final exam. The final score is determined from the points obtained during the semester (max. 40 points) and the final exam (max. 60 points).
Course inclusion in study plans