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FEKT-MPA-SYSAcad. year: 2026/2027
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.
Language of instruction
Number of ECTS credits
Mode of study
Guarantor
Department
Offered to foreign students
Entry knowledge
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.
Rules for evaluation and completion of the course
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).
Aims
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
Study aids
Prerequisites and corequisites
Basic literature
Recommended reading
Classification of course in study plans
specialization NHPC , 0 year of study, summer semester, electivespecialization NVER , 0 year of study, summer semester, electivespecialization NIDE , 0 year of study, summer semester, electivespecialization NISY , 0 year of study, summer semester, electivespecialization NEMB , 0 year of study, summer semester, electivespecialization NSPE , 0 year of study, summer semester, electivespecialization NEMB , 0 year of study, summer semester, electivespecialization NBIO , 0 year of study, summer semester, electivespecialization NSEN , 0 year of study, summer semester, electivespecialization NVIZ , 0 year of study, summer semester, electivespecialization NGRI , 0 year of study, summer semester, electivespecialization NADE , 0 year of study, summer semester, electivespecialization NISD , 0 year of study, summer semester, electivespecialization NMAT , 0 year of study, summer semester, electivespecialization NSEC , 0 year of study, summer semester, electivespecialization NNET , 0 year of study, summer semester, electivespecialization NMAL , 0 year of study, summer semester, electivespecialization NCPS , 0 year of study, summer semester, elective
specialization MPC-BIO_TECH , 1 year of study, summer semester, compulsory-optional
Lecture
Teacher / Lecturer
Syllabus
1. An Introduction to Systems Biology2. Laboratory Techniques3. Model Organisms, Biological Networks and Pathways4. Basics of Dynamic Analysis of Continuous Models5. Enzyme Kinetics6. Transcriptional Regulation7. Prediction of Network Motifs, Autoregulation Motif8. Network Motif FFL9. Other Network Motifs10. Gene Regulatory Network Inference 11. Parameter Estimation12. Gene Ontology13. Project Presentation
Exercise in computer lab
1. An Introduction to Systems Biology2. Databases for Systems Biology3. Graph Theory, Data Formats, Cytoscape4. Dynamic analysis (Copasi)5. Enzyme Kinetics, Michaelis-Menten6. Transcriptional Regulation7. Prediction of Network Motifs8. Static and Dynamic Analysis of FFL Motif9. Cell Collective I, project assignments10. Cell Collective II, project briefing and consultation11. Cell Collective III, project briefing and consultation12. Cell Collective IV, project briefing and consultation13. Consultations, compensation for missed exercises
Project
Work on a group project (1-3 member groups).
Individual preparation for an ending of the course
Final preparation for the oral exam from the provided study materials (lecture and exercise presentations), your own notes and reports of computer exercises, or from basic literature.