FI:PB050 Modelling in Bioinformatics - Course Information
PB050 Modelling and Prediction in Systems BiologyFaculty of Informatics
- Extent and Intensity
- 1/1. 2 credit(s) (plus extra credits for completion). Type of Completion: zk (examination).
- RNDr. David Šafránek, Ph.D. (lecturer)
- Guaranteed by
- prof. Ing. Václav Přenosil, CSc.
Department of Machine Learning and Data Processing - Faculty of Informatics
- Wed 16:00–17:50 B410
- This is an interdisciplinary course that extends the knowledge of bachelor students. The course is especially recommended for students of Bioinformatics.
- Course Enrolment Limitations
- The course is also offered to the students of the fields other than those the course is directly associated with.
- fields of study / plans the course is directly associated with
- there are 22 fields of study the course is directly associated with, display
- Course objectives
- At the end of the course, students will be able to apply abstract computer-scientific thinking to in silico modeling and analysis of living organisms. Students will become familiar with a variety of tools devoted to modeling and simulation in systems biology. Relevant practical skills will be obtained by working on a semestral project.
- History and scope of systems biology.
- Basic notions: living organism as a system with precisely given structure and functionality, in silico model, abstraction, simulation and prediction, model validation.
- Sources of biological data: databases of biological knowledge.
- Specification of a biological model: biological networks and pathways, SBML language.
- Static analysis of biological systems: analysis of biological networks and pathways, network motifs and biological circuits.
- Modeling and simulation of biological systems dynamics: hypotheses prediction.
- Modeling of Escherichia coli bacteria: genetic regulatory network, models of loccomotion organ synthesis and chemotaxis, nutritional stress response models.
- Robustness and parameter sensitivity.
- Teaching methods
- Lectures and optional homeworks. Group projects.
- Assessment methods
- Written final examination (50%), semester project (50%).
- Language of instruction
- Follow-Up Courses
- Further Comments
- Study Materials
The course is taught annually.