FI:PB050 Modelling in Bioinformatics - Course Information
PB050 Modelling and Prediction in Systems Biology
Faculty of InformaticsAutumn 2024
- Extent and Intensity
- 1/1. 2 credit(s) (plus extra credits for completion). Recommended Type of Completion: zk (examination). Other types of completion: k (colloquium).
- Teacher(s)
- doc. RNDr. David Šafránek, Ph.D. (lecturer)
RNDr. Matej Troják, Ph.D. (assistant) - Guaranteed by
- doc. RNDr. David Šafránek, Ph.D.
Department of Machine Learning and Data Processing – Faculty of Informatics
Supplier department: Department of Machine Learning and Data Processing – Faculty of Informatics - Timetable
- Thu 19. 9. to Thu 12. 12. Thu 10:00–11:50 B411
- Prerequisites
- This is an interdisciplinary course that extends the knowledge of bachelor students of all study branches. 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 36 fields of study the course is directly associated with, display
- Course objectives
- At the end of the course, students will be able to:
understand basic principles of quantitative modeling,
understand dynamic computational models of complex systems in the domain of biological processes;
apply abstract computer-scientific thinking to modeling and analysis of complex systems with special focus to biological systems;
practically use state-of-the-art modeling and analysis software tools;
model and analyze dynamic properties of complex interaction networks. - Learning outcomes
- At the end of the course, students will be able to:
describe basic principles of quantitative modeling,
constract dynamic computational models of complex systems in the domain of biological processes;
apply abstract computer-scientific thinking to modeling and analysis of complex systems with special focus to biological systems;
use state-of-the-art modeling and analysis software tools. - Syllabus
- 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.
- Specification of a biological model: biological networks and pathways, languages SBML and SBGN.
- Emergent properties of systems dynamics, their specification and encoding.
- Modeling and simulation of biological systems dynamics: hypotheses prediction.
- Modeling of Escherichia coli bacteria: genetic regulatory network, models of locomotion organ synthesis and chemotaxis, nutritional stress response models.
- Notion of stochasticity in biological dynamics, basic principles of stochastic models, chemical master equation, Monte Carlo simulation.
- Model parameters, robustness and parameter sensitivity.
- Literature
- recommended literature
- VRIES, Gerda de. A course in mathematical biology : quantitative modeling with mathematical and computational methods. Philadelphia, Pa.: Society for Industrial and Applied Mathematics, 2006, xii, 309. ISBN 0898716128. URL info
- ALON, Uri. An Introduction to Systems Biology: Design Principles of Biological Circuits. Chapman & Hall/Crc, 2006. info
- WILKINSON, Darren James. Stochastic modelling for systems biology. Boca Raton: Chapman & Hall/CRC, 2006, 254 s. ISBN 1584885408. info
- not specified
- NOBLE, Denis. Music of life : biology beyond the genome. Oxford: Oxford University Press, 2006, xiii, 153. ISBN 9780199295739. info
- System modeling in cell biology : from concepts to nuts and bolts. Edited by Zoltan Szallasi - Jorg Stelling - Vipul Periwal. Cambridge, Mass.: MIT Press, 2006, xiv, 448. ISBN 0262195488. info
- Computational modeling of genetic and biochemical networks. Edited by James M. Bower - Hamid Bolouri. Cambridge: Bradford Book, 2001, xx, 336. ISBN 0262524236. info
- Teaching methods
- Lectures and optional homeworks. Semestral projects. In the case of online teaching lectures are implemented synchronously through a suitable videoconferencing software.
- Assessment methods
- Written final examination (50%), semester project (50%). In case of online teaching the exam is oral.
- Language of instruction
- Czech
- Follow-Up Courses
- Further Comments
- The course is taught annually.
- Teacher's information
- http://www.fi.muni.cz/~xsafran1/PB050/
- Enrolment Statistics (recent)
- Permalink: https://is.muni.cz/course/fi/autumn2024/PB050