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FI:PA054 Formal Methods in Biology - Course Information

## PA054 Formal Methods in Systems Biology

**Faculty of Informatics**

Spring 2020

**Extent and Intensity**- 2/0. 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)
**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**- Mon 17. 2. to Fri 15. 5. Thu 12:00–13:50 B411
**Prerequisites**- The course requires elementary knowledge of formal techniques achieved at bachelor level. This is an interdisciplinary course. The course is recommended especially for students of Bioinformatics. The course is also suitable for students of all other applied and theoretical study branches, namely Parallel and Distributed Systems and Theoretical Computer Science.
**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 49 fields of study the course is directly associated with, display
**Course objectives**- At the end of this course students should be able to: understand the actual trends and open problems in the domain of formal methods for complex systems modeling; apply formal methods in the modern biological research in systems biology; employ relevant software tools to solve particular problems in modeling and simulation of biological systems.
**Learning outcomes**- At the end of this course students should be able to:

- define the actual problems solved in the domain of formal methods for complex systems modelling and analysis;

- apply formal methods in systems biology;

- use relevant software tools to solve particular problems in modeling and simulation of biological systems. **Syllabus**- Problem definition: Modeling and analysis in systems biology. Motivation for application of formal methods.
- Overview of formal methods employed for analysis of biological hypotheses. Model specification. Model size and state explosion problem.
- Modeling and simulation: Deterministic vs. non-deterministic models. Continuous vs. discrete models. Models with parameter uncertainty. Approximation and abstraction. Simulation and analysis.
- Qualitative models: Boolean networks, Petri nets.
- Quantitative models: Timed Boolean networks, Markov chains, Stochastic Petri nets, relations to continuous and hybrid models.
- Formal specification of models: Kappa-calculus, Stochastic Petri nets, Stochastic Pi-Calculus and related formalisms.
- Model checking: Application in the process of model validation. Properties of in silico models vs. in vivo/in vitro experiments. Model checking tools for biological models.
- Models with parameter uncertainty: Parameter estimation. Robustness analysis.

**Literature***Formal methods for computational systems biology : 8th International School on Formal Methods for the Design of Computer, Communication and Software Systems, SFM 2008 : Bertinoro, Italy, June 2-7, 2008 : advanced lectures*. Edited by Marco Bernardo - Pierpaolo Degano - Gianluigi Zavattaro. Berlin: Springer, 2008. x, 523. ISBN 9783540688921. info*Computational modeling of genetic and biochemical networks*. Edited by James M. Bower - Hamid Bolouri. Cambridge: Bradford Book, 2001. xx, 336. ISBN 0262524236. info

*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. info - ALON, Uri.
*An Introduction to Systems Biology: Design Principles of Biological Circuits*. : Chapman & Hall/Crc, 2006. info - PALSSON, Bernhard.
*Systems biology : properties of reconstructed networks*. 1st pub. Cambridge [England]: Cambridge University Press, 2006. xii, 322. ISBN 9780521859035. info

*not specified***Teaching methods**- Lectures, group projects. Optional homeworks.
**Assessment methods**- oral exam (40%), semester project (60%)
**Language of instruction**- Czech
**Further Comments**- Study Materials

The course is taught annually.

- Enrolment Statistics (recent)

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