NCBR001 Systems Biology and Modeling Methods

Faculty of Science
Spring 2022
Extent and Intensity
0/2/0. 2 credit(s) (plus 2 credits for an exam). Type of Completion: zk (examination).
Teacher(s)
Tomáš Helikar, PhD. (lecturer)
prof. RNDr. Michaela Wimmerová, Ph.D. (lecturer)
Mgr. Veronika Papoušková, Ph.D. (assistant)
Guaranteed by
prof. RNDr. Michaela Wimmerová, Ph.D.
National Centre for Biomolecular Research – Faculty of Science
Contact Person: Mgr. Veronika Papoušková, Ph.D.
Supplier department: National Centre for Biomolecular Research – Faculty of Science
Prerequisites
No prior math or computer science classes are required.
Course Enrolment Limitations
The course is offered to students of any study field.
Course objectives
The course aims at immersing life sciences students in the field of computational modeling of biochemical and biological network systems and their complex dynamics. Students will learn about network processes in living organisms and computational methods hand-in-hand on several biological and biochemical systems (e.g., regulation of bacterial chemotaxis, signal transduction, etc.). Students will learn and utilize a popular logical modeling framework and related software tools on the computational modeling side. The course will primarily consist of hands-on activities that will involve the construction, manipulation, simulation, and analysis of computational models of biological systems. By the end of the course, students will be expected to have created, analyzed, and presented a computational model of a biological system of their interest.
Syllabus
  • 1. Computational systems modeling: Overview. 2. Towards multi-scale models of the immune system: Exploring the capacity of T cell differentiation. 3. Introduction to logical modeling and Cell Collective. 4. Modeling and simulating the dynamics of network motifs (positive/negative feedback loops), Part 1. 5. Modeling and simulating the dynamics of network motifs (positive/negative feedback loops), Part 2. 6. Nuts and bolts of logical modeling, Part 1. 7. Nuts and bolts of logical modeling, Part 2. 8. Modeling and simulating the dynamics of bacterial chemotaxis. 9. Modeling and simulating the dynamics of gene regulation (lac operon). 10. Modeling Challenge: Build, validate, and simulate a model of regulation of T cell differentiation (3 blocks). 11. Announcement of winners of the modeling challenge.
Assessment methods
Attendance at the whole course and active participation.
Language of instruction
English
Further Comments
The course is taught only once.
The course is taught: in blocks.
  • Enrolment Statistics (recent)
  • Permalink: https://is.muni.cz/course/sci/spring2022/NCBR001