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Computational Systems Biology: Stochastic Approaches
Last Updated: 2026-06-03 00:07:32
Abstract
This course is concerned with the development of computational methods for modeling, simulation, and analysis of stochasticity in living cells. Using these tools, the course explores the richness of stochastic phenomena, how it arises from the interactions of dynamics and noise, and its biological implications.
Objective
To understand the origins and implications of stochastic noise in living cells, and to learn the computational tools for the modeling, simulation, analysis, and identification of stochastic biochemical reaction networks.
Content
The cellular environment is abuzz with noise. A key source of this noise is the randomness that characterizes the motion of cellular constituents at the molecular level. Cellular noise not only results in random fluctuations (over time) within individual cells, but it is also a main source of phenotypic variability among clonal cell populations. Review of basic probability and stochastic processes; Introduction to stochastic gene expression; deterministic vs. stochastic models; the stochastic chemical kinetics framework; a rigorous derivation of the chemical master equation; moment computations; linear vs. nonlinear propensities; linear noise approximations; Monte Carlo simulations; Gillespie's Stochastic Simulation Algorithm (SSA) and variants; direct methods for the solution of the Chemical Master Equation; moment closure methods; intrinsic and extrinsic noise in gene expression; parameter identification from noise; propagation of noise in cell networks; noise suppression in cells; the role of feedback; exploiting noise; bimodality and stochastic switches.
Resources
Literature
Literature will be distributed during the course as needed.
General Information
- Language
- English
- Levels
- DR , MSC
- Frequency
- Yearly recurring
Examination
- Type
- session examination
- Mode
- written 180 minutes
- Aids
- None
Course Components
| Type | Title | Time & Place | Hours |
|---|---|---|---|
| lecture with exercise |
Computational Systems Biology: Stochastic Approaches
Does not take place this semester.
|
No time listed | 3 h weekly |
Offered In
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Computational Biology and Bioinformatics Master (More information at: )
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Core Courses (The list of core courses is a closed list - no other courses can be added in this category. The assignment of the courses to the respective subcategory cannot be changed. Students must pass at least one course in each subcategory. A total of 40 ECTS must be acquired in the core course category, including the mandatory CBB seminar.)
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Doctorate Biosystems Science and Engineering (More Information at: )
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Biotechnology Master (More information at: )
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Electives (Open list - other courses (ETH or UNIBAS) may be taken as electives upon approval of the mentor.)
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