Schedule BioSB course Dynamic Modelling in Systems Biology (December 08-12, 2025)
General schedule BioSB course
(More information on this course can be found through this link)
| 9:30-12:30 | lecture |
| 12:30-14:00 | lunch + meet-the-teacher |
| 14:00-16:00 | pen & paper exercises and/or computer practical |
| 16:15-17:00 | research talk + wrap up |
Except Friday: 9.30-12.30 lecture & practical; 14.00 – 15.00 wrap up
Day 1 (8 December)
Introduction Systems Biology, math tools, optimization – Dragan Bošnački
Topics:
- brief intro participants at the start of the course
- introduction of modelling with (ordinary) differential equations
- introduction of optimization concepts and methods
- practical (1): phase plane analysis
- practical (2): Matlab intro (Hans Stigter)
Research talk: Dragan Bošnački discusses the topic linked to the assignment
Day 2 (9 December)
How to build a model – Rob Smith
Topics:
- translating pictures into reaction kinetics and ODEs
- simulating ODE systems in MATLAB
- qualitatively comparing simulations with data
- predicting new experiments from initial models
- practical using MATLAB software
TBD
Day 3 (10 December)
Networks, Network motifs, Network inference – Aalt-Jan van Dijk
Topics:
- network structure, motifs, dynamics
- network inference
- bias/variance: overfitting
Practical (Matlab): network inference with thickening – thinning
Research talk: TBD
Day 4 (11 December)
Numerical optimization, Parameter estimation, Sensitivity analysis – Hans Stigter
Topics:
- Maximum Likelihood Estimation (MLE)
- linear and nonlinear least squares
- optimization algorithms (local and global), steepest descent, Gauss-Newton, Levenberg-Marquardt
- sensitivity (local)
- Fisher Information Matrix
- confidence intervals
- experimental design
- practical (Matlab)
Research talk: TBD
16:30 Social event
Day 5 (12 December)
Parameter sensitivity analysis (PSA) – Natal van Riel
Topics:
- Local PSA
- Sampling (Latin hypercube sampling)
- Global PSA
Discussion about the assignment (Dragan Bošnački)