A4: Introduction to Systems Biology
The module introduces mathematical approaches and systems biology concepts of cellular processes, as they are important for therapeutically relevant systems. The overall aim of the module is to learn and understand how prior knowledge on the targeted system (e.g., based on in vitro data or systems biology models of endogenous compounds) can be exploited for and integrated into the analysis of preclinical and clinical data.
The module includes important deterministic and stochastic approaches to biochemical reaction kinetics, model reduction techniques (e.g., the quasi-steady state approach/singular perturbation analysis), network motifs and the integration of cell-level models and pharmacokinetic models. This allows us to establish the link to empirical models as introduced in the A1 module Introduction to pharmacokinetics and pharmacodynamics (PK/PD) (Emax, non-linear CL etc) and important physiological processes as part of PBPK models (establishing the link to the A2 Introduction to physiologically-based pharmacokinetics. Techniques are exemplified for the EGFR signalling system and the drug-host-virus system in HIV disease.
Frequency: Every year in September/October.
Language: English
Module in 2024: 02-06 Sept, University of Potsdam/Germany. The schedule below is generic. For each PhD student year, the specific schedule will be sent via email to the participants.
Illustrative schedule
| Time | Monday | Tuesday | Wednesday | Thursday | Friday |
|---|---|---|---|---|---|
| 8:45 – 10:45 | Introduction to Systems Biology | Hands-on: Matlab recap on solving ODEs; ligand-receptor binding (theory) | Mathematical modelling tools II: Model reduction techniques (QSSA) | Introduction to disease modelling: HIV infection models | Network motifs and modules |
| 30 min | Coffee break | ||||
| 11:15 - 13:00 | Mathematical modelling tools I: Deterministic reaction kinetics | Mathematical modelling tools I: Deterministic reaction kinetics (con't) | Hands-on: cell-level PK/PD modelling | Hands-on: deterministic HIV infection models (incl. mutants) | Hands-on: targeting a signalling cascade |
| 60 min | Lunch break | ||||
| 14:00 - 16:00 | Guest discussion on ethical aspect in pharmacometrics | Hands-on: ligand- receptor binding (implementation) | Hands-on: cell-level PK/PD modelling (con't) | Mathematical modelling tools III: Stochastic reaction kinetics + hybrid models | Hands-on: targeting a signalling cascade (con't); Summary & closing; end |
| 15 min | Coffee break | ||||
| 16:15 - 17:45 | Guest talk & discussion (con't), end: 17:00. | Integration of systems biology models into PK/PD models | Understanding and reducing complex systems pharmacology models | Hands-on: deterministic HIV infection models (incl. drugs); stochastic HIV infection models | |
| Evening | Social Event (either during A3 or A4 module) | ||||
Contributions:
- Prof. Wilhelm Huisinga; theoretical lectures
- PharMetrX PhD students (2nd/3rd year); hands-on exercises
- External contributions by our faculty members
Hard- and software
- Please bring your own laptop.
- MATLAB® (The MathWorks), will be provided during the module.
- Detailed references will be provided during the course.
- Edda Klipp et al.,''Systems Biology - A Textbook'', Wiley-Blackwell, 2009.
- Uri Alon, ''An Introduction to Systems Biology: Design Principles of Biological Circuits'', Chapman & Hall, 2006.