Course Discovering Systems Biology Principles


23-27 November 2015


VU University, Amsterdam


Teachers: Evert Bosdriesz (NKI, Amsterdam), Jacky Snoep (Stellenbosch, SA) and Frank Bruggeman (VU, Amsterdam)

Study load

Course description

A large part of systems biology is concerned with studying how the molecular networks inside living cells function. What they do. How their molecular interactions, including feedback circuitry, give rise to cellular properties, such as sensing, adaptation, division and death, that transcend those of single molecules. This includes figuring out how gene mutations, causing changes in proteins, cause networks, and their cellular hosts, to malfunction. In order to do this, systems biology focusses on the dynamics of molecular networks, using quantitative experiments and mathematical modeling. Mathematical models help systems biologists to figure out: i. how molecular properties relate to the functional, systemic properties of molecular networks, and ii. how molecular networks assist in the survival and functioning of cells.
This 1-week course serves as an introduction to mathematical modeling as it is used in systems biology.

Target audience

This course does not require any introductory reading or courses, it should be accessible to students with diverse backgrounds.

Course Programme

We start from physical and chemical principles of molecules, cells and reactions. Next, you will learn how you can relate the changes in the concentrations of molecules over time to the activity of reactions and the underlying molecular properties. You will be introduced to enzyme kinetics and the dynamics of small enzyme systems, in metabolism and signal transduction. We also briefly deal with models of genetic circuits. We will illustrate a number of unexpected, functional properties of molecular networks that can be studied with simple mathematical models. You will make and analyse models yourself, on paper and with software. We will close the week with a short overview of some more advanced topics, to introduce you to approaches and concepts that you will often hear about in systems biology.
The course material concerns a syllabus (with exercises and answers), handouts, and computer exercises. At the end of this 1-week course, you will have a good understanding how mathematical models are made, what biology they require and how you can use them in systems-biology research.

Course schedule

Monday, Nov 23
09:30-10:30 Diffusion
11:00-12:30 Diffusion
13:30-15:00 Mass balances and kinetics
15:30-17:00 Mass balances and kinetics

Tuesday, Nov 24
09:30-10:30 Mathematica or JWS online, basics
11:00-12:30 Mathematica or JWS online, basics
13:30-15:00 Simulating differential equation models
15:30-17:00 Simulating differential equation models

Wednesday, Nov 25
09:30-10:30 Enzyme kinetics
11:00-12:30 Enzyme kinetics
13:30-15:00 Rate characteristics
15:30-17:00 Supply demand theory and ultrasensitivity

Thursday, Nov 26
09:30-12:30 Cool systems: kinetic proofreading, TF-DNA search, robustness, fold-change detection,
optimal gene expression
13:30-17:00 Making models in JWS online or Mathematica

Friday, Nov 27
09:30-10:30 Stoichiometric analysis, N, K, L
11:00-12:30 Flux balance analysis
13:30-15:00 Stability analysis, phase-plane analysis
15:30-17:00 Bistability and oscillations with JWS Online or Mathematica

Further information

You are encouraged to bring your own laptop to be able to do the computer exercises.
Information about the course schedule, course rooms and map can be found here