SSB-31806 Advanced Systems Biology


Credits 6.00

Teaching methodContact hours
Independent study0
Course coordinator(s)dr. E Saccenti
Lecturer(s)dr. ADJ van Dijk
dr. E Saccenti
dr. M Suarez Diez
dr. RW Smith
Examiner(s)dr. M Suarez Diez

Language of instruction:


Assumed knowledge on:

BCT-20306 Modelling Dynamic Systems, SSB-30306 Molecular Systems Biology

Continuation courses:

SSB-31312 Toolbox in Systems and Synthetic Biology; SSB MSc thesis in Systems and Synthetic Biology


Mathematical modelling is becoming an increasingly valuable tool for molecular cell biology. Consequently, it is important for life scientists to have a background in the relevant mathematical techniques, so that they can participate in the construction, analysis, and critique of available models. The course will cover different topics in Systems and Synthetic Biology such as Modelling of chemical reaction networks, Biochemical kinetics, Analysis of dynamic mathematical models, Metabolic networks and Gene regulatory networks. The course alternates lectures on theoretical aspects of Systems Biology with exercises and computer/computational practicals where the students will develop programming and analysis skills by modeling and investigating biological systems.  

The scripting language used during the course is Matlab: introductions and scripts will be provided and no previous Matlab experience is required.

Learning outcomes:

After successful completion of this course students are expected to be able to:

  • Describe and analyze a biological system in terms of ordinary or partial  differential equations.

  • Describe the properties of a dynamic biological system given its mathematical formulation

  • Recognize the different properties of the tools used to simulated and analyse biological systems

  • Recognize the advantages and limitations of different tools and apply them critically given a problem

  • Implement the model(s) using Matlab


- lectures;

- read and discuss literature;

- assignments;

- solve exercises;

- extensive practicals;

- computer programming.


- exercises (30%);

- written report on project work  (40%)

- oral-presentations of project work  (30%).


A suggested supporting textbook for this course is “Mathematical Modeling in Systems Biology” by Brian P. Ingalls (ISBN-13: 978-0262018883). A preprint pdf version of the book is freely available online. Additional material (articles, tutorials, references and suggested readings) will be made available at the Brightspace site of the course.

Restricted Optional for: MBFBioinformaticsMSc5MO