Lecture: Computational Systems Biology – SS12

Lecturer: Dr. Jürgen Pahle
Assistants: Alexandr Andreychenko, Linar Mikeev

First lecture on 24th April 2012!
No lectures on Tuesday 1st, May 2012 (“Tag der Arbeit”) and Tuesday 10th July 2012
Lectures: Tuesdays 16:00-17:30, MPI, room 021
Tutorials/Exercises: Thursdays 16:00-17:30, E1 3, room 015 (in selected weeks)

Exam on 31st July 2012, 10:00-12:00, room HS001, E1 3

Credits: 6 ECTS points

This lecture is designed for bioinformatics and computer science students.

Systems biology aims at integrating the knowledge about single biological components (e.g. molecules, cells, organs) into one coherent picture, focusing on the interactions between the components and their dynamic interplay. Computational modelling of biochemical networks is one of the key tools in this endeavour.

This lecture will introduce students to the commonly used work flow in this context ranging from model formulation and refinement to simulation and analysis approaches. Some of the methods that will be covered are

  • model formulation and kinetic functions,
  • software, databases and standards (e.g. SBML, SBGN),
  • steady state analysis and time course simulation (deterministic, stochastic and hybrid),
  • structural analysis (conservation relations, elementary flux modes),
  • sensitivity analysis (including metabolic control analysis),
  • parameter scanning/sampling,
  • parameter estimation and
  • (global) optimisation techniques.

Exercises will be carried out mostly using the software COPASI (www.copasi.org).

Learning outcomes:
The students will be familiar with the basic work flow in computational systems biology. They will have a firm grasp of the commonly used methods and approaches, e.g. they will know about the purposes, algorithmic and mathematical background, respective strengths, as well as potential hurdles and pitfalls of these methods.


  • Klipp, Liebermeister, Wierling, Kowald, Lehrach and Herwig. Systems Biology – A textbook. Wiley-Blackwell, June 2009, ISBN 978-3-527-31874-2
  • S. Hoops, S. Sahle, R. Gauges, C. Lee, J. Pahle, N. Simus, M. Singhal, L. Xu, P. Mendes and U. Kummer (2006) COPASI – a COmplex PAthway SImulator. Bioinformatics 22(24):3067, doi:10.1093/bioinformatics/btl485


Course material:

CSB_01_Introduction, Worksheet_01_Introduction (24.4.2012)
Tag der Arbeit (1.5.2012)
CSB_02_ModelsOfBiochemicalSystems_part1, Worksheet_02_ModelsOfBiochemicalSystems_part1 (8.5.2012)
CSB_03_ModelsOfBiochemicalSystems_part2, Worksheet_03_ModelsOfBiochemicalSystems_part2 (15.5.2012)
CSB_04_StandardsSoftwareDatabases (22.5.2012)
CSB_05_StructuralAnalysis, Worksheet_04_Standards_and_StructuralAnalysis (29.5.2012)
CSB_06_ParameterScanning_DiscreteEvents_Rules (5.6.2012)
CSB_07_SensitivitiesMCA, Worksheet_05_SensitivitiesMCA (12.6.2012)
CSB_08_CaseStudies (19.6.2012)

CSB_09_StochasticModelling, Worksheet_06_StochasticModelling (26.6.2012)

CSB_10_Optimisation, Worksheet_07_Optimisation (3.7.2012)
CSB_11_ParameterEstimation, Worksheet_08_ParameterEstimation (17.7.2012)

CSB_12_WrapUp (24.7.2012)
Exam (31.7.2012), 10:00-12:00, HS001, E1 3
Results of the course evaluation: EvaluationLectureComputationalSystemsBiology.pdf

Update 2012-08-28:
Exam solution: solution.pdf
Results and grades: results.pdf
If you want to have a look at your exam please send me a brief email or come to my office.
I will offer oral exams ONLY for people who have failed the written exam, or who had indicated before the written exam that they cannot attend due to an important reason. If you want to take an oral exam please send me an email as soon as possible. Oral exams will take place on Tuesday, 27th of September 2012 (subject to change).