Tools for Systems biology modeling and data exchange: COPASI, CellNetAnalyzer, SABIO-RK, FAIRDOMHub/SEEK


Educators: Axel von Kamp, Steffen Klamt, Sven Thiele (MPI Magdeburg), Frank T. Bergmann, Ursula Kummer (University of Heidelberg), Maja Rey, Andreas Weidemann, Ulrike Wittig (HITS)


18-MAR-2019 10:00 am – 20-MAR-2019 5:00pm


Seminar Room 42, BioQUANT, Im Neuenheimer Feld 267, 69120 Heidelberg

See also: How to get there

Learning goals:

During this 3-day course, attendees will learn basic techniques for modeling of biochemical networks including data access and storage due to the FAIR principles. The first day introduces kinetic modeling techniques which will be illustrated and exercised with COPASI. The second day continues with principles of stoichiometric and constraint-based modeling coupled with hands on exercises using CellNetAnalyzer. The third day SABIO-RK is used as a resource for kinetic data and FAIRDOMHub/SEEK is introduced as a data and model management platform fitted to the needs of systems biologists. The hands on exercises throughout the three days will ensure that attendees become familiar with the software tools and with analyzing, creating, editing, importing, simulating and storing biochemical networks.


Some knowledge of mathematical modeling will be advantageous. The participants should bring their own laptop with MATLAB installed (if you do not have MATLAB please let us know during registration). Download and preinstallation of COPASI and CellNetAnalyzer is recommended but not mandatory.


There are a number of hotels closeby, we recommend on of the following:


There is no registration fee.

More information

COPASI Tutorial

For the hands on exercises to the parameter estimation part, please download the following data file.