Tools for Systems Biology Modeling and Data Exchange: COPASI, CellNetAnalyzer, SABIO-RK, SEEK

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Tools for Systems Biology Modeling and Data Exchange: COPASI, CellNetAnalyzer, SABIO-RK, SEEK

  • Beginn: 24.04.2018 10:00
  • Ende: 26.04.2018 15:00
  • Vortragender: 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)
  • Ort: Max-Planck-Institut Magdeburg
  • Raum: Großer Seminarraum "Prigogine"
  • Kontakt:

The 'German Network for Bioinformatics Infrastructure – de.NBI' is a national infrastructure supported by the Federal Ministry of Education and Research providing comprehensive, high-quality bioinformatics services to users in life sciences research and biomedicine. The partners organize training events, courses and summer schools on tools, standards and compute services provided by de.NBI to assist researchers to more effectively exploit their data.


Key concepts of stoichiometric and kinetic modeling of biochemical networks:
- stoichiometric matrix and stoichiometric networks
- steady state flux distributions
- principles of constraint-based modeling
- metabolic flux analysis and flux optimization (flux balance analysis)
- metabolic pathway analysis with elementary flux modes
- metabolic network design via minimal cut sets
- simulation of dynamic (kinetic) models
- sensitivity analysis
- carrying out parameter estimation tasks
- model exchange using SBML

Data and model management:
- manual/programmatic access to reaction kinetics data from SABIO-RK
- storage and exchange of data and models using FAIRDOM Hub/SEEK
- modeling specific functionalities in FAIRDOM Hub/SEEK

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 principles of stoichiometric and constraint-based modeling coupled with hands on exercises using CellNetAnalyzer. The second day continues with kinetic modeling techniques which will be illustrated and exercised with COPASI. The third day SABIO-RK is used as a resource for kinetic data and FAIRDOM Hub/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.