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

Date:
21. - 23 September 2020

Location:
MPI Magdeburg
Sandtorstrasse 1
39106 Magdeburg

or online

Contents:
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 FAIRDOMHub/SEEK
- modeling specific functionalities in FAIRDOMHub/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 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 second day introduces principles of stoichiometric and constraint-based modeling coupled with hands on exercises using CellNetAnalyzer. The third day continues with kinetic modeling techniques which will be illustrated and exercised with COPASI

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.

Prerequisites:
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.

Keywords:
CellNetAnalyzer (CNA), COPASI, SBML, FAIR, modeling, kinetic data access, database, data and model management

Tools:
CellNetAnalyzer, COPASI, Matlab, SABIO-RK, FAIRDOMHub/SEEK