Steffen Klamt, Axel von Kamp, Sven Thiele, Ursula Kummer, Frank T. Bergmann (de.NBI-SysBio)
12-SEP-2017 10:00 am – 13-SEP-2017 5:00pm
BioQUANT, Im Neuenheimer Feld 267, 69120 Heidelberg
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
During this 2-day course, attendees will learn basic techniques for modeling of biochemical networks. 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 hands on exercises throughout the two days will ensure that attendees become familiar with the software tools and with analyzing, creating, editing, importing and simulating 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.
CellNetAnalyzer (CNA), COPASI, SBML, Modeling
CellNetAnalyzer, COPASI, Matlab.