Workshops und Schulungen

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

9. bis 11. August 2022
9:30 bis 17 Uhr

SR42, BioQUANT, Heidelberg

Veranstaltet von

Vortragende Person/Vortragende Personen:

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 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.

Tools for Systems biology modeling and data exchange: COPASI, CellNetAnalyzer, SABIO-RK, FAIRDOMHub/SEEK 2022

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

More information and registration