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Manchester Centre for Integrative Systems Biology

Workshop on Modelling and Simulation using COPASI


Manchester Centre for Integrative Systems Biology, 28-30 July 2009

A hands-on workshop designed to teach modelling and simulation of biochemical networks using the software COPASI and the SBML language. The Workshop is directed both at beginners as well as advanced users and there will be sessions directed at each of these groups. The workshop will also be an important means for the COPASI development team to collect feedback from users to improve the software.

This workshop is sponsored by the Manchester Centre for Integrative Systems Biology which is funded by the BBSRC and EPSRC.

Participation in this workshop is free but registration is mandatory. To register please click . Travel and lodging arrangements must be made by the participants, useful information found at the bottom of this page.

The programme of the workshop will cover several aspects of modelling and simulation by using models previously published and retrieved from the Biomodels model database. The topics covered are:

  • Basic Modeling and Simulation - How to create biochemical kinetic models, and find out their dynamic behavior and steady-state properties.
  • Stochastic Simulation - COPASI's capabilities for running Gillespie's algorithm, as well as for automatically converting ODE-based models to the stochastic representation.
  • Sensitivity Analysis - Study of the importance of parameters in determining the values of model variables. This includes local as well as global sentivity analysis.
  • Parameter Scans - How to easily program COPASI to 1) carry out many simulations at different parameter values; 2) random sampling of parameter values, and 3) determine distributions in stochastic models.
  • Optimization - How to use numerical optimization methods to explore the properties of large and complex models. This includes the use of optimization in strategies for metabolic engineering.
  • Parameter Estimation - How to use experimental data to calibrate models to represent real biological systems accurately. This includes analysis of enzyme kinetic experiments, and in vivo time courses of cell biology experiments, among other applications.
  • Data Visualization and Reports - COPASI has a flexible means of defining customized reports and plots, including trajectories, phase planes, and histograms.
  • Batch Processing - An advanced feature of COPASI is that it can be run unattended from a command line, which allows for the creation of complex workflows, including batch processing and parallel execution in clusters or Condor pools.
  • Integration with other Software Packages - How to use COPASI together with other applications that support SBML (e.g. Biomodels database, CellDesigner and SBW)
  • Web Services - How to access COPASI functionality in other software through using the web services technology.

The workshop will be led by Prof. Pedro Mendes, Dr. Juergen Pahle and others (TBA).

COPASI is a free, open-source, software package for creating and simulating systems biology models. COPASI runs on Windows, Mac, Linux and Solaris and it is a user-friendly software that allows for construction of kinetic models without much knowledge of mathematics. However COPASI is also equipped with advanced algorithms and is a powerful tool for modeling and simulation, with some features that are not available in other simulators. COPASI is available at http://www.copasi.org.

Travel Information. The workshop will take place in the Manchester Integrative Biocentre (MIB) building, 131 Princess St., Manchester M1 7DN. Nearby hotels are featured in this Google map; the IBIS and the Manchester Conference Centre (Days Hotel) are the nearest. The MIB is about a 5 minute walk from Manchester Piccadilly train station. Manchester is served by an International Airport with easy rail connections to Piccadilly train station (15 minutes journey).