COPASI Modelling and Simulation Workshop in Manchester, June 14-16, 2011

mendes: 2011-03-28 09:03:00 +0000

The MCISB announces a COPASI User Workshop for the summer 2011. The 3 day Modeling and Simulation in Systems Biology course will be offered at the MIB, University of Manchester, UK.

This is the first of two 3-day workshops to take place in the Summer (watch out for the announcement of the second one in the USA)

'’Modelling and Simulation in Systems Biology’‘
June 14 - 16, 2011 at Manchester Interdisciplinary Biocentre, Manchester, UK
Led by Pedro Mendes and Juergen Pahle
free registration

This workshop is for current or prospective users of the COPASI modeling and simulation package for system biology. The workshop will take place in the UK (there will be another one in the USA in July).

The workshop is directed both at beginners as well as advanced users and there will be sessions directed at each of these groups (in parallel if needed). The workshop will also be an important means for the COPASI development team to collect feedback from users about improving the software.

COPASI is a free, open-source, software package for creating and simulating systems biology models. COPASI runs on Windows, Mac, and Linux 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

The workshop will cover several features of modeling and simulation by using examples of previously published models. The set of topics covered:

  • 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 sensitivity 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 work flows, 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.

Details about registration and travel for this workshop can be obtained at the web page:

This workshop is sponsored by the Manchester Centre for Integrative Systems Biology with funding from the BBSRC and EPSRC.