The COPASI team announces the User Workshop for the summer 2012. The 3 day Modeling and Simulation in Systems Biology course will be offered at VBI, Blacksburg, USA

Modelling and Simulation in Systems Biology

July 30 - August 1, 2012 at Virginia Bioinformatics Institute, Blacksburg, VA, USA
http://www.copasi.org/UserWorkshop2012
Led by Pedro Mendes and Stefan Hoops

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 USA. It is sponsored by the MIEP project led by Josep Bassaganya-Riera.

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 http://www.copasi.org

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 of this workshop can be obtained at the web page: http://www.copasi.org/UserWorkshop2012 (small registration fee (includes lodging) and possibility of getting financial support)