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
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
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
- 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
- carry out many simulations at different parameter values;
- random sampling of parameter values, and
- 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