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Events | Past Events | COPASI User Workshop Manchester January 2013

COPASI User Workshop Manchester January 2013


This workshop, sponsored by the EU FP7 project BioPreDyn, is aimed at current and prospective users of the COPASI modeling and simulation package for system biology. 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.

The workshop will cover several features of modeling and simulation by using examples of previously published models from the BioModels database . Some of the features highlighted during this hands-on workshop will be:
  • Basic Modeling and Simulation - How to create biochemical kinetic models, and find out their dynamic behavior and steady-state properties.
  • Sensitivity Analysis - Study of the importance of parameters in determining the values of model variables. This includes local as well as global sensitivity analysis.
  • 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.
  • Stochastic Simulation - COPASI's capabilities for running Gillespie's algorithm, as well as for automatically converting ODE-based models to the stochastic representation.
  • Integration with other Software Packages - How to use COPASI together with other applications that support SBML (e.g. Biomodels database, CellDesigner and SBW)
  • Advanced topics – several features such as the command line version, using COPASI on distributed computing, and web services.


The registration is free. To register please visit the registration page.


The workshop will start at 10:00 on Monday January 21, and will end at 16:30 Wednesday January 23.

Jan 21
10:00-10:30CaféWelcome and coffee
10:30-12:30LG.010Introduction to modelling and COPASIPedro Mendes
13:30-15:00LG.010Time course simulation, SBML, plots, reportsFrank Bergmann
15:00-15:20CaféCoffee break
15:20-17:00LG.010Steady state analysis, MCA, sensitivity analysisKieran Smallbone
Jan 22
09:00-10:20LG.010Scanning and sampling parametersPedro Mendes
10:20-10:40CaféCoffee break
10:40-12:30LG.010OptimizationPedro Mendes
13:30-15:00LG.010Parameter estimation 1Pedro Mendes
15:00-15:20CaféCoffee break
15:20-17:00LG.010Parameter estimation 2Pedro Mendes
Jan 23
09:00-10:30LG.010Stochastic and hybrid simulationsJuergen Pahle
10:30-10:50CaféCoffee break
10:50-12:30LG.010Command line, Condor, Web servicesPedro Mendes
13:30-14:15LG.010User feedback sessionPedro Mendes
14:15-15:00LG.010Open sessionPedro Mendes
15:00-15:30CaféCoffee break
15:30-16:30Lecture TheatreSeminar: Identification and control in computational systems biologyJulio Banga, CSIC Vigo


The primary target for this workshop are current and prospective users of COPASI as a modeling tool. Prior knowledge of COPASI is not required.


January 21-23, 2013


Manchester Institute of Biotechnology
University of Manchester
131 Princess Street
Manchester M1 7DN
United Kingdom

Travel and accommodation:

Each participant will have to organize and pay their own travel and accommodation.
Manchester is served by an International Airport. Train service is to Manchester Piccadilly train station.

Nearby hotels to the location of the workshop are:

Course Size:

The number of participants is limited to 20.

Computer Equipment:

Participants are strongly encouraged to bring their own laptops for which network access will be available.


If you need further information or have any question please contact us by .


We are grateful to the BioPreDyn project for sponsoring this workshop.