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Events | Past Events | COPASI User Workshop Manchester May, 2015

COPASI User Workshop Manchester May, 2015

University of Manchester, UK, May 5-7, 2015


This workshop 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: using events for monitoring simulation progression, bifurcation analysis, using COPASI on distributed computing, and web services.


The registration is free. To register please visit the registration page. Registration includes free lunch and refreshments on all three days.


The workshop will start at 10:00 on Tuesday May 5, and will end at 17:00 Thursday May 7. The topics on the agenda below can be adapted according to the needs of the participants.

May 5
10:00-10:30Welcome and coffee
10:30-12:30Introduction to modelling with COPASI (time course)Pedro Mendes
13:30-15:00Steady state analysis, MCA, sensitivity analysisEttore Murabito
15:00-15:20Coffee break
15:20-17:00Scanning and sampling parameters, slidersEttore Murabito
May 6
09:00-10:20Stochastic simulation 1Juergen Pahle
10:20-10:40Coffee break
10:40-12:30Stochastic simulation 2 & linear noise approx.Juergen Pahle
13:30-15:00OptimizationPedro Mendes
15:00-15:20Coffee break
15:20-17:00Parameter estimationPedro Mendes
May 7
09:00-10:30advanced modelling & analysis: eventsPedro Mendes
10:30-10:50Coffee break
10:50-12:30Advanced modelling and analysis: bifurcation analysisPedro Mendes
13:30-14:15User feedback sessionall
14:15-15:00COPASI for programmersPedro Mendes
15:00-15:30Coffee break
15:30-17:00"Bring your own models": modelling clinic Pedro Mendes


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


May 5-7, 2015


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

Google Maps view of location

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 or Manchester Oxford Road train stations.

Nearby hotels to the location of the workshop are:

Other hotels not too far (less than 10 min walk):
Google Maps view of location, hotels and train stations

Course Size:

The number of participants is limited to 20.

Computer Equipment:

Participants should bring their own laptops for which network access will be provided.


If you need further information or have any question please contact us at:


We are grateful to the BBSRC for sponsoring this workshop through grant BB/J019259.