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Events | Past Events | COPASI User Workshop Manchester September 2013

COPASI User Workshop Manchester September 2013

University of Manchester, September 9-11, 2013


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.


The workshop will start at 10:00 on Monday September 9, and will end at 17:00 Wednesday September 11.

Sept 9
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 analysisKieran Smallbone
15:00-15:20Coffee break
15:20-17:00Scanning and sampling parameters, slidersJuergen Pahle
Sept 10
09:00-10:20OptimizationPedro Mendes
10:20-10:40Coffee break
10:40-12:30Optimization & Parameter estimationPedro Mendes
13:30-15:00Parameter estimationPedro Mendes
15:00-15:20Coffee break
15:20-17:00Stochastic and hybrid simulationsJuergen Pahle
Sept 11
09:00-10:30advanced modelling & analysis: bifurcation analysis, linear noise approx.Pedro Mendes & Juergen Pahle
10:30-10:50Coffee break
10:50-12:30Advanced modelling and analysis (cont.)Pedro Mendes
13:30-14:15User feedback sessionPedro Mendes
14:15-15:00Command line, Web services, API, CondorJoseph Dada
15:00-15:30Coffee break
15:30-17:00Open session/applicationsvarious


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


September 9-11, 2013


School of Computer Science
University of Manchester
Kilburn Building
Oxford Road
Manchester M13 9PL
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:

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 BBSRC for sponsoring this workshop through grant BB/J019259.