Outline:
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.
Registration:
The registration is free. To register please visit the
registration page.
Agenda
The workshop will start at 10:00 on Monday January 21, and will end at 16:30 Wednesday January 23.
| Time | Room | Activity | Leader |
| Jan 21 | | | |
| 10:00-10:30 | Café | Welcome and coffee | |
| 10:30-12:30 | LG.010 | Introduction to modelling and COPASI | Pedro Mendes |
| 12:30-13:30 | Café | Lunch | |
| 13:30-15:00 | LG.010 | Time course simulation, SBML, plots, reports | Frank Bergmann |
| 15:00-15:20 | Café | Coffee break | |
| 15:20-17:00 | LG.010 | Steady state analysis, MCA, sensitivity analysis | Kieran Smallbone |
| Jan 22 | | | |
| 09:00-10:20 | LG.010 | Scanning and sampling parameters | Pedro Mendes |
| 10:20-10:40 | Café | Coffee break | |
| 10:40-12:30 | LG.010 | Optimization | Pedro Mendes |
| 12:30-13:30 | Café | Lunch | |
| 13:30-15:00 | LG.010 | Parameter estimation 1 | Pedro Mendes |
| 15:00-15:20 | Café | Coffee break | |
| 15:20-17:00 | LG.010 | Parameter estimation 2 | Pedro Mendes |
| Jan 23 | | | |
| 09:00-10:30 | LG.010 | Stochastic and hybrid simulations | Juergen Pahle |
| 10:30-10:50 | Café | Coffee break | |
| 10:50-12:30 | LG.010 | Command line, Condor, Web services | Pedro Mendes |
| 12:30-13:30 | Café | Lunch | |
| 13:30-14:15 | LG.010 | User feedback session | Pedro Mendes |
| 14:15-15:00 | LG.010 | Open session | Pedro Mendes |
| 15:00-15:30 | Café | Coffee break | |
| 15:30-16:30 | Lecture Theatre | Seminar: Identification and control in computational systems biology | Julio Banga, CSIC Vigo |
| 16:30 | Farewell | | |
Audience:
The primary target for this workshop are current and prospective users of COPASI as a modeling tool. Prior knowledge of COPASI is not required.
Date:
January 21-23, 2013
Location:
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.
Contact
If you need further information or have any question please contact us by .
Sponsorship
We are grateful to the
BioPreDyn project for sponsoring this workshop.
