University of Manchester, September 9-11, 2013
Outline:
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.
Registration:
The registration is free. To register please visit the
registration page.
Agenda
The workshop will start at 10:00 on Monday September 9, and will end at 17:00 Wednesday September 11.
| Time | Activity | Leader |
| Sept 9 | | |
| 10:00-10:30 | Welcome and coffee | |
| 10:30-12:30 | Introduction to modelling with COPASI (time course) | Pedro Mendes |
| 12:30-13:30 | Lunch | |
| 13:30-15:00 | Steady state analysis, MCA, sensitivity analysis | Kieran Smallbone |
| 15:00-15:20 | Coffee break | |
| 15:20-17:00 | Scanning and sampling parameters, sliders | Juergen Pahle |
| Sept 10 | | |
| 09:00-10:20 | Optimization | Pedro Mendes |
| 10:20-10:40 | Coffee break | |
| 10:40-12:30 | Optimization & Parameter estimation | Pedro Mendes |
| 12:30-13:30 | Lunch | |
| 13:30-15:00 | Parameter estimation | Pedro Mendes |
| 15:00-15:20 | Coffee break | |
| 15:20-17:00 | Stochastic and hybrid simulations | Juergen Pahle |
| Sept 11 | | |
| 09:00-10:30 | advanced modelling & analysis: bifurcation analysis, linear noise approx. | Pedro Mendes & Juergen Pahle |
| 10:30-10:50 | Coffee break | |
| 10:50-12:30 | Advanced modelling and analysis (cont.) | Pedro Mendes |
| 12:30-13:30 | Lunch | |
| 13:30-14:15 | User feedback session | Pedro Mendes |
| 14:15-15:00 | Command line, Web services, API, Condor | Joseph Dada |
| 15:00-15:30 | Coffee break | |
| 15:30-17:00 | Open session/applications | various |
| 17:00 | 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:
September 9-11, 2013
Location:
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.
Contact
If you need further information or have any question please contact us by .
Sponsorship
We are grateful to the
BBSRC for sponsoring this workshop through grant BB/J019259.
