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. Registration includes free lunch and refreshments on all three days.
Agenda
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.
Time
Activity
Leader
May 5
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
Ettore Murabito
15:00-15:20
Coffee break
15:20-17:00
Scanning and sampling parameters, sliders
Ettore Murabito
May 6
09:00-10:20
Stochastic simulation 1
Juergen Pahle
10:20-10:40
Coffee break
10:40-12:30
Stochastic simulation 2 & linear noise approx.
Juergen Pahle
12:30-13:30
Lunch
13:30-15:00
Optimization
Pedro Mendes
15:00-15:20
Coffee break
15:20-17:00
Parameter estimation
Pedro Mendes
May 7
09:00-10:30
advanced modelling & analysis: events
Pedro Mendes
10:30-10:50
Coffee break
10:50-12:30
Advanced modelling and analysis: bifurcation analysis
Pedro Mendes
12:30-13:30
Lunch
13:30-14:15
User feedback session
all
14:15-15:00
COPASI for programmers
Pedro Mendes
15:00-15:30
Coffee break
15:30-17:00
"Bring your own models": modelling clinic
Pedro Mendes
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.
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:
