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PROGRAM
Last Update
13.02.2018

The course poster (version 13.02.2018) can be downloaded HERE in pdf format.

The program (version 13.02.2018) can be downloaded HERE in pdf format.

 

COPASI (Complex Pathway Simulator) is the main topic of the BioModelling Spring Riga in 2018. The  first COPASI version is published in 2006. The peculiarity of COPASI is the graphical user interface that enables modelling without programming skills. That is important while building interaction between biologists and mathematicians. Another important aspect is that COPASI is free of charge for academic use and needs no other software product to be run.  The named aspects and some more ones have helped COPASI to become a popular tool for modelling as well as education. COPASI has also developed community and support.  COPASI has been also the first software used by Computational Systems Biology Group, the organiser of BioModeling Spring Riga.

This modelling course is dedicated to the introduction in COPASI as well as showing a number of advanced options that can be demonstrated by interesting use cases. Course topics include:

- basic introduction in kinetic modeling

- global stochastic optimization methods in parameter estimation and optimisation

- total optimization potential (TOP) approach

- introduction of constraints in parameter estimation and optimization tasks

- sample COPASI models of metabolism, signaling, pharmacokinetics

 

LECTURERS

Dr. Jürgen Pahle (COPASI developer),

-       Center for Modelling and Simulation in the Biosciences (BIOMS)

-       Center for Quantitative Analysis of Molecular and Cellular Biosystems (BioQuant)
Heidelberg University, Germany 

Prof. Egils Stalidzans (COPASI user),

-        Institute of Microbiology and BiotechnologyUniversity of Latvia, Latvia

-        Latvian Biomedical Research and Study Centre, Latvia

 

PROGRAM 

Day 1  (May 15, 2018)

COPASI intro

9:00-10:30 Development of COPASI model, time course (Pahle)

10:30-11:00 Coffee break

11:00-12:30 Stochastic simulation (Pahle)

12:30-14:00 Lunch

14:00-15:30 Parameter estimation of COPASI model (Stalidzans)

15:30-16:00 Coffee break

16:00-17:30 Optimization of COPASI model (Stalidzans)

 

Day 2  (May 16, 2018)

COPASI advanced options

9:00-10:30 Parameter estimation (Stalidzans)

-       parallel optimization runs;

-       several experiments with different conditions.

10:30-11:00 Coffee break

11:00-12:30 Parameter estimation (Stalidzans)

-       parameter identifiability analysis;

-       total optimization potential (TOP) approach with Space Scanner.

12:30-14:00 Lunch

14:00-15:30 COPASI R Connector (Pahle)

15:30-16:00 Coffee break

16:00-17:30 Discussion: Success stories of modelling (Pahle and Stalidzans)

 

Day 3 (May 17, 2018)

Versatility of kinetic modeling applications on COPASI

 

9:00-10:30 Optimization (Stalidzans)

-       convergence properties of global stochastic optimization methods in larger models;

-       application of parallel optimization runs.

10:30-11:00 Coffee break

11:00-12:30 Optimization (Stalidzans)

-       total enzyme activity constraint;

-       metabolite concentration (homeostatic) constraint.

12:30-14:00 Lunch

14:00-15:30 Models of metabolism (Stalidzans)

15:30-16:00 Coffee break

16:00-17:30  Models of pharmacokinetics, models of signaling (Stalidzans)