Program

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 Biotechnology, University 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 and optimization of COPASI model (Stalidzans)

15:30-16:00 Coffee break

16:00-17:30 Collective building of “surprise” model (coordinated by Stalidzans)

 

Day 2  (May 16, 2018)

COPASI advanced options

 

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

10:30-11:00 Coffee break

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

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 modelling applications on COPASI

 

9:00-10:30 Optimization (Stalidzans)

10:30-11:00 Coffee break

11:00-12:30 Optimization (Stalidzans)

12:30-14:00 Lunch

14:00-15:30 COPASI applications (Stalidzans)

15:30-16:00 Coffee break

16:00-17:30 Multiscale modelling (Stalidzans)