ICSB2024 Copasi Tutorial

COPASI – The Complex Pathway Simulator

Copasi logo

COPASI website: https://www.copasi.org
There, you can download COPASI, find documentation and examples and our COPASI user forum.

If you use COPASI, please cite:
S. Hoops, S. Sahle, R. Gauges, C. Lee, J. Pahle, N. Simus, M. Singhal, L. Xu, P. Mendes and U. Kummer (2006)
COPASI – a COmplex PAthway SImulator.
Bioinformatics 22(24):3067, doi:10.1093/bioinformatics/btl485

We will be using one of the example models provided by Copasi:
File → Examples → COPASI Files → CircadianClock.cps

Parameter Estimation

Additional example:

CoRC – The COPASI R Connector

You can find much more information on CoRC at https://jpahle.github.io/CoRC. There, we provide installation instructions, documentation and many examples. CoRC is free and open source and the code is available as a github repository at https://github.com/jpahle/CoRC.

If you use CoRC, please cite our publication:
J. Förster, F.T. Bergmann and J. Pahle (2021)
CoRC: the COPASI R Connector.
Bioinformatics 37(17):2778-2779, doi:10.1093/bioinformatics/btab033

In case you are interested in creating dynamic publication media with RMarkdown, Shiny and/or Jupyter, we provide many practical examples for that at

https://jpahle.github.io/DynamiCoRC/

and our publication:
J.C.J. Daas, J.D. Förster and J. Pahle (2022)
Dynamic Publication Media with the COPASI R Connector (CoRC)
Mathematical Biosciences 348:108822, doi:10.1016/j.mbs.2022.108822

We recommend you install RStudio, which provides a comfortable graphical user interface for R with support for plotting, package management, git, etc.
The basic version is free and open source.

ICSB 2024 COPASI tutorial files: