Simulating models from command line (or without using the GUI)

[Torkel Loman]

Hello,

I am looking to simulate models using COPASI. I have found instructions for running it from the command line: http://copasi.org/Support/User_Manual/Model_Creation/Commandline_Version_and_Commandline_Options/

These, however, only seem to cover loading models and files. When I look at the simulation options, I see nothing about the command line.

Is there a way to simulate Copasi without using the GUI?

Cheers,

Torkel

[Hoops, Stefan (sh9cq)]

Hello Torkel,

I am sorry that the instructions are not clear enough. All activated
tasks will be processed. In order to activate a task your will have
mark the executable check box of the task you like to run.

Thanks,
Stefan

--
Stefan Hoops, Ph.D.
Research Associate Professor
Biocomplexity Institute & Initiative
University of Virginia
995 Research Park Boulevard
Charlottesville, VA 22911

Phone: +1 540 570 1301
Email: sho...@virginia.edu

[Torkel Loman]

Thanks Stefan

By marking the checkbox, do you mean that I should create a file first in the GUI, where I mark the task, and then run the file from the commandline?

Cheers,

Torkel

[Hoops, Stefan (sh9cq)]

Hello Torkel,

Yes you always have to specify the task's parameters first. You will
also have to define a report so that your results will be captured.

Thanks,
Stefan

[Mendes,Pedro]

Torkel,

the other option you have is to use one of the scripting languages that
we provide support for:

in R there is CoRC https://jpahle.github.io/CoRC/
and in python there is basiCO  https://github.com/copasi/basico

These allow you to specify new models or modify existing models and then
use COPASI to carry out the simulations (they have functions to run the
various tasks of COPASI).

To run the command line version itself, you have to be able to create
and modify the copasi files (.cps). The best way for that, as Stefan
said, is to use the COPASI GUI and save the files with the "execute"
flag on the task you want to run.

Pedro

Pedro Mendes, PhD
Professor and Director,
Richard D. Berlin Center for Cell Analysis and Modeling
University of Connecticut School of Medicine
group website: http://www.comp-sys-bio.org

[Torkel Loman]

Thank both of you, this was very useful, I got it working now.

Torkel