Multiline INI file issue

[Alexandre de Assis Bento Lima]

Hello, everybody.

I am trying with no success to use "CopasiSE --reparameterize" with a multiline .ini file. Copasi reads only the file's first line, ignoring the other ones. I am using the same species' names Copasi itself generatres with --exportIni. Could anyone give me some help?

Thanks in advance!

Best,

Alexandre.

[Frank Bergmann]

Could you send me an example model  / ini file? Then i'd be able to better analyze the issue here. 

thank you

Frank

[Frank Bergmann]

I've had another look at this, as it turns out, the reparameterize option currently only changes initial compartment volumes, initial particle numbers, initial values of global parameters and local reaction parameters. 

We'll fix it for the next version, so that initial concentrations can be set as well. 

best

Frank

[Alexandre de Assis Bento Lima]

Thanks for your answer. We'll wait for the next version.

Please, allow me to make a remark: if we define an initial species concentration in the first line of the INI file, COPASI reads and uses it, ignoring the remaining lines. We are working on a simpler model that illustrates this behavior and will soon send it to you.

Best

Alexandre.

[Alexandre de Assis Bento Lima]

Hi!

Here it goes a toy model to illustrate this issue. Three files are attached to this post: one model file (Modelo.cps) and two INI files. When COPASI runs the model, a file named "output" is produced by its "Time Course" task. The model has 3 species: A, B and C, with their initial concentrations set to 1. The "output" file has 3 columns: time, A, B and C.

When I run

CopasiSE --reparameterize params_1.ini Modelo.cps

the value for A in the first line of the report file is 20, while B and C remain unchanged (=1). The first line in params_1.ini specifies a new value for A (=20).

On the other hand, the first line in params_2.ini is a new value for B (=30). When I run

CopasiSE --reparameterize params_2.ini Modelo.cps

the value for B initial concentration changes (=30), while A and C remain unchanged (=1).

So, COPASI does get the initial concentration value specified in an INI file for a species. However, it just considers the INI file's first line.

Best Regards,
Alexandre.

[Frank Bergmann]

This is still the same issue, that has since been resolved. We have created a new snapshot of COPASI (4.40.276) that fixes the issue and we hope to release it soon. In the meantime you can get the snapshot from: 

https://drive.google.com/open?id=1hJ60lCXxPM0OTAXrBLfGUuMHIk_CasQk

best

Frank

[Alexandre de Assis Bento Lima]

Thanks a lot, Frank!

I'll give it a try.

Best,

Alexandre

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