Combinatorial expansion functionality in COPASI

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Roma Smirnov

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Oct 13, 2022, 3:21:53 PM10/13/22
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Dear colleges, 

I'm wondering, is it possible to write few reactions and expand it up to full possible combinations of reactants? In other words, can I write implicitly reactions such that the COPASI autocompleted another part of a reaction scheme?

Let's say, I would like to explicitly write only 6 reaction highlighted in a red and based on them restore all others (fig.1). Will it be possible in COPASI?

I will be grateful for your help!
Roma
full reaction scheme.png

Roma Smirnov

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Oct 13, 2022, 3:25:33 PM10/13/22
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Colleagues* (I apologize for the mistake)

Frank Bergmann

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Oct 13, 2022, 4:42:23 PM10/13/22
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Hello Roma, 

the COPASI graphical user interface will not infer any reactions. What you could do is to script model creation using either


that would make it easy to create such networks. 

let us know if you need more help with either frameworks. 

best
Frank

Roma Smirnov

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Oct 15, 2022, 9:46:10 AM10/15/22
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Hello Frank!

Sorry for the late answer. I have tried to find some guide/examples concerning an expanding of a model among these two tools, but have found nothing. Do I have to make an expanded model from scratch somehow? Hope, there is a manual about it. Otherwise, I guess it won't be so easy, considering that I need to learn and get used to the script-based interface.

Regards,
Roma 

Frank Bergmann

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Oct 15, 2022, 10:22:34 AM10/15/22
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Hello Roma, 

if you look for a ready solution, you would have to look at BNGL[1] or PySB[2]. They define rules and patterns and out of those generate the full SBML model (which you then could import in COPASI). With the scripting languages i mentioned, you'd manually encode the construction of the full model with loops and `add_reaction` calls and the like[3]. 

best
Frank

Roma Smirnov

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Oct 15, 2022, 11:09:55 AM10/15/22
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Thank you, for such a fast and clear answer! I'll try to use tools with a ready solution, which you recommended.

Wish you all the best,
Roma

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Roma Smirnov

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Oct 16, 2022, 1:47:00 PM10/16/22
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Hello, Frank!

I have searched some ways to export SBML from BNGL format, but found only one answer in a FAQ section of VCell[1, fig.1]. However, by some reasons, it didn't work for me. Do you know some alternative approaches concerning BNGL to SBML conversion? Or maybe you can point out possible reasons of this problem?

Regards,
Roma

[1]: http://vcell.org/bionetgen/faq.html
fig.1.png

Frank Bergmann

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Oct 16, 2022, 2:46:50 PM10/16/22
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hello Roma, 

i'm afraid i have not used either BNGL nor PySB. I vaguely recall that there was a command line tool that would convert their native language to SBML. But I have not used it myself. Maybe others on the list know. Otherwise, it might be a good idea to ask them directly. 

best
Frank

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Roma Smirnov

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Oct 16, 2022, 3:35:21 PM10/16/22
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Thanks for the advice! I have asked Bionetgen group, and I'm waiting for an answer. If I get something useful in this regard, I will share with you.


Best wishes,
Roma

Roma Smirnov

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Oct 16, 2022, 4:03:16 PM10/16/22
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I figured out the problem: I have to paste 'writeSBML({})' command after the model generation function (e.g., generate_network) in BNGL script. Anyway, I'm glad that it's possible to do!
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