working on cobrapy mat import

[Uri David Akavia]

Hi

I've been working on cobrapy mat import/export, and I have some questions about the model format.

osense - what values are allowed? Does -1 mean "min" or "max" for objective direction?

What database/website does metSMILES refer to? I understand it is SMILES, but is there a link where I can find the SMILES database?

what do metPdMap, metSBOTerm refer to? I thought that SBOTerm is about processes.

Thank you,

Uri David

[Ronan M.T. Fleming]

Hi Uri,

SMILES are database independent
https://en.wikipedia.org/wiki/Simplified_molecular-input_line-entry_system
https://github.com/EBI-BioModels/SBO
See also
https://github.com/opencobra/cobratoolbox/blob/master/docs/source/notes/COBRAModelFields.md

metPdMap is nonstandard, you can ignore it.

Regards,

Ronan

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Mr. Ronan MT Fleming B.V.M.S. Dip. Math. Ph.D.
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[Uri David Akavia]

Thanks Ronan.

What about osense? I've tried importing Recon3D_301.mat into cobrapy, and it has osense, not osenseStr. So I'm wondering what that means.

Thank you,

Uri David

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[Ronan M.T. Fleming]

https://github.com/opencobra/cobratoolbox/blob/master/src/base/solvers/solveCobraLP.m

On Thu, 31 Mar 2022 at 20:06, Uri David Akavia

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[Uri David Akavia]

Thank you.

One question about groups - it seems like groups are stored as subSystems, and cobra doesn't make distinction between groups and subsystems. Is that correct? Does this mean that only reactions have groups?

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[Thomas Pfau]

Hi Uri David,

Yes, at the moment only subSystems are mapped to groups in sbml files. No other groups have been implemented in the COBRA Toolbox model structure (for all I know at least).
This file:
https://github.com/opencobra/cobratoolbox/blob/master/docs/source/notes/COBRAModelFields.md
should contain most field information

And this file:
https://github.com/opencobra/cobratoolbox/blob/master/src/base/io/definitions/COBRA_structure_fields.tab
Should contain all computational definitions on how fields have to look.
There are of course models around that have additional fields but for those fields there is no clear definition (at least none specified in the toolbox).

This function:

https://github.com/opencobra/cobratoolbox/blob/master/src/base/io/utilities/generateFieldDescriptionFile.m

creates the description file from the definition file and thus, if used as intended the above two files should be in sync.

I hope this helps

Thomas

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[Uri David Akavia]

Hi Thomas and Ronan,

Thank you for all your help.

I was wondering if you could help me get a test model. I was thinking about Recon3, since it has most of the fields. If you can trim it down to less metabolites, reactions, genes, so it would be easy to have it be part of the cobrapy test suite without being too large, that would be great.

I'm thinking around 100KB gzipped compressed if that is possible.

Also, if you can do that, can you please export it as SBML from cobratoolbox? I'll compare the mat and the SBML to make sure they are both read correctly.

Thank you so much

Yours,

Uri David

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[Uri David Akavia]

Actually,  never mind. I'l use the models in COBRA.models if that's okay with you. 

[Ronan M.T. Fleming]

Hi Uri,
yes, perfect, because COBRA.models was designed to share models for
code testing purposes, rather than a means of model dissemination.
Regards,
Ronan

On Tue, 12 Apr 2022 at 14:20, Uri David Akavia

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[Uri David Akavia]

Hi Ronan,

Can you please do me a quick favor?

I've been trying to import Recon2.v04.mat into cobrapy, and I'm having some issues. I'm not sure if it is my code or the original .mat file. Can you please tell me what the grRules and rules field is for reaction H2CO3D?

That one is tripping up my cobrapy code. I want to see what it is in cobratoolbox.

I'd check it myself, but I no longer have access to MATLAB.

Thank you,

Uri David

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[Ronan M.T. Fleming]

Hi Uri,
see the "Associated human genes" section of:
https://www.vmh.life/#reaction/H2CO3D
Regards,
Ronan

On Sat, 16 Apr 2022 at 19:48, Uri David Akavia

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