iMAT+MTA functions on Python

[RolandLendsley]

is the iMAT (https://github.com/opencobra/cobratoolbox/blob/6c1ba69dfd7adbf121a3b987a3446b3d7fdc15ed/src/dataIntegration/transcriptomics/iMAT/iMAT.m) and MTA algorithm from cobratoolbox(matlab) available on cobrapy too?

If not, would you think about implementing it soon on cobrapy?
If that's not the case, could you provide a swift alternative to run iMAT/MAT within a Python based project?

Thank you,
Roland

[cdiener]

Most of the metabolic reconstruction algorithms were slated to be added to driven. However, that has been stalled since nobody wanted to pick this up. There is an implementation of iMAT in there but I would not bet that it still works (last updated several years ago). There are sone actively maintained alternatives on https://opencobra.github.io/cobrapy/tags/reconstruction/ you could check out.

[RolandLendsley]

Dear Christian, thank you very much,

I found iMAT but no MTA or rMTA in Cobrapy, am I missing something out here?

Since they should be used in conjuction in my case, then I would be still directed into using matlab because one of those two runs on matlab only

Let me know, thank you,
Roland

[cdiener]

Not sure what exactly you mean by MTA since there are several algorithms with that acronym. If you mean the metabolic transformation algorithm, no, there is no implementation in cobrapy I am aware of 😢 Though it should not be too hard to write a package that implements them if you would like to take a stab at it. Optlang helps quite a bit.

[y1zhou]

Late to the discussion, but it seems several more algorithms were implemented in the driven devel branch.