Proteimics integration

[Nicolas Mendoza Mejia]

Dear all,

I am interested in integrating transcriptomics and proteomics into a generic model. And by looking at the documentation, transcriptomic data integration is supported.

But, I have not been able to find anything about proteomics integration, even thought, there are some algorithms already implemented inside COBRA that support both transcriptomic and proteomic data integration, such as iMAT and MBA.

Any help will be truly appreciated.

[dtm.van...@gmail.com]

Dear Nicolas,

Maybe you mixed up COBRApy and the COBRA Toolbox (which is a Matlab Toolbox and can be found here).

If you prefer to work in python, reframed has GIMME, MARGE and eFlux coded. And there is also troppo which has multiple methods coded in.

Hope this sets you on the right track,

Dennis

[Neha Rohatgi]

Hi All, 

Has anyone tried using troppo to integrate expression data with RECON3 to generate a specific model?
I have downloaded the code and data from github but I am not able to reproduce this. I have used FASTCORE in MATLAB with cobra toolbox but am new to python so any help would be great. 

Thanks!

Neha 

[Stephen Chapman]

Great stuff regarding reframed, I soon hope to be using eFLux, I can't find any tutorial however, any pointers?

[Moritz Beber]

If you are feeling adventurous, there is also the development version of driven

https://github.com/opencobra/driven

but it hasn't been developed in some time. So there be dragons!

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[ch.d...@gmail.com]

And there are a few packages at https://opencobra.github.io/cobrapy/tags/reconstruction/ as well...