Draw the flux of tuberculosis organism with e.coli map

[Agustin Maria Pardo]

Hello,

I am running FBA using a mycobacterium tuberculosis model from BIGG (http://bigg.ucsd.edu/models/iEK1008).

After run FBA I using the e.coli map of the COBRA tutorial (https://opencobra.github.io/cobratoolbox/stable/tutorials/tutorialEcoliCoreModel_part1.html) to map the flux results:

"""

map=readCbMap('ecoli_Textbook_ExportMap.txt')

options.zeroFluxWidth = 0.1;

options.rxnDirMultiplier = 10;

drawFlux(map, model, FBAsolution.x, options); 

"""

I am new in the area and have some questions:

🚩 1) Is there some way to actualize the "ecoli_Textbook_ExportMap.txt" map to tuberculosis reactions/genes? Or anyone knows a map like the e.coli closer to tuberculosis organism pathways/reactions?

🚩 2) Do you think that e.coli draw flux map is a good approximation (biologically speaking) to draw the flux of tuberculosis? Should I take into account other technical aspects?

🚩 3) How I could check if some reactions of tuberculosis have a different id to e.coli map and they could not be drawn because they don't match the id of the map?

🚩 4) Is this (draw the fluxes result) the best way to debug my model an see if is working in the correct biology way? 

Regards

Agustin Pardo

[Ronan M.T. Fleming]

Hi Augustin,

the mapping functionality described in (https://opencobra.github.io/cobratoolbox/stable/tutorials/tutorialEcoliCoreModel_part1.html) is legacy code that is no longer maintained. Instead, there has been substantial effort put into interfacing with cell designer, there are several tutorials under "visualisation" that you could use instead.

https://opencobra.github.io/cobratoolbox/latest/tutorials/index.html

You need a different map than e.coli core to use for tb.

If anyone is interested in writing an interface to use escher https://escher.github.io/#/ please go ahead. It would be a welcome addition.

Regards,

Ronan

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[Agustin Maria Pardo]

Hi Ronan,

Thanks for the answer!

Finally, I export the fluxes of the reactions of the model in .json format and I use Escher(https://escher.github.io/#/) to create the draw! I found some tuberculosis maps in .json format in this paper:  https://bmcsystbiol.biomedcentral.com/articles/10.1186/s12918-018-0557-y

Many Regards

[Agustin Maria Pardo]

Regarding to this:
"""
If anyone is interested in writing an interface to use Escher https://escher.github.io/#/ please go ahead. It would be a welcome addition.

"""

I think that the most difficult/problematic part is to get a "map" in json from the COBRA model to use in Escher.

Regards