How to build a metabolic map from an SBML file?

[Sudipta Dash]

Hi!

I am new to Cobrapy. I have an SBML file (BiGG: iJN1463) with more than 1000 reactions, but the metabolic map has not been drawn previously. Is there a way I can create a 2D network map with the file?

I have tried using Escher, but there I have to manually draw networks for each reaction separately and hence not feasible for the type of model I am working on.

Thanks,

-Sudipta

[Moritz Beber]

Hi Sudipta,

Creating well laid out maps for metabolic networks is indeed a big pain point in this field. There are a couple of approaches:

• Since iJN1463 uses BiGG identifiers, you can try the existing Escher maps for E. coli, for example, and see if most of the reactions on those maps match your model. Take a look here https://github.com/SBRG/escher-maps
• An alternative are automatic layout tools that can work with the entire network at once but often create unfavourable layouts. Some tools are:
• https://www2.mpi-magdeburg.mpg.de/projects/cna/cna.html
• https://fluxer.umbc.edu/tutorial
• https://doi.org/10.1186/s12859-019-2779-4
• You can also bite the bullet and design your own map. I recommend adjust existing Escher maps or you can try https://sammipy.readthedocs.io/ which was made for this purpose.

Hope that helps,

Moritz

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