pairwise interaction model setting constraints to simulate media

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Sofi Z

Feb 1, 2023, 11:11:22 AMFeb 1
to COBRA Toolbox

Dear Community,


I have a pairwise interaction model with two species. In addition to the exchange reaction IDs from the original SBML file, exchange reactions of those same extracellular metabolites are included beginning with an EX and ending with an [u] such as 'EX_s_4204[u]’. If I understood correctly, the latter exchange reaction type is the flux available from the shared environment/media? 

However, for shared extracellular metabolites (that have the same IDs in both models) there are two media exchange reactions as such: ‘EX_s_4204[u]’ and ‘EX_s_4204[u][u]’, for each of the species respectively.  

Is there a way to only have one media exchange reaction for the whole community and not for each species part of the community? 


Best wishes,



Almut Heinken

Feb 2, 2023, 8:08:44 AMFeb 2
Hi Sophie,
the community exchange reactions are formulated based on the metabolites.You have to be careful what the metabolites in each model are exactly called after changing the namespaces.
Best regards,


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Sofi Z

Feb 7, 2023, 11:05:12 AMFeb 7
to COBRA Toolbox
Dear Almut,

thank you for the response.

Best wishes,


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