predict all secreted metabolites under 20 Rhodo+ Azo- biolog conditions and intersect with Azo+ biolog conditions

PNNL-CompBio / CONCERTO

Continuous integration and validation for genome-scale metabolic model consortia

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predict all secreted metabolites under 20 Rhodo+ Azo- biolog conditions and intersect with Azo+ biolog conditions #96

Closed djinnome closed 1 year ago

djinnome commented 1 year ago

From @JamesPino :

Out of the 20, RT can grow on EX_gly_e, which then exports EX_inost_e, that AV can grow on. This is using minimal media without carbon, same media used for biolog tests.

djinnome commented 1 year ago

According to the actual data,

Rhodo can consume xylose
Azo cannot consume xylose
Rhodo can secrete gluconate
Azo can consume gluconate

If our model cannot reproduce this effect, then the question is: why not?

Is it the case that Rhodo cannot consume xylose?
Or does Rhodo not secrete gluconate?
Or does Azo not consume gluconate?

djinnome commented 1 year ago

PR for this is on Consortium models: https://github.com/PNNL-CompBio/ConsortiumModels/pull/1