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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

djinnome opened this issue · comments

commented

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.

commented

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?
commented

PR for this is on Consortium models: PNNL-CompBio/ConsortiumModels#1