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PNNL-CompBio / CONCERTO

Continuous integration and validation for genome-scale metabolic model consortia
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Convert Pavlo's cyano-rhodo data to binary consortia unit tests #84

Open djinnome opened 1 year ago

djinnome commented 1 year ago

Previously we used Pavlo's cyano-rhodo data to check whether metabolite excretion and import was possible for each individual organism. Now we want to use the data to test for metabolic exchange between two organisms.

The unit tests would be as follows:

  1. If it there is evidence that metabolite X is exchanged from organism A to B, then check whether a flux exists from A to B for metabolite X.

  2. If there is only evidence that metabolite X is in the media, then check whether organism A OR organism B can excrete that metabolite.

JamesPino commented 1 year ago

Working on generating binary models (in https://github.com/PNNL-CompBio/ConsortiumModels/issues/2) to have them updated. Currently generated manually with older models. Should be streamlined right when this is done.