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simulate ternary consortium model to confirm no growth under tested media conditions #3

Open vladpetyuk opened 1 year ago

vladpetyuk commented 1 year ago

we should confirm that azotobacter takes over rhodosporidium

mcnaughtonadm commented 1 year ago

Working Example found: https://github.com/PNNL-CompBio/ConsortiumModels/blob/main/Notebooks/Tertiary_Model.ipynb

mcnaughtonadm commented 1 year ago
Compartments abundance growth_rate reactions metabolites
Azotobacter 0.333333 0.14959 2469 2003
Rhodosporidium 0.333333 0.00000 2398 2051
Synechococcus 0.333333 0.00000 851 768
medium NaN NaN 464 464

In this growth, Synechococcus produces sucrose that is all taken up by Azotobacter

SUCROSE EXPORT FROM SYN

compartment
Azotobacter            NaN
Rhodosporidium         NaN
Synechococcus    -1.457401
medium                 NaN
Name: SUCRt2, dtype: float64

SUCROSE UPTAKE AZOTOBACTER vs RHODOSPORIDIUM

compartment
Azotobacter       1.427503
Rhodosporidium         NaN
Synechococcus          NaN
medium                 NaN
Name: SUCRtex, dtype: float64

This shows that Azotobacter is taking all of the carbon being produced in the system and therefore preventing community growth.

djinnome commented 1 year ago

We want growth for cyano and Azo, but not (necessarily) Rhodo

djinnome commented 1 year ago

Link to Milestone https://github.com/PNNL-CompBio/CONCERTO/milestone/5