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

[vladpetyuk]

No description provided.

[vladpetyuk]

we should confirm that azotobacter takes over rhodosporidium

[mcnaughtonadm]

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

[mcnaughtonadm]

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]

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

[djinnome]

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