visualization-friendly version of Carbon dioxide flux

[mcnaughtonadm]

• [x] Create a source CO2 flux that is distinguishable from CO2 exchange
• [x] Remove bicarbonate <-> CO2 reaction from Rhodosporidium (or restrict the maximum flux) to prevent Cyano from getting more carbon that it should

[mcnaughtonadm]

Addresses https://github.com/PNNL-CompBio/CONCERTO/issues/99

[mcnaughtonadm]

Modifications would create the addition of a source carbon metabolite and exchange.

[ShantMahserejian]

Visualization for a test attempt at carbon source treatment:

Flux file used: test_source_carbon.csv

Generated PNG file

Interactive HTML version also available (sent to Andrew directly)

[djinnome]

Why is Leu__L a source metabolite?

[djinnome]

And why is glc__D a source metabolite? I thought this was supposed to be only carbon dioxide as the nitrogen source?

[mcnaughtonadm]

Sorry that was my fault, I was more focused on seeing the co2 so the method I used to implement the specific carbon just loaded the 3-member model directly and made the edits to the co2_source and ran it with the rest of the medium default.

This exercise was just to see if the new co2 worked, which after talking to Shant may need to be edited with a new feature that the exchange between the medium and each individual organism may need it's own "source co2".

We can run one with the proper minimal carbon-nitrogen medium. I was going to make a method for that once we figured out which source co2 reactions were needed.

[mcnaughtonadm]

Altered approach to make sure the "source" co2 is actually being captured by visualization. Left comment on merge request.

https://github.com/PNNL-CompBio/ConsortiumModels/pull/5#issuecomment-1698780934

[mcnaughtonadm]

I'm anticipating this to return a more visualization friendly carbon source as after optimization the fluxes for the co2 return like this:

Compartment	EX_co2_e	EX_co2_m	EX_co2_source_e	EX_co2_source_m
Azotobacter	5.02887247		0
Rhodosporidium	-3.72924568		0
Synechococcus	1.299626789		1.89995819
medium		0		-1.8999582

So this to me shows that the source carbon is going into the Synechococcus (now it flowing here may not be the preferred outcome, but that means this co2 diagnostic visualization would be working and we can make tweaks to get the carbon where it needs to go)