ModelSEED/Model-SEED-core — Issue #127: ./mdl-loadbiomass
Author: samseaver
Created: 2012-01-24 15:51:32+00:00
State: open

If I create my own biomass file, with my own biomass equation, and use ./mdl-loadbiomass to load that equation for a particular model (from file), then the equation gets added to the BIOMASS table, but it does not get added to the model's local provenance.

If I were to include the same biomass equation in a makeshift model which I then import, and I then print out the same biomass file (which now has its own id in ModelSEED), I can then use ./mdl-loadbiomass to load this new file. So it seems that for a biomass equation to be added to a model, it must already practically exist in ModelSEED.

To compound things further, I cannot simply use the id of a biomass already in ModelSEED to load it into a model, I have to print out the biomass to file (via ./mdl-printmodel) and use that.

So, effectively, this issue boils down to two, well, three, OK, four things:

1) We need a ./mdl-createbiomass that will load from file
-- it probably should generate a biomass id rather than let the user dictate it.

2) We need a ./mdl-loadbiomass that can simply take the id of a biomass already in ModelSEED.

3) We need a ./mdl-printbiomass

4) We could do with a ./mdl-findbiomass function that will take a comma-separated string of compounds, and find all the biomass equations that have all the compounds queried.