Fix model objective functions

SBRG / bigg_models

The BiGG Models website server

http://bigg.ucsd.edu

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Fix model objective functions #188

Closed zakandrewking closed 7 years ago

zakandrewking commented 8 years ago

Models are importing with incorrect objective functions for a couple reasons:

Objective function not included in the published model file
- iJR904, iRC1080
SBML in published file has conflicting information about the objective
- iAF987

draeger commented 8 years ago

This is most likely caused by the renaming of the biomass reaction's id to upper case. It should already be fixed in the trunk of ModelPolisher. I'll test this.

zakandrewking commented 8 years ago

@draeger I think these errors happen on import, before the IDs are renamed

draeger commented 8 years ago

On import in what?

zakandrewking commented 8 years ago

The issue is the the original model files from supplements to these papers did not specify objectives, so when we import them with COBRApy to load them into BiGG, there are already errors.

zakandrewking commented 7 years ago

Fixed for iJR904. not fixing the others because they are defined this way in published models.