Eduard Kerkhoven

Does not strictly have to be JSON, but it should be flat-text so that it is diff-able.

For reference, [this](https://dev-metatlas.csbi.chalmers.se/api/v2/gotenzymes/enzymes?filters[organism]=sce&pagination[page]=1&pagination[pageSize]=500) is what GotEnzymes output looks like (showing only the first 28 lines here): ``` {"enzymes":[{"gene":"YAL012W","organism":"sce","domain":"E","ko":"K01758","reaction_id":"R04770","ec_number":"4.4.1.1;4.4.1.11","compound":"C00109","kcat_values":1.1646}, {"gene":"YAL012W","organism":"sce","domain":"E","ko":"K01758","reaction_id":"R04770","ec_number":"4.4.1.1;4.4.1.11","compound":"C00014","kcat_values":4.2309}, {"gene":"YAL012W","organism":"sce","domain":"E","ko":"K01758","reaction_id":"R09366","ec_number":"4.4.1.1;4.4.1.13","compound":"C05703","kcat_values":1.5564}, {"gene":"YAL012W","organism":"sce","domain":"E","ko":"K01758","reaction_id":"R00782","ec_number":"4.4.1.1;4.4.1.13;4.4.1.28","compound":"C00022","kcat_values":0.7785}, {"gene":"YAL012W","organism":"sce","domain":"E","ko":"K01758","reaction_id":"R09366","ec_number":"4.4.1.1;4.4.1.13","compound":"C00022","kcat_values":0.7785}, {"gene":"YAL012W","organism":"sce","domain":"E","ko":"K01758","reaction_id":"R02408","ec_number":"4.4.1.1;4.4.1.13;4.4.1.35","compound":"C01962","kcat_values":2.2991}, {"gene":"YAL012W","organism":"sce","domain":"E","ko":"K01758","reaction_id":"R04930","ec_number":"4.4.1.1","compound":"C00109","kcat_values":1.1646}, {"gene":"YAL012W","organism":"sce","domain":"E","ko":"K01758","reaction_id":"R00782","ec_number":"4.4.1.1;4.4.1.13;4.4.1.28","compound":"C00283","kcat_values":2.2484}, {"gene":"YAL012W","organism":"sce","domain":"E","ko":"K01758","reaction_id":"R09366","ec_number":"4.4.1.1;4.4.1.13","compound":"C00014","kcat_values":4.2309}, {"gene":"YAL012W","organism":"sce","domain":"E","ko":"K01758","reaction_id":"R02408","ec_number":"4.4.1.1;4.4.1.13;4.4.1.35","compound":"C00022","kcat_values":0.7785}, {"gene":"YAL012W","organism":"sce","domain":"E","ko":"K01758","reaction_id":"R04930","ec_number":"4.4.1.1","compound":"C05699","kcat_values":1.3478}, {"gene":"YAL012W","organism":"sce","domain":"E","ko":"K01758","reaction_id":"R09366","ec_number":"4.4.1.1;4.4.1.13","compound":"C05689","kcat_values":1.3304}, {"gene":"YAL012W","organism":"sce","domain":"E","ko":"K01758","reaction_id":"R04930","ec_number":"4.4.1.1","compound":"C00014","kcat_values":4.2309},...

Last thing to fix here, although not just related to using different carbon sources, is that if `generate_protModels` runs for multiple conditions is overwrites the model file in every iteration,...

The changes intended here have been superseded by various developments as part of GECKO3.

In GECKO3, the original model information remains intact.

This scaling is solved in #147

Inactive for > 2 years, and also addressed in GECKO3 protocol

Use of model-specified EC numbers is now implemented in GECKO3.

Thanks for the explanation, this could go directly in the documentation! :) What if no Pax-DB data is available for my organism of interest? Requiring defining the location of the...

This will be completely revamped with GECKO3, the discussion here is obsolete.