Benjamín Sánchez

fix: inconsistency in the gene name storage in SBML files

1

#### Problem description As noted in https://github.com/SysBioChalmers/yeast-GEM/pull/216, currently there's an inconsistency with how cobratoolbox and cobrapy store gene names in the xml file: cobratoolbox uses the `fbc:label` field, whereas cobrapy...

fix: avoid scrambling of group members

9

#### Problem description When going through an I/O cycle with a model that has subsystems stored as groups, the members of each group in the sbml file get scrambled on...

fix: subSystems field

35

Currently the fields `rxnECNumbers` & `subSystems` are retrieved from KEGG & Swissprot, using an [automatic script](https://github.com/SysBioChalmers/gem-scripts/blob/master/yeast7scripts/missingFields/getMissingFields.m). However, this leads to many cases in which there is more than one match,...

feat: apply curations from mitoYeast-GEM paper

1

@CarlMalina made significant curation in the mitochondrial compartment for his project. @CarlMalina would you mind sharing your changes so they can be integrated to the full model? You can make...

fix: biomass tests from memote

1

### Description of the issue: From the latest [memote report](https://github.com/SysBioChalmers/yeast-GEM/files/2191823/index_SBO.zip), the following biomass tests are giving unexpected results: - [ ] Biomass consistency = 0 - [x] GAM ~is not...

feat: yeast-GEM maps in caffeine platform

7

### Description of the issue: For improved visualization of the _S. cerevisiae_ model, the files available at [SysBioChalmers/Yeast-maps](https://github.com/SysBioChalmers/Yeast-maps) could be uploaded to https://caffeine.dd-decaf.eu/, a platform for simulating + visualizing GEM...

fix: remove generic reactions

5

### Description of the issue: Reaction `r_4308` uses a generic `phospholipid` species, not specifying which type of phospholipid it is. As this creates confusion with the rest of the model,...

feat: allow contributions from python users

1

### Description of the issue: Continuation of #102: Currently both matlab and python users can load the model without loosing any fields, but only matlab users can contribute. This issue...

### Description of the issue: In PR #216 we are forcing the model to save the `proteins` COBRA field with the same information as `geneNames`, in order to allow both...

### Description of the issue: In the consistency tests from the [memote report](https://github.com/SysBioChalmers/yeast-GEM/files/2191823/index_SBO.zip), the "Stoichiometric Consistency" dropped significantly after adding [SLIME reactions](https://github.com/SysBioChalmers/yeast-GEM/pull/112), as these reactions are by definition mass unbalanced....