iYali v4.1.2: update few gene associations, format repo as standard-GEM

• Curation:
  • correct gene associations of BAT1/2 (doi:10.1128/AEM.00644-07) and Jen genes (doi:10.1002/mbo3.225)
• Refactoring:
  • reorganize folder structure to fit standard-GEM

4.1.1: fix SBML, standardized repo

• Curation:
  • most chemical formulae are without brackets.
  • remove reactions that were not connected to remaining network and had no gene annotation
  • partial correct KEGG and subSystem annotations
  • correct metabolite charge and annotations
• Refactoring:
  • fbc_label is now specified for each gene.
  • x_BIOMASS is set as default objective function.
  • move towards a standardized format of versioning, inspired by yeast-GEM, including not tracking binaries in devel
• New features:
  • scripts newCommit and newRelease for updating repository.
  • add .gitignore.

4.1.0: Significant update by new reconstruction

Significant update to version 4.1.0 by new reconstruction

* Model is completely reconstructed from scratch, using Yeast 7.6 as template.
* Standardized reaction IDs are introduced, referencing where the reaction came from (y0 is derived from yeast concensus network, y1 is modified from yeast concensus network, y2 is from other Yarrowia lipolytica reconstructions, y3 is manual curation).
* Gap-filling during model reconstruction was automated via MENECO. Some reactions from the previous model that were identified through gap-filling are omitted in this version.

4.0.3: Correct grRules, metFormula, additional annotation (InChi, ChEBI, KEGG)

* Removed incorrect annotation of FAD:ubiquinone oxidoreductse (yli0053), while allowing flux through NADH:ubiquinone oxidoreductse (773).
* Some complex grRules were incorrect. Some metFormula gave error message when loaded as SBML.
* Cytosolic and mitochondrial branched-chain amino-acid transaminases are encoded by different genes (BAT2 and BAT1, respectively).
* Metabolite annotation (InChi, ChEBI, KEGG) that were previously lost during conversion from RAVEN to COBRA format are now included by exporting the file in RAVEN format. This format is now fully COBRA compatible.

4.0.2: Correct energetics, SBML L3V1 FBCv2

Changed equations of complex III, IV and V of oxidative phosphorylation to correct the transport of protons over the mitochondrial membrane (reactions 226, 438, 439). This was incorrectly represented in the template model.

Made asparate transport over the mitochondrial membrane irreversible (reaction 1117), otherwise this would transport protons for 'free' over the mitochondrial membrane. This was already identified in the Yeast consensus network.

Updated SBML to L3V1 with FBCv2, also using updated RAVEN functions. This changed the compartment IDs slightly (removed C_). Amended README.md to reflect the changes.

4.0.1: Corrected metabolite names

Fixed metabolite names

Due to an error in model generation, some of the metabolite names were
appended with "_ActiveX VT_ERROR:". This is now removed.

4.0.0: Published model

This is the model as published in

Kerkhoven EJ, Pomraning KR, Baker SE, Nielsen J (2016) "Regulation of amino-acid metabolism controls flux to lipid accumulation in Yarrowia lipolytica." npj Systems Biology and Applications 2:16005. doi:10.1038/npjsba.2016.5