chore: new version

ModelFiles/xml/yeastGEM.xml

@@ -1,6 +1,6 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:groups="http://www.sbml.org/sbml/level3/version1/groups/version1" level="3" version="1" fbc:required="false" groups:required="false">
-  <model metaid="yeastGEM.xml" id="COBRAModel" name="Model Exported from COBRA Toolbox" fbc:strict="true">
+  <model metaid="yeastGEM_v7.8.2" id="COBRAModel" name="Model Exported from COBRA Toolbox" fbc:strict="true">
     <listOfUnitDefinitions>
       <unitDefinition id="mmol_per_gDW_per_hr">
         <listOfUnits>

history.md

@@ -0,0 +1,34 @@
+# History
+
+### yeast 7.8.0:
+First release of the yeast model
+
+* Format changes:
+  * FBCv2 compliant
+  * Compatible with latest COBRA and RAVEN parsers
+  * Biomass clustered by 5 main groups: protein, carbohydrate, lipid, RNA and DNA
+* Added information:
+  * `subSystems` and `rxnECnumbers` added to reactions based on [KEGG](http://www.genome.jp/kegg/) & [Swissprot](http://www.uniprot.org/uniprot/?query=*&fil=organism%3A%22Saccharomyces+cerevisiae+%28strain+ATCC+204508+%2F+S288c%29+%28Baker%27s+yeast%29+%5B559292%5D%22+AND+reviewed%3Ayes) data
+  * `geneNames` added to genes based on [KEGG](http://www.genome.jp/kegg/) data
+  * `rxnKEGGID` added from old version
+  * `rxnNotes` enriched with Pubmed ids (`pmid`) from old version
+  * `rxnConfidenceScores` added based on [automatic script](https://github.com/SysBioChalmers/YeastMetabolicNetwork-GEM/blob/f7870589d16c08e18057a8f6cc880466373b77a7/ComplementaryScripts/getConfidenceScores.m)
+  * Boundary metabolites tracked (available in [`ComplementaryScripts`](https://github.com/SysBioChalmers/yeast-metabolic-network-7.6/blob/master/ComplementaryScripts/boundaryMets.txt))
+* Simulation improvements:
+  * Glucan composition fixed in biomass pseudo-rxn
+  * Proton balance in membrane restored
+  * Ox.Pho. stoichiometry fixed
+  * NGAM rxn introduced
+  * GAM in biomass pseudo-rxn fixed and refitted to chemostat data
+
+### yeast 7.8.1:
+* started following dependencies
+* started keeping track of the version in the repo (`version.txt`)
+* included `.gitignore`
+* dropped `.mat` storage for `devel` + feature branches (but kept it in `master`)
+
+### yeast 7.8.2:
+* fixed subSystems bug: now they are saved as individual groups
+* solved inter-OS issues
+* remade license to follow GitHub format
+* added `history.md` and made it a requirement to update when increasing version

version.txt

@@ -1 +1 @@
-7.8.1
+7.8.2