Merge pull request #46 from SysBioChalmers/devel

final doc changes

ComplementaryScripts/saveYeastModel.m

@@ -1,13 +1,13 @@
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-% saveYeastModel(model,version)
+% saveYeastModel(model)
 % Saves model as a .mat, .xml and .txt file.
 %
 % Benjamín J. Sánchez. Last edited: 2018-01-18
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 
-function saveYeastModel(model,version)
+function saveYeastModel(model)
 
-model.description = ['yeastGEM_' version];
+model.description = 'yeastGEM';
 
 %Remove any space in rxnECNumbers:
 model.rxnECNumbers = strrep(model.rxnECNumbers,' ','');

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="yeast_7.8.xml" id="COBRAModel" name="Model Exported from COBRA Toolbox" fbc:strict="true">
+  <model metaid="yeastGEM" id="COBRAModel" name="Model Exported from COBRA Toolbox" fbc:strict="true">
     <listOfUnitDefinitions>
       <unitDefinition id="mmol_per_gDW_per_hr">
         <listOfUnits>

README.md

@@ -13,6 +13,9 @@ This repository contains the current genome-scale metabolic model of _Saccharomy
   * 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.
@@ -25,7 +28,7 @@ This repository contains the current genome-scale metabolic model of _Saccharomy
 
 **GEM Category:** Species; **Utilisation:** maximising growth; **Field:** metabolic-network reconstruction; **Type of Model:** curated, reconstruction; **Model Source:** [Yeast 7.6](https://sourceforge.net/projects/yeast/); **Taxonomy:** _Saccharomyces cerevisiae_; **Metabolic System:** General Metabolism; **Bioreactor**
 
-* Last update: 2017-12-28
+* Last update: 2018-01-18
 
 * The model: