chore: new version

SysBioChalmers · May 30, 2018 · 7f9346e · 7f9346e
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Showing 5 changed files with 13 additions and 2 deletions.
diff --git a/ModelFiles/mat/yeastGEM.mat b/ModelFiles/mat/yeastGEM.mat
diff --git a/ModelFiles/xlsx/yeastGEM.xlsx b/ModelFiles/xlsx/yeastGEM.xlsx
diff --git a/ModelFiles/xml/yeastGEM.xml b/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_v8.0.2" id="COBRAModel" name="Model Exported from COBRA Toolbox" fbc:strict="true">
+  <model metaid="yeastGEM_v8.1.0" id="COBRAModel" name="Model Exported from COBRA Toolbox" fbc:strict="true">
     <listOfUnitDefinitions>
       <unitDefinition id="mmol_per_gDW_per_hr">
         <listOfUnits>

diff --git a/history.md b/history.md
@@ -1,5 +1,16 @@
 # History
 
+### yeast 8.1.0:
+* New features:
+  * SLIME reactions added to the model using [SLIMEr](https://github.com/SysBioChalmers/SLIMEr), to properly account for constraints on lipid metabolism (fixes #21):
+    * SLIME rxns replace old ISA rxns for lumping lipids. They create 2 types of lipid pseudometabolites: backbones and acyl chains.
+    * There are now 3 lipid pseudoreactions: 1 constrains backbones, 1 constrains acyl chains, 1 merges both.
+* Fixes:
+  * All metabolite formulas made compliant with SBML (fixes #19). Model is now a valid SBML object.
+  * Biomass composition was rescaled to experimental data from [Lahtvee et al. 2017](https://www.sciencedirect.com/science/article/pii/S2405471217300881), including protein and RNA content, trehalose and glycogen concentrations, lipid profile and FAME data. Biomass was fitted to add up to 1 g/gDW by rescaling total carbohydrate content (unmeasured).
+* Refactoring:
+  * Organized all files in `ComplementaryData`
+
 ### yeast 8.0.2:
 * New features:
   * Model can now be used with cobrapy by running `loadYeastModel.py`

diff --git a/version.txt b/version.txt
@@ -1 +1 @@
-8.0.2
+8.1.0