Merge pull request #54 from SysBioChalmers/devel

GECKO 1.3.3

README.rst

@@ -11,7 +11,7 @@ The **GECKO** toolbox is a Matlab/Python package for enhancing a **G**\ enome-sc
 - ``geckomat``: Matlab+Python scripts to fetch online data and build/simulate enzyme-constrained models.
 - ``geckopy``: a Python package which can be used with `cobrapy <https://opencobra.github.io/cobrapy/>`_ to obtain a ecYeastGEM model object, optionally adjusted for provided proteomics data.
 
-Last update: 2018-10-12
+Last update: 2018-11-02
 
 This repository is administered by Benjamin J. Sanchez (`@BenjaSanchez <https://github.com/benjasanchez>`_), Division of Systems and Synthetic Biology, Department of Biology and Biological Engineering, Chalmers University of Technology.
 
@@ -45,19 +45,21 @@ Usage
 
   - Update the following data files in ``/databases`` with your organism infomation:
 
-    - ``databases/chemostatData.tsv``: Chemostat data for estimating GAM	(optional).
-    - ``databases/manual_data.txt``: Kcat data from eventual manual curations	(optional).
     - ``databases/prot_abundance.txt``: Protein abundance Data from Pax-DB.
     - ``databases/uniprot.tab``: Gene-proteins data from uniprot.
+    - ``databases/chemostatData.tsv``: Chemostat data for estimating GAM (optional, called by ``fitGAM.m``).
+    - ``databases/manual_data.txt``: Kcat data from eventual manual curations (optional, called by ``manualModifications.m``).
 
   - Adapt the following functions in ``/geckomat`` to your organism:
 
-    - ``geckomat/get_enzyme_data/preprocessModel.m``
-    - ``geckomat/change_model/manualModifications.m``	(optional)
-    - ``geckomat/change_model/removeIncorrectPathways.m``
-    - ``geckomat/limit_proteins/sumBioMass.m``	(If chemostat data is provided)
-    - ``geckomat/limit_proteins/scaleBioMass.m``	(If chemostat data is provided)
+    - ``geckomat/enhanceGEM.m``
+    - ``geckomat/change_model/manualModifications.m``
+    - ``geckomat/limit_proteins/sumProtein.m``
+    - ``geckomat/limit_proteins/scaleBioMass.m``
     - ``geckomat/kcat_sensitivity_analysis/changeMedia_batch.m``
+    - ``geckomat/change_model/removeIncorrectPathways.m`` (optional, called by ``manualModifications.m``)
+    - ``geckomat/limit_proteins/sumBioMass.m`` (optional, called by ``sumProtein.m`` & ``scaleBiomass.m``)
+    - ``geckomat/limit_proteins/fitGAM.m`` (optional, called by ``scaleBiomass.m``)
 
   - Run ``geckomat/get_enzyme_data/updateDatabases.m`` to update ``ProtDatabase.mat``.
   - Run ``geckomat/enhanceGEM.m`` with your metabolic model as input.
@@ -97,8 +99,9 @@ Usage
 Contributors
 ------------
 
-- Benjamin J. Sanchez (`@BenjaSanchez <https://github.com/benjasanchez>`_), Chalmers University of Technology, Gothenburg Sweden
 - Ivan Domenzain (`@IVANDOMENZAIN <https://github.com/IVANDOMENZAIN>`_), Chalmers University of Technology, Gothenburg Sweden
+- Eduard Kerkhoven (`@edkerk <https://github.com/edkerk>`_), Chalmers University of Technology, Gothenburg Sweden
+- Benjamin J. Sanchez (`@BenjaSanchez <https://github.com/benjasanchez>`_), Chalmers University of Technology, Gothenburg Sweden
 - Moritz Emanuel Beber (`@Midnighter <https://github.com/Midnighter>`_), Danish Technical University, Lyngby Denmark
 - Henning Redestig (`@hredestig <https://github.com/hredestig>`_), Danish Technical University, Lyngby Denmark
 - Cheng Zhang, Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm Sweden

docs/conf.py

@@ -54,9 +54,9 @@
 # built documents.
 #
 # The short X.Y version.
-version = u'1.3.2'
+version = u'1.3.3'
 # The full version, including alpha/beta/rc tags.
-release = u'1.3.2'
+release = u'1.3.3'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

geckomat/enhanceGEM.m

@@ -1,9 +1,9 @@
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-% [ecModel,model_data,kcats] = enhanceGEM(model,toolbox,name,version)
+% [ecModel,ecModel_batch] = enhanceGEM(model,toolbox,name,version)
 %
-% Benjamin J. Sanchez & Ivan Domenzain. Last edited: 2018-09-27
+% Benjamin J. Sanchez & Ivan Domenzain. Last edited: 2018-10-25
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-function [ecModel,model_data,kcats] = enhanceGEM(model,toolbox,name,version)
+function [ecModel,ecModel_batch] = enhanceGEM(model,toolbox,name,version)
 
 if nargin < 3
     name    = '';
@@ -30,7 +30,6 @@
 cd ../get_enzyme_data
 model_data = getEnzymeCodes(model);
 kcats      = matchKcats(model_data,org_name);
-save(['../../models/' name '/data/' name '_enzData.mat'],'model_data','kcats','version')
 
 %Integrate enzymes in the model:
 cd ../change_model
@@ -49,7 +48,7 @@
 %Save output models:
 cd ../../models
 ecModel = saveECmodel(ecModel,toolbox,name,version);
-saveECmodel(ecModel_batch,toolbox,[name '_batch'],version);
+ecModel_batch = saveECmodel(ecModel_batch,toolbox,[name '_batch'],version);
 cd ../geckomat
 
 end