Merge pull request #8 from SysBioChalmers/develop

Rat 1.3

.gitattributes

@@ -0,0 +1,19 @@
+# Set the default behavior, in case people don't have core.autocrlf set.
+* text=auto
+
+
+# Explicitly declare text files you want to always be normalized and converted
+# to native line endings on checkout.
+*.tsv text
+*.yml text
+*.xml text
+*.md text
+*.txt text
+*.json text
+*.rst text
+
+
+# Denote all files that are truly binary and should not be modified.
+*.xlsx
+*.docx
+*.mat

.github/ISSUE_TEMPLATE.md

@@ -17,9 +17,7 @@
 ```
 
 **I hereby confirm that I have:**
-- [ ] Tested my code with [all requirements](https://github.com/SysBioChalmers/yeast-GEM#required-software---user) for running the model
-- [ ] Done this analysis in the `master` branch of the repository
+- [ ] Done this analysis in the `main` branch of the repository
 - [ ] Checked that a similar issue does not exist already
-- [ ] If needed, asked first in the [Gitter chat room](https://gitter.im/SysBioChalmers/yeast-GEM) about the issue
 
 *Note: replace [ ] with [X] to check the box. PLEASE DELETE THIS LINE*

.github/PULL_REQUEST_TEMPLATE.md

@@ -4,6 +4,6 @@
 **I hereby confirm that I have:**
 
 - [ ] Tested my code on my own computer for running the model
-- [ ] Selected `devel` as a target branch
+- [ ] Selected `develop` as a target branch
 
 *Note: replace [ ] with [X] to check the box. PLEASE DELETE THIS LINE*

README.md

@@ -11,7 +11,7 @@ This repository contains the latest version of Rat-GEM, a rat genome-scale metab
 
 #### Citation
 
-Manuscript under preparation
+ > H. Wang, J. L. Robinson, P. Kocabaş, J. Gustafsson, M. Anton, P.-E. Cholley, et al. Genome-scale metabolic network reconstruction of model animals as a platform for translational research. _PNAS_ 118, e2102344118 (2021). [doi.org/10.1073/pnas.2102344118](https://doi.org/10.1073/pnas.2102344118)
 
 #### Model Keywords
 
@@ -52,15 +52,15 @@ Manuscript under preparation
 
 
 ### Installation Instructions
-* Clone the [master branch](https://github.com/SysBioChalmers/Rat-GEM/tree/master) of this repository, or [download the latest release](https://github.com/SysBioChalmers/Rat-GEM/releases/latest).
+* Clone the [main branch](https://github.com/SysBioChalmers/Rat-GEM/tree/main) of this repository, or [download the latest release](https://github.com/SysBioChalmers/Rat-GEM/releases/latest).
 * Add the directory to your MATLAB path (instructions [here](https://se.mathworks.com/help/matlab/ref/addpath.html?requestedDomain=www.mathworks.com)).
 
 
 ## Usage
 
 #### Loading/saving the model
 
-`Rat-GEM.mat` (Recommended if on `master` branch)
+`Rat-GEM.mat` (Recommended if on `main` branch)
 * Load and save using the built-in MATLAB `load()` and `save()` functions.
 
 `Rat-GEM.xml` (SBML format)

code/README.md

@@ -0,0 +1,5 @@
+# Rat-GEM code
+
+- `masterScriptRatGEM.m`:  The master script for GEM generation.
+
+

code/masterScriptRatGEM.m

@@ -42,6 +42,8 @@
     exportTsvFile(metAssoc,'../model/metabolites.tsv');
 end
 
+ratGEM = annotateGEM(ratGEM,'../model',{'rxn','met'});  % add annotation data to structure
+ratGEM.id = regexprep(ratGEM.id,'-','');  % remove dash from model ID since it causes problems with SBML I/O
 save('../model/Rat-GEM.mat', 'ratGEM');
 exportYaml(ratGEM, '../model/Rat-GEM.yml');
 exportModel(ratGEM, '../model/Rat-GEM.xml');