Merge pull request #6 from SysBioChalmers/develop

Fruitfly 1.2

.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

@@ -7,7 +7,7 @@
 
 
 #### Current feature/value/output:
-*How the reaction/metabolite/gene/simulation actually looks in the `master` branch. PLEASE DELETE THIS LINE.*
+*How the reaction/metabolite/gene/simulation actually looks in the `main` branch. PLEASE DELETE THIS LINE.*
 
 
 #### Reproducing these results:
@@ -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

@@ -11,8 +11,7 @@ This repository contains the latest version of Fruitfly-GEM, a fruit fly genome-
 
 #### 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
 
@@ -53,15 +52,15 @@ Manuscript under preparation
 
 
 ### Installation Instructions
-* Clone the [master branch](https://github.com/SysBioChalmers/Fruitfly-GEM/tree/master) of this repository, or [download the latest release](https://github.com/SysBioChalmers/Fruitfly-GEM/releases/latest).
+* Clone the [main branch](https://github.com/SysBioChalmers/Fruitfly-GEM/tree/main) of this repository, or [download the latest release](https://github.com/SysBioChalmers/Fruitfly-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
 
-`Fruitfly-GEM.mat` (Recommended if on `master` branch)
+`Fruitfly-GEM.mat` (Recommended if on `main` branch)
 * Load and save using the built-in MATLAB `load()` and `save()` functions.
 
 `Fruitfly-GEM.xml` (SBML format)

code/masterScriptFruitflyGEM.m

@@ -44,7 +44,10 @@
     exportTsvFile(metAssoc,'../model/metabolites.tsv');
 end
 
+fruitflyGEM = annotateGEM(fruitflyGEM,'../model',{'rxn','met'});  % add annotation data to structure
+fruitflyGEM.id = regexprep(fruitflyGEM.id,'-','');  % remove dash from model ID since it causes problems with SBML I/O
 save('../model/Fruitfly-GEM.mat', 'fruitflyGEM');
 exportYaml(fruitflyGEM, '../model/Fruitfly-GEM.yml');
+fruitflyGEM.genes = strcat('G_',fruitflyGEM.genes);
 exportModel(fruitflyGEM, '../model/Fruitfly-GEM.xml');
 

data/fruitflySpecificMets.tsv

@@ -1,10 +1,10 @@
 mets	metNames	metFormulas	metCharges	compartments	metKEGGID	metPubChemID	metChEBIID	metMetaCycID	metMetaNetXID	metsNoComp
 "MAM20003c"	"L-Allothreonine"	"C4H9NO3"	0	"c"	"C05519"	"99289"	"CHEBI:28718"	"L-ALLO-THREONINE"	"MNXM2125"	"MAM20003"
-"MAM01104p"	"5-hydroxyisourate"	"C5H4N4O4"	0	"p"	"C11821"	"250388"	"CHEBI:250388"	"5-HYDROXYISOURATE"	"MNXM1137"	"MAM01104"
-"MAM10018p"	"5-Hydroxy-2-oxo-4-ureido-2,5-dihydro-1H-imidazole-5-carboxylate"	"C5H5N4O5"	-1	"p"	"C12248"	"443736"	"CHEBI:58639"	"CPD-5821"	"MNXM1805"	"MAM10018"
+"MAM01104x"	"5-hydroxyisourate"	"C5H4N4O4"	0	"x"	"C11821"	"250388"	"CHEBI:250388"	"5-HYDROXYISOURATE"	"MNXM1137"	"MAM01104"
+"MAM10018x"	"5-Hydroxy-2-oxo-4-ureido-2,5-dihydro-1H-imidazole-5-carboxylate"	"C5H5N4O5"	-1	"x"	"C12248"	"443736"	"CHEBI:58639"	"CPD-5821"	"MNXM1805"	"MAM10018"
 "MAM10018c"	"5-Hydroxy-2-oxo-4-ureido-2,5-dihydro-1H-imidazole-5-carboxylate"	"C5H5N4O5"	-1	"c"	"C12248"	"443736"	"CHEBI:58639"	"CPD-5821"	"MNXM1805"	"MAM10018"
-"MAM20005p"	"1,3,7-Trimethyluric acid"	"C8H10N4O3"	0	"p"	"C16361"	"47205669"	"CHEBI:691622"	"CPD-12480"	"MNXM2761"	"MAM20005"
-"MAM20006p"	"3,6,8-Trimethylallantoin"	"C7H12N4O3"	0	"p"	"C16362"	"47205670"	"CHEBI:80471"	"CPD-12485"	"MNXM6778"	"MAM20006"
+"MAM20005x"	"1,3,7-Trimethyluric acid"	"C8H10N4O3"	0	"x"	"C16361"	"47205669"	"CHEBI:691622"	"CPD-12480"	"MNXM2761"	"MAM20005"
+"MAM20006x"	"3,6,8-Trimethylallantoin"	"C7H12N4O3"	0	"x"	"C16362"	"47205670"	"CHEBI:80471"	"CPD-12485"	"MNXM6778"	"MAM20006"
 "MAM20010c"	"pseudouridine"	"C9H12N2O6"	0	"c"	"C02067"	"15047"	"CHEBI:17802"	"CPD-497"	"MNXM1094063;MNXM4794"	"MAM20010"
 "MAM02807c"	"pseudouridine-5-phosphate"	"C9H11N2O9P"	-2	"c"	"C01168"	"25245232"	"CHEBI:18116"	"PSEUDOURIDINE-5-P"	"MNXM2276"	"MAM02807"
 "MAM20027c"	"L-arginine-phosphate"	"C6H14N4O5P"	-1	"c"	"C05945"	"92150"	"CHEBI:58477"	"L-ARGININE-P"	"MNXM3663"	"MAM20027"

data/fruitflySpecificRxns.tsv

@@ -1,10 +1,10 @@
 rxns	equations	ub	lb	eccodes	subSystems	grRules	rxnReferences	rxnConfidenceScores	rxnKEGGID	rxnMetaCycID	rxnREACTOMEID	rxnMetaNetXID
 "MAR20001"	"NAD+[m] + threonine[m] => NADH[m] + H+[m] + L-2-amino-3-oxobutanoic acid[m]"	1000	0	"1.1.1.103"	"Glycine, serine and threonine metabolism"	"CG5955"	"PMID:26492815"	4	"R01465"	"THREODEHYD-RXN"	"R-HSA-6798667"	"MNXR103402"
 "MAR20003"	"L-Allothreonine[c] <=> glycine[c] + acetaldehyde[c]"	1000	-1000	"4.1.2.48;4.1.2.49"	"Glycine, serine and threonine metabolism"	"CG10184"	""	2	"R06171"	"LTAA-RXN"	""	"MNXR104834"
-"MAR20004"	"H2O[p] + 5-hydroxyisourate[p] => 5-Hydroxy-2-oxo-4-ureido-2,5-dihydro-1H-imidazole-5-carboxylate[p] + H+[p]"	1000	0	"3.5.2.17"	"Purine metabolism"	"CG30016"	"PMID:17085964"	4	"R06601"	"3.5.2.17-RXN"	""	"MNXR100652"
-"MAR20005"	"5-hydroxyisourate[p] <=> 5-hydroxyisourate[c]"	1000	-1000	""	"Transport"	""	""	0	""	""	""	""
-"MAR20006"	"5-Hydroxy-2-oxo-4-ureido-2,5-dihydro-1H-imidazole-5-carboxylate[p] <=> 5-Hydroxy-2-oxo-4-ureido-2,5-dihydro-1H-imidazole-5-carboxylate[c]"	1000	-1000	""	"Transport"	""	""	0	""	""	""	""
-"MAR20007"	"2 H2O[p] + O2[p] + 1,3,7-Trimethyluric acid[p] <=> CO2[p] + H2O2[p] + 3,6,8-Trimethylallantoin[p]"	1000	-1000	"1.7.3.3"	"Caffeine metabolism"	"Uro"	""	2	"R07981"	""	""	"MNXR111564"
+"MAR20004"	"H2O[x] + 5-hydroxyisourate[x] => 5-Hydroxy-2-oxo-4-ureido-2,5-dihydro-1H-imidazole-5-carboxylate[x] + H+[x]"	1000	0	"3.5.2.17"	"Purine metabolism"	"CG30016"	"PMID:17085964"	4	"R06601"	"3.5.2.17-RXN"	""	"MNXR100652"
+"MAR20005"	"5-hydroxyisourate[x] <=> 5-hydroxyisourate[c]"	1000	-1000	""	"Transport"	""	""	0	""	""	""	""
+"MAR20006"	"5-Hydroxy-2-oxo-4-ureido-2,5-dihydro-1H-imidazole-5-carboxylate[x] <=> 5-Hydroxy-2-oxo-4-ureido-2,5-dihydro-1H-imidazole-5-carboxylate[c]"	1000	-1000	""	"Transport"	""	""	0	""	""	""	""
+"MAR20007"	"2 H2O[x] + O2[x] + 1,3,7-Trimethyluric acid[x] <=> CO2[x] + H2O2[x] + 3,6,8-Trimethylallantoin[x]"	1000	-1000	"1.7.3.3"	"Caffeine metabolism"	"Uro"	""	2	"R07981"	""	""	"MNXR111564"
 "MAR20013"	"ATP[c] + pseudouridine[c] <=> ADP[c] + pseudouridine-5-phosphate[c] + H+[c]"	1000	-1000	"2.7.1.83"	"Pyrimidine metabolism"	"CG2794"	""	2	"R03315"	"PSEUDOURIDINE-KINASE-RXN"	""	"MNXR108088;MNXR162394"
 "MAR20014"	"NADH[c] + O2[c] + H+[c] + cholesterol[c] => 2 H2O[c] + NAD+[c] + provitamin D3[c]"	1000	0	"1.14.19.21"	"Hormone biosynthesis"	"nvd"	""	2	"R11007"	"RXN-16379"	""	"MNXR120043"
 "MAR20015"	"NADPH[c] + O2[c] + H+[c] + cholesterol[c] => 2 H2O[c] + NADP+[c] + provitamin D3[c]"	1000	0	"1.14.19.21"	"Hormone biosynthesis"	"nvd"	""	2	"R11008"	"RXN-16379"	""	"MNXR120043"