Merge pull request #164 from SysBioChalmers/devel

yeast 8.3.1

ComplementaryData/modelCuration/Metabolomics_newRxnMatrix.tsv

@@ -0,0 +1,96 @@
+ID	coefficient	standard_name	type	compartment
+MNXR111769	1	2-hydroxyglutarate	reactant	cytoplasm
+MNXR111769	1	NAD	reactant	cytoplasm
+MNXR111769	1	H+	product	cytoplasm
+MNXR111769	1	NADH	product	cytoplasm
+MNXR111769	1	2-oxoglutarate	product	cytoplasm
+MNXR134240	1	2-hydroxyglutarate	reactant	cytoplasm
+MNXR134240	3	H+	product	cytoplasm
+MNXR134240	1	glyoxylate	product	cytoplasm
+MNXR134240	1	propionyl-CoA	product	cytoplasm
+MNXR95862	1	beta-alanine	reactant	cytoplasm
+MNXR95862	1	2-oxoglutarate	reactant	cytoplasm
+MNXR95862	1	3-oxopropanoate	product	cytoplasm
+MNXR95862	1	L-glutamate	product	cytoplasm
+MNXR101665	1	coenzyme A	reactant	cytoplasm
+MNXR101665	1	3-oxopropanoate	reactant	cytoplasm
+MNXR101665	1	NAD	reactant	cytoplasm
+MNXR101665	1	NADH	product	cytoplasm
+MNXR101665	1	carbon dioxide	product	cytoplasm
+MNXR101665	1	acetyl-CoA	product	cytoplasm
+MNXR106650	1	coenzyme A	reactant	cytoplasm
+MNXR106650	1	3-oxopropanoate	reactant	cytoplasm
+MNXR106650	1	NADP(+)	reactant	cytoplasm
+MNXR106650	1	carbon dioxide	product	cytoplasm
+MNXR106650	1	acetyl-CoA	product	cytoplasm
+MNXR106650	1	NADPH	product	cytoplasm
+MNXR110693	1	H+	reactant	cytoplasm
+MNXR110693	1	3-oxopropanoate	reactant	cytoplasm
+MNXR110693	1	carbon dioxide	product	cytoplasm
+MNXR110693	1	acetaldehyde	product	cytoplasm
+MNXR100904	1	(R)-2,3-dihydroxy-3-methylbutanoate	reactant	cytoplasm
+MNXR100904	1	NADP(+)	reactant	cytoplasm
+MNXR100904	1	H+	product	cytoplasm
+MNXR100904	1	3-hydroxy-3-methyl-2-oxobutanoate	product	cytoplasm
+MNXR100904	1	NADPH	product	cytoplasm
+MNXR137278	1	3-methyl-2-oxobutanoate	reactant	cytoplasm
+MNXR137278	1	3-hydroxy-3-methyl-2-oxobutanoate	product	cytoplasm
+MNXR137279	1	2-acetyllactic acid	reactant	cytoplasm
+MNXR137279	1	NADPH	reactant	cytoplasm
+MNXR137279	1	H+	product	cytoplasm
+MNXR137279	1	3-hydroxy-3-methyl-2-oxobutanoate	product	cytoplasm
+MNXR137279	1	NADP(+)	product	cytoplasm
+MNXR95271	1	H+	reactant	cytoplasm
+MNXR95271	2	pyruvate	reactant	cytoplasm
+MNXR95271	1	(2S)-2-acetolactate	product	cytoplasm
+MNXR95271	1	carbon dioxide	product	cytoplasm
+MNXR100390	1	H+	reactant	cytoplasm
+MNXR100390	1	6-phospho-D-gluconate	reactant	cytoplasm
+MNXR100390	1	ADP	reactant	cytoplasm
+MNXR100390	1	ATP	product	cytoplasm
+MNXR100390	1	D-gluconate	product	cytoplasm
+MNXR97523	1	(R)-2,3-dihydroxy-3-methylbutanoate	reactant	cytoplasm
+MNXR97523	1	NADP(+)	reactant	cytoplasm
+MNXR97523	1	H+	product	cytoplasm
+MNXR97523	1	(2S)-2-acetolactate	product	cytoplasm
+MNXR97523	1	NADPH	product	cytoplasm
+MNXR106779	1	(2R,3S)-3-methylmalate	reactant	cytoplasm
+MNXR106779	1	NAD	reactant	cytoplasm
+MNXR106779	1	NADH	product	cytoplasm
+MNXR106779	1	carbon dioxide	product	cytoplasm
+MNXR106779	1	2-oxobutanoate	product	cytoplasm
+MNXR121603	1	H2O	reactant	cytoplasm
+MNXR121603	1	glyoxylate	reactant	cytoplasm
+MNXR121603	1	propionyl-CoA	reactant	cytoplasm
+MNXR121603	1	H+	product	cytoplasm
+MNXR121603	1	coenzyme A	product	cytoplasm
+MNXR121603	1	(2R,3S)-3-methylmalate	product	cytoplasm
+MNXR99136	1	H2O	reactant	cytoplasm
+MNXR99136	1	trans-2,cis-9-octadecadienoyl-CoA	reactant	cytoplasm
+MNXR99136	1	H+	product	cytoplasm
+MNXR99136	1	coenzyme A	product	cytoplasm
+MNXR99136	1	(9Z,12Z)-octadecadienoate	product	cytoplasm
+MNXR99175	1	coenzyme A	reactant	cytoplasm
+MNXR99175	1	(9Z,12Z)-octadecadienoate	reactant	cytoplasm
+MNXR99175	1	ATP	reactant	cytoplasm
+MNXR99175	1	diphosphate	product	cytoplasm
+MNXR99175	1	AMP	product	cytoplasm
+MNXR99175	1	trans-2,cis-9-octadecadienoyl-CoA	product	cytoplasm
+MNXR100010	1	stachyose	reactant	cytoplasm
+MNXR100010	1	H2O	reactant	cytoplasm
+MNXR100010	1	D-galactose	product	cytoplasm
+MNXR100010	1	raffinose	product	cytoplasm
+MNXR122225	2	raffinose	product	cytoplasm
+MNXR122225	1	stachyose	reactant	cytoplasm
+MNXR122225	1	sucrose	reactant	cytoplasm
+MNXR123213	1	6-phospho-D-gluconate	reactant	cytoplasm
+MNXR123213	1	D-gluconate	product	cytoplasm
+MNXR123213	1	phosphate	product	cytoplasm
+MNXR110535	1	H+	reactant	cytoplasm
+MNXR110535	1	phenylacetic acid	reactant	cytoplasm
+MNXR110535	1	4-hydroxyphenyl acetate	product	cytoplasm
+MNXR110621	1	H+	reactant	cytoplasm
+MNXR110621	1	acetate	reactant	cytoplasm
+MNXR110621	1	Hydroquinone	reactant	cytoplasm
+MNXR110621	1	H2O	product	cytoplasm
+MNXR110621	1	4-hydroxyphenyl acetate	product	cytoplasm

ComplementaryData/modelCuration/Metabolomics_newRxnMetAnnotation.tsv

@@ -0,0 +1,15 @@
+NewMetName	Charged formula	Charge	compartment	KEGG ID	CHEBI ID	Remark	Ref
+2-hydroxyglutarate [cytoplasm]	C5H6O5	-2	cytoplasm	C02630	CHEBI:11596	MNXM1210	DOI: 10.1002/biot.201500613; DOI: 10.1021/ac302881e; DOI: 10.1186/jbiol54
+propionyl-CoA [cytoplasm]	C24H36N7O17P3S	-4	cytoplasm	C00100	CHEBI:57392	MNXM86	exist in model, but in another compartment
+3-oxopropanoate [cytoplasm]	C3H3O3	-1	cytoplasm	C00222	CHEBI:33190	MNXM244	DOI: 10.1186/s12918-016-0350-8; DOI: 10.1007/s11306-017-1195-x
+(R)-2,3-dihydroxy-3-methylbutanoate [cytoplasm]	C5H9O4	-1	cytoplasm	C04272	CHEBI:49072	MNXM114097	exist in model, but in another compartment
+3-hydroxy-3-methyl-2-oxobutanoate [cytoplasm]	C5H7O4	-1	cytoplasm	C04181	CHEBI:11812	MNXM1638	DOI: 10.1186/s12918-016-0350-8; DOI: 10.1007/s11306-017-1195-x
+2-acetyllactic acid [cytoplasm]	C5H7O4	-1	cytoplasm	C00900	CHEBI:57774	MNXM426	exist in model, but in another compartment
+(2S)-2-acetolactate [cytoplasm]	C5H7O4	-1	cytoplasm	C06010	CHEBI:58476	MNXM114079	DOI: 10.1186/s12918-016-0350-8; DOI: 10.1007/s11306-017-1195-x
+(2R,3S)-3-methylmalate [cytoplasm]	C5H6O5	-2	cytoplasm	C06032	CHEBI:58511	MNXM2512	DOI: 10.1186/s12918-016-0350-8; DOI: 10.1007/s11306-017-1195-x
+trans-2,cis-9-octadecadienoyl-CoA [cytoplasm]	C39H62N7O17P3S	-4	cytoplasm	C02050	CHEBI:57383	MNXM638	exist in model, but in another compartment
+(9Z,12Z)-octadecadienoate [cytoplasm]	C18H31O2	-1	cytoplasm	C01595	CHEBI:30245	MNXM293	DOI: 10.1186/s12918-016-0350-8; DOI: 10.1007/s11306-017-1195-x; DOI: 10.1016/j.procbio.2017.04.003; DOI: 10.1038/srep42659
+stachyose [cytoplasm]	C24H42O21	0	cytoplasm	C01613	CHEBI:17164	MNXM1503	DOI: 10.1186/s12918-016-0350-8; DOI: 10.1007/s11306-017-1195-x
+raffinose [cytoplasm]	C18H32O16	0	cytoplasm	C00492	CHEBI:16634	MNXM621	exist in model, but in another compartment
+4-hydroxyphenyl acetate [cytoplasm]	C8H8O3	0	cytoplasm	C00642	CHEBI:18101	MNXM3863	DOI: 10.1186/s12918-016-0350-8; DOI: 10.1007/s11306-017-1195-x
+Hydroquinone [cytoplasm]	C6H6O2	0	cytoplasm	C00530	CHEBI:17594	MNXM376	exist in model, but in another compartment

ComplementaryData/modelCuration/Metabolomics_newRxnProp.tsv

@@ -0,0 +1,22 @@
+RxnID	rev	RxnName	EC	rxnID_kegg	Source
+MNXR100390	0	ATP:D-Gluconate 6-phosphotransferase	2.7.1.12	R01737	rhea:19433
+MNXR123213	0	6-phosphogluconate phosphatase	3.1.3.-;3.1.3.2;3.1.3.29		metacyc:RXN0-5185
+MNXR110535	0	R06790		R06790	seed:rxn04605
+MNXR110621	0	Carboxylic ester hydrolases	3.1.1.-;3.1.1.2		rhea:47384
+MNXR111769	1	phosphoglycerate dehydrogenase	1.1.1.95	R08198	rhea:13449
+MNXR134240	1	seed:rxn00681			seed:rxn00681
+MNXR95862	1	beta-alanine:2-oxoglutarate aminotransferase	2.6.1.19;2.6.1.55	R00908	rhea:30699
+MNXR101665	0	3-Oxopropanoate:NAD+ oxidoreductase (decarboxylating, CoA-acetylating)	1.2.1.-;1.2.1.18;1.2.1.27	R00705	rhea:22992
+MNXR106650	0	3-Oxopropanoate:NADP+ oxidoreductase (decarboxylating, CoA-acetylating)	1.2.1.-;1.2.1.18	R00706	rhea:22988
+MNXR110693	0	3-oxopropanoate carboxy-lyase	4.1.1.-;4.2.1.155	R06973	rhea:45160
+MNXR100904	1	(R)-2,3-Dihydroxy-3-methylbutanoate:NADP+ oxidoreductase (isomerizing)	1.1.1.86	R04440	rhea:31139
+MNXR137278	0	Dihydroxy-acid dehydratase, mitochondrial			seed:rxn13007
+MNXR137279	0	Ketol-acid reductoisomerase, mitochondrial			seed:rxn13008
+MNXR95271	0	pyruvate:pyruvate acetaldehydetransferase (decarboxylating); (S)-2-acetolactate pyruvate-lyase (carboxylating)	2.2.1.6	R00226	rhea:25249
+MNXR97523	1	(R)-2,3-dihydroxy-3-methylbutanoate:NADP+ oxidoreductase (isomerizing)	1.1.1.383;1.1.1.86	R04439	rhea:22068
+MNXR106779	0	(2R,3S)-3-methylmalate:NAD+ oxidoreductase	1.1.1.-;1.1.1.85	R00994	rhea:32715
+MNXR121603	0	malate/β-methylmalate synthase	2.3.3.-		metacyc:RXN-18333
+MNXR99136	0	palmitoyl-CoA hydrolase	3.1.2.-;3.1.2.2		rhea:40143
+MNXR99175	0	long-chain-fatty-acid---CoA ligase	6.2.1.3		rhea:33651
+MNXR100010	0	a-galactosidase (stachyose)	3.2.1.22		seed:rxn02596
+MNXR122225	0	stachyose synthase	2.4.1.-		metacyc:RXN-8287

ComplementaryData/physiology/biomassComposition_Forster2003.tsv

@@ -0,0 +1,38 @@
+model_id	name	abundance_mmol/gDW	MW_g/mol	group
+s_0001[ce]	(1->3)-beta-D-glucan	0.8506	180.16	carbohydrate
+s_0004[ce]	(1->6)-beta-D-glucan	0.2842	180.16	carbohydrate
+s_0404[c]	alanine	0.4588	89.09	protein
+s_0423[c]	AMP	0.046	347.22	RNA
+s_0428[c]	arginine	0.1607	174.2	protein
+s_0430[c]	asparagine	0.1017	132.12	protein
+s_0432[c]	aspartic acid	0.2975	133.11	protein
+s_0509[c]	chitin	0.000001	221.21	carbohydrate
+s_0526[c]	CMP	0.0447	323.2	RNA
+s_0542[c]	cysteine	0.0066	121.16	protein
+s_0584[c]	dAMP	0.0036	331.22	DNA
+s_0589[c]	dCMP	0.0024	307.2	DNA
+s_0615[c]	dGMP	0.0024	345.21	DNA
+s_0649[c]	dTMP	0.0036	322.21	DNA
+s_0747[c]	glutamine	0.1054	146.14	protein
+s_0748[c]	glutamic acid	0.3018	147.13	protein
+s_0757[c]	glycine	0.2904	75.07	protein
+s_0773[c]	glycogen	0.5185	180.16	carbohydrate
+s_0782[c]	GMP	0.046	363.22	RNA
+s_0832[c]	histidine	0.0663	155.15	protein
+s_0847[c]	isoleucine	0.1927	131.17	protein
+s_1077[c]	leucine	0.2964	131.17	protein
+s_1099[c]	lysine	0.2862	146.19	protein
+s_1107[c]	mannan	0.8079	180.16	carbohydrate
+s_1148[c]	methionine	0.0507	149.21	protein
+s_1314[c]	Phenylalanine	0.1339	165.19	protein
+s_1379[c]	proline	0.1647	115.13	protein
+s_1405[c]	riboflavin	0.00099	376.36	other
+s_1428[c]	serine	0.1854	105.09	protein
+s_1467[c]	sulphate	0.02	96.06	other
+s_1491[c]	threonine	0.1914	119.12	protein
+s_1520[c]	trehalose	0.0234	342.296	carbohydrate
+s_1527[c]	tryptophan	0.0284	204.23	protein
+s_1533[c]	tyrosine	0.102	181.19	protein
+s_1545[c]	UMP	0.0599	324.18	RNA
+s_1561[c]	valine	0.2646	117.15	protein
+s_3714[c]	heme a	0.000001	852.83	other

ComplementaryData/physiology/biomassComposition_Lahtvee2017.tsv

@@ -0,0 +1,9 @@
+model_id	name	abundance_g/gDW
+s_1520[c]	trehalose	0.050958
+s_0773[c]	glycogen	0.0666
+s_3717[c]	protein	0.46
+s_3719[c]	RNA	0.061
+s_3740[c]	C16:0chain	0.00808584
+s_3741[c]	C16:1chain	0.02373021
+s_3742[c]	C18:0chain	0.002266316
+s_3743[c]	C18:1chain	0.008706639

ComplementaryData/physiology/chemostatData_VanHoek1998.tsv

@@ -0,0 +1,5 @@
+Drate	GlucoseUptake	O2uptake	CO2production
+0.025	0.30	0.80	0.80
+0.05	0.60	1.30	1.40
+0.10	1.10	2.50	2.70
+0.15	1.70	3.90	4.20

ComplementaryScripts/increaseVersion.m

@@ -1,10 +1,19 @@
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-% increaseVersion(bumpType)
-%
-% Benjamín J. Sánchez
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-
 function increaseVersion(bumpType)
+% increaseVersion
+%   Upgrades the model to a new version. Run this function after merging
+%   changes to the master branch for making a new release.
+%
+%   bumpType    One of the following 3 strings: "major", "minor" or
+%               "patch", indicating the type of increase of version to be
+%               performed.
+%
+%   NOTE: This function requires a git wrapper added to the MATLAB search
+%         path: https://github.com/manur/MATLAB-git
+%
+%   Usage: increaseVersion(bumpType)
+%
+%   Benjamin Sanchez, 2018-09-25
+%
 
 %Check if in master:
 currentBranch = git('rev-parse --abbrev-ref HEAD');
@@ -74,7 +83,7 @@ function increaseVersion(bumpType)
         'then merge to master, and try again.'])
 end
 
-%Allow .mat & .xls storage:
+%Allow .mat & .xlsx storage:
 copyfile('../.gitignore','backup')
 fin  = fopen('backup','r');
 fout = fopen('../.gitignore','w');
@@ -95,6 +104,14 @@ function increaseVersion(bumpType)
 
 %Convert to RAVEN format and store model as .xlsx:
 model = ravenCobraWrapper(model);
+model.annotation.defaultLB    = -1000;
+model.annotation.defaultUB    = +1000;
+model.annotation.taxonomy     = 'taxonomy/559292';
+model.annotation.givenName    = 'Benjamin';
+model.annotation.familyName   = 'Sanchez';
+model.annotation.email        = '[email protected]';
+model.annotation.organization = 'Chalmers University of Technology';
+model.annotation.note         = 'Saccharomyces cerevisiae - strain S288C';
 exportToExcelFormat(model,'../ModelFiles/xlsx/yeastGEM.xlsx');
 
 %Update version file:
@@ -103,5 +120,3 @@ function increaseVersion(bumpType)
 fclose(fid);
 
 end
-
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

ComplementaryScripts/modelCuration/SubstrateUsage.m

@@ -2,7 +2,7 @@
 % SubstrateUsage
 %
 % Automatically adds exchange reactions for every metabolite in 
-% ComplementaryData/modelCuration/Biolog_substrate.tsv and checks whether
+% ComplementaryData/physiology/Biolog_substrate.tsv and checks whether
 % it can be used as a "solo" substrate.
 %
 % NOTE: requires COBRA
@@ -15,7 +15,7 @@
 model = loadYeastModel;
 
 % Load data:
-fid2 = fopen('../ComplementaryData/modelCuration/Biolog_substrate.tsv');
+fid2 = fopen('../ComplementaryData/physiology/Biolog_substrate.tsv');
 substrate = textscan(fid2,'%s %s %s %s %s %s','Delimiter','\t','HeaderLines',1);
 SubBiologName = substrate{1};
 SubModelName  = substrate{2};
@@ -139,7 +139,7 @@
 
 % Update results from model:
 cd ..
-fid2 = fopen('../ComplementaryData/modelCuration/Biolog_substrate.tsv','w');
+fid2 = fopen('../ComplementaryData/physiology/Biolog_substrate.tsv','w');
 formatSpec = '%s\t%s\t%s\t%s\t%s\n';
 fprintf(fid2,formatSpec,'Substrate','Name_in_Model','Substrate_type','Growth_Biolog','Growth_Model');
 for i = 1:length(FBAresult)