From f88f507ed3e0704b61f0dfe2b293f454bb3a09c9 Mon Sep 17 00:00:00 2001 From: FEIRANL Date: Tue, 4 Dec 2018 17:16:51 +0100 Subject: [PATCH 1/4] style-data:add a title to the file 'biomassComposition_Cofactor_Ion.tsv' Add a title for the data file --- ComplementaryData/physiology/biomassComposition_Cofactor_Ion.tsv | 1 + 1 file changed, 1 insertion(+) diff --git a/ComplementaryData/physiology/biomassComposition_Cofactor_Ion.tsv b/ComplementaryData/physiology/biomassComposition_Cofactor_Ion.tsv index 4ab2f660..6a948332 100644 --- a/ComplementaryData/physiology/biomassComposition_Cofactor_Ion.tsv +++ b/ComplementaryData/physiology/biomassComposition_Cofactor_Ion.tsv @@ -1,3 +1,4 @@ +model_id name abundance_mmol/gDW MW_g/mol group reference s_3880[c] Ca(2+) 2.17E-04 40.08 ion DOI: 10.22161/ijeab/2.2.2 s_3778[c] chloride 1.29E-03 35.45 ion DOI: 10.3103/S106836741702015X s_4019[c] Cu2(+) 6.59E-04 63.55 ion DOI: 10.22161/ijeab/2.2.2 From 1715d0a0e2770e7ac92324bd646aeac28e5aaf6d Mon Sep 17 00:00:00 2001 From: FEIRANL Date: Tue, 4 Dec 2018 20:58:56 +0100 Subject: [PATCH 2/4] fix-data: update the data with Ca2+ exchange reaction Add a exchange reaction for Ca 2+ --- ComplementaryData/modelCuration/Biomass_newRxnMatrix.tsv | 1 + ComplementaryData/modelCuration/Biomass_newRxnProp.tsv | 1 + 2 files changed, 2 insertions(+) diff --git a/ComplementaryData/modelCuration/Biomass_newRxnMatrix.tsv b/ComplementaryData/modelCuration/Biomass_newRxnMatrix.tsv index 419ceaf3..63d8de54 100644 --- a/ComplementaryData/modelCuration/Biomass_newRxnMatrix.tsv +++ b/ComplementaryData/modelCuration/Biomass_newRxnMatrix.tsv @@ -26,3 +26,4 @@ Cu2(+) exchange 1 Cu2(+) reactant extracellular Mn(2+) exchange 1 Mn(2+) reactant extracellular Zn(2+) exchange 1 Zn(2+) reactant extracellular Mg(2+) exchange 1 Mg(2+) reactant extracellular +Ca(2+) exchange 1 Ca(2+) reactant extracellular diff --git a/ComplementaryData/modelCuration/Biomass_newRxnProp.tsv b/ComplementaryData/modelCuration/Biomass_newRxnProp.tsv index edb28e21..fafebfc6 100644 --- a/ComplementaryData/modelCuration/Biomass_newRxnProp.tsv +++ b/ComplementaryData/modelCuration/Biomass_newRxnProp.tsv @@ -10,3 +10,4 @@ Cu2(+) exchange 1 Cu2(+) exchange Mn(2+) exchange 1 Mn(2+) exchange Zn(2+) exchange 1 Zn(2+) exchange Mg(2+) exchange 1 Mg(2+) exchange +Ca(2+) exchange 1 Ca(2+) exchange From c6dc07bb85c093e7439fd81d23d94c0d641c5c8f Mon Sep 17 00:00:00 2001 From: FEIRANL Date: Tue, 4 Dec 2018 21:02:11 +0100 Subject: [PATCH 3/4] feat-rxns: add Ca2+ exchange reaction change the function to let Ca2+ can enter into the cell freely update in the model --- .../modelCuration/minimal_Y6.m | 3 +- ModelFiles/boundaryMets.txt | 1 + ModelFiles/dependencies.txt | 2 +- ModelFiles/txt/yeastGEM.txt | 5 +-- ModelFiles/xml/yeastGEM.xml | 33 ++++++++++++++++--- ModelFiles/yml/yeastGEM.yml | 19 ++++++++--- README.md | 4 +-- 7 files changed, 52 insertions(+), 15 deletions(-) diff --git a/ComplementaryScripts/modelCuration/minimal_Y6.m b/ComplementaryScripts/modelCuration/minimal_Y6.m index 39b37fc2..b9f686b5 100755 --- a/ComplementaryScripts/modelCuration/minimal_Y6.m +++ b/ComplementaryScripts/modelCuration/minimal_Y6.m @@ -27,6 +27,7 @@ 'r_4597'; ... % Mg(2+) exchange 'r_2049'; ... % sodium exchange 'r_4594'; ... % Cu(2+) exchange + 'r_4600'; ... % Ca(2+) exchange 'r_2020' }; % potassium exchange blockedExchanges = {'r_1663'; ... % bicarbonate exchange @@ -39,7 +40,7 @@ glucoseExchangeIndex = findRxnIDs(model,glucoseExchange); BlockedRxnIndex = findRxnIDs(model,blockedExchanges); -if length(find(uptakeRxnIndexes~= 0)) ~= 14 +if length(find(uptakeRxnIndexes~= 0)) ~= 15 warning('Not all exchange reactions were found.') end diff --git a/ModelFiles/boundaryMets.txt b/ModelFiles/boundaryMets.txt index c8c2baca..a2d06263 100644 --- a/ModelFiles/boundaryMets.txt +++ b/ModelFiles/boundaryMets.txt @@ -243,3 +243,4 @@ s_4201[e] Cu2(+) [extracellular] s_4202[e] Mn(2+) [extracellular] s_4203[e] Zn(2+) [extracellular] s_4204[e] Mg(2+) [extracellular] +s_4199[e] Ca(2+) [extracellular] diff --git a/ModelFiles/dependencies.txt b/ModelFiles/dependencies.txt index 91284b25..ff6db5c2 100644 --- a/ModelFiles/dependencies.txt +++ b/ModelFiles/dependencies.txt @@ -1,4 +1,4 @@ -MATLAB 9.5.0.944444 (R2018b) +MATLAB 9.1.0.441655 (R2016b) libSBML 5.17.0 RAVEN_toolbox 2.1.0 COBRA_toolbox 3.0.2 diff --git a/ModelFiles/txt/yeastGEM.txt b/ModelFiles/txt/yeastGEM.txt index f11d12a6..33cb9e2d 100644 --- a/ModelFiles/txt/yeastGEM.txt +++ b/ModelFiles/txt/yeastGEM.txt @@ -3415,7 +3415,7 @@ r_4044 s_3716[e] -> 0.00 1000.00 0.00 r_4041 55.3 s_0434[c] + 55.3 s_0803[c] + s_1096[c] + s_3717[c] + s_3718[c] + s_3719[c] + s_3720[c] + s_4205[c] + s_4206[c] -> 55.3 s_0394[c] + s_0450[c] + 55.3 s_0794[c] + 55.3 s_1322[c] 0.00 1000.00 0.00 r_4046 s_0434[c] + s_0803[c] -> s_0394[c] + s_0794[c] + s_1322[c] 0.70 0.70 0.00 r_4047 0.527012 s_0404[c] + 0.184592 s_0428[c] + 0.11682 s_0430[c] + 0.341731 s_0432[c] + 0.00758126 s_0542[c] + 0.12107 s_0747[c] + 0.34667 s_0748[c] + 0.333575 s_0757[c] + 0.0761572 s_0832[c] + 0.22135 s_0847[c] + 0.340467 s_1077[c] + 0.328751 s_1099[c] + 0.0582379 s_1148[c] + 0.153808 s_1314[c] + 0.189187 s_1379[c] + 0.212964 s_1428[c] + 0.219857 s_1491[c] + 0.0326224 s_1527[c] + 0.117165 s_1533[c] + 0.30394 s_1561[c] -> 0.527012 s_1582[c] + 0.184592 s_1583[c] + 0.11682 s_1585[c] + 0.341731 s_1587[c] + 0.00758126 s_1589[c] + 0.12107 s_1590[c] + 0.34667 s_1591[c] + 0.333575 s_1593[c] + 0.0761572 s_1594[c] + 0.22135 s_1596[c] + 0.340467 s_1598[c] + 0.328751 s_1600[c] + 0.0582379 s_1602[c] + 0.153808 s_1604[c] + 0.189187 s_1606[c] + 0.212964 s_1607[c] + 0.219857 s_1608[c] + 0.0326224 s_1610[c] + 0.117165 s_1612[c] + 0.30394 s_1614[c] + s_3717[c] 0.00 1000.00 0.00 -r_4048 0.748532 s_0001[ce] + 0.250097 s_0004[ce] + 0.361423 s_0773[c] + 0.710956 s_1107[c] + 0.138279 s_1520[c] -> s_3718[c] 0.00 1000.00 0.00 +r_4048 0.748515 s_0001[ce] + 0.250092 s_0004[ce] + 0.361415 s_0773[c] + 0.71094 s_1107[c] + 0.138276 s_1520[c] -> s_3718[c] 0.00 1000.00 0.00 r_4049 0.0445348 s_0423[c] + 0.0432762 s_0526[c] + 0.0445348 s_0782[c] + 0.0579921 s_1545[c] -> s_3719[c] 0.00 1000.00 0.00 r_4050 0.0036 s_0584[c] + 0.0024 s_0589[c] + 0.0024 s_0615[c] + 0.0036 s_0649[c] -> s_3720[c] 0.00 1000.00 0.00 r_4051 s_3721[g] -> s_3722[c] 0.00 1000.00 0.00 @@ -3960,4 +3960,5 @@ r_4595 s_4202[e] <=> -1000.00 1000.00 0.00 r_4596 s_4203[e] <=> -1000.00 1000.00 0.00 r_4597 s_4204[e] <=> -1000.00 1000.00 0.00 r_4598 0.00019 s_0529[c] + 1e-05 s_0687[c] + 0.00265 s_1198[c] + 0.00015 s_1203[c] + 0.00057 s_1207[c] + 0.0027 s_1212[c] + 0.00099 s_1405[c] + 1.2e-06 s_1475[c] + 6.34e-05 s_1487[c] + 1e-06 s_3714[c] -> s_4205[c] 0.00 1000.00 0.00 -r_4599 3.04e-05 s_0924[c] + 0.00363 s_1373[c] + 0.00397 s_1437[c] + 0.02 s_1467[c] + 0.00129 s_3778[c] + 0.00273 s_3801[c] + 0.000748 s_3822[c] + 0.00124254 s_4013[c] + 0.000659 s_4019[c] -> s_4206[c] 0.00 1000.00 0.00 +r_4599 3.04e-05 s_0924[c] + 0.00363 s_1373[c] + 0.00397 s_1437[c] + 0.02 s_1467[c] + 0.00129 s_3778[c] + 0.00273 s_3801[c] + 0.000748 s_3822[c] + 0.000217 s_3880[c] + 0.00124254 s_4013[c] + 0.000659 s_4019[c] -> s_4206[c] 0.00 1000.00 0.00 +r_4600 s_4199[e] <=> -1000.00 1000.00 0.00 diff --git a/ModelFiles/xml/yeastGEM.xml b/ModelFiles/xml/yeastGEM.xml index c9164cc3..0d388fd4 100644 --- a/ModelFiles/xml/yeastGEM.xml +++ b/ModelFiles/xml/yeastGEM.xml @@ -175476,11 +175476,11 @@ - - - - - + + + + + @@ -192668,6 +192668,7 @@ + @@ -192675,6 +192676,28 @@ + + + +

Confidence Level: 1

+

NOTES:added for BiomassUpdate (PR #174)

+ + + + + + + + + + + + + + + + + diff --git a/ModelFiles/yml/yeastGEM.yml b/ModelFiles/yml/yeastGEM.yml index 314a65ad..80c1dfc5 100644 --- a/ModelFiles/yml/yeastGEM.yml +++ b/ModelFiles/yml/yeastGEM.yml @@ -86148,10 +86148,10 @@ - id: r_4048 - name: carbohydrate pseudoreaction - metabolites: !!omap - - s_0001: -0.74853 - - s_0004: -0.2501 - - s_0773: -0.36142 - - s_1107: -0.71096 + - s_0001: -0.74851 + - s_0004: -0.25009 + - s_0773: -0.36141 + - s_1107: -0.71094 - s_1520: -0.13828 - s_3718: 1 - lower_bound: 0 @@ -93987,6 +93987,7 @@ - s_3778: -0.00129 - s_3801: -0.00273 - s_3822: -0.000748 + - s_3880: -0.000217 - s_4013: -0.0012425 - s_4019: -0.000659 - s_4206: 1 @@ -93995,6 +93996,16 @@ - annotation: !!omap - sbo: SBO:0000395 - confidence_score: 0 + - !!omap + - id: r_4600 + - name: Ca(2+) exchange + - metabolites: !!omap + - s_4199: -1 + - lower_bound: -1000 + - upper_bound: 1000 + - annotation: !!omap + - sbo: SBO:0000627 + - confidence_score: 1 - genes: - !!omap - id: GR191W diff --git a/README.md b/README.md index 502eebb5..f44b6b24 100644 --- a/README.md +++ b/README.md @@ -10,13 +10,13 @@ This repository contains the current consensus genome-scale metabolic model of _ **GEM Category:** species; **Utilisation:** experimental data reconstruction, multi-omics integrative analysis, _in silico_ strain design, model template; **Field:** metabolic-network reconstruction; **Type of Model:** reconstruction, curated; **Model Source:** YeastMetabolicNetwork; **Omic Source:** genomics, metabolomics; **Taxonomy:** _Saccharomyces cerevisiae_; **Metabolic System:** general metabolism; **Bioreactor**; **Strain:** S288C; **Condition:** aerobic, glucose-limited, defined media; -* Last update: 2018-11-26 +* Last update: 2018-12-04 * Main Model Descriptors: |Taxonomy | Template Model | Reactions | Metabolites| Genes | |:-------:|:--------------:|:---------:|:----------:|:-----:| -|_Saccharomyces cerevisiae_|[Yeast 7.6](https://sourceforge.net/projects/yeast/)|3962|2691|1139| +|_Saccharomyces cerevisiae_|[Yeast 7.6](https://sourceforge.net/projects/yeast/)|3963|2691|1139| This repository is administered by Benjamín J. Sánchez ([@BenjaSanchez](https://github.com/benjasanchez)), Division of Systems and Synthetic Biology, Department of Biology and Biological Engineering, Chalmers University of Technology. From c1ecddcd734d13fbe24d579e5fb46acef2ee1acf Mon Sep 17 00:00:00 2001 From: FEIRANL Date: Wed, 5 Dec 2018 21:57:28 +0100 Subject: [PATCH 4/4] fix-rxnannot:fix the rxnconfidence scores for those reactions in this update fix the rxnconfidence scores for those reactions in this update:exchange reactions: NAN; reactions for modeling: 1 --- .../modelCuration/addBiomassUpdate.m | 3 +++ ModelFiles/dependencies.txt | 2 +- ModelFiles/xml/yeastGEM.xml | 16 ++++++++-------- ModelFiles/yml/yeastGEM.yml | 10 ++-------- README.md | 2 +- 5 files changed, 15 insertions(+), 18 deletions(-) diff --git a/ComplementaryScripts/modelCuration/addBiomassUpdate.m b/ComplementaryScripts/modelCuration/addBiomassUpdate.m index 29b984db..219d2c91 100644 --- a/ComplementaryScripts/modelCuration/addBiomassUpdate.m +++ b/ComplementaryScripts/modelCuration/addBiomassUpdate.m @@ -142,6 +142,8 @@ model.rxnNotes{rxnIndex} = 'NOTES:added for BiomassUpdate (PR #174)'; if ~isempty(model.rules{rxnIndex}) model.rxnConfidenceScores(rxnIndex) = 2; %reactions has GPR rules + elseif contains(model.rxnNames(rxnIndex),'exchange') + model.rxnConfidenceScores(rxnIndex) = NaN; %exchange rxns else model.rxnConfidenceScores(rxnIndex) = 1; %reactions without gene but needed for modelling end @@ -213,6 +215,7 @@ rxnIndex = strcmp(model.rxns,rxnID); end model.rxnNotes{rxnIndex} = 'NOTES:added for BiomassUpdate (PR #174)'; + model.rxnConfidenceScores(rxnIndex) = 1; %needed for modeling model = rmfield(model,'grRules'); end diff --git a/ModelFiles/dependencies.txt b/ModelFiles/dependencies.txt index ff6db5c2..94f39789 100644 --- a/ModelFiles/dependencies.txt +++ b/ModelFiles/dependencies.txt @@ -1,7 +1,7 @@ MATLAB 9.1.0.441655 (R2016b) libSBML 5.17.0 RAVEN_toolbox 2.1.0 -COBRA_toolbox 3.0.2 +COBRA_toolbox 3.0.3 SBML_level 3 SBML_version 1 fbc_version 2 diff --git a/ModelFiles/xml/yeastGEM.xml b/ModelFiles/xml/yeastGEM.xml index 0d388fd4..3acc245d 100644 --- a/ModelFiles/xml/yeastGEM.xml +++ b/ModelFiles/xml/yeastGEM.xml @@ -192501,7 +192501,7 @@ -

Confidence Level: 1

+

Confidence Level: NaN

NOTES:added for BiomassUpdate (PR #174)

 @@ -192523,7 +192523,7 @@ -

Confidence Level: 1

+

Confidence Level: NaN

NOTES:added for BiomassUpdate (PR #174)

 @@ -192545,7 +192545,7 @@ -

Confidence Level: 1

+

Confidence Level: NaN

NOTES:added for BiomassUpdate (PR #174)

 @@ -192567,7 +192567,7 @@ -

Confidence Level: 1

+

Confidence Level: NaN

NOTES:added for BiomassUpdate (PR #174)

 @@ -192589,7 +192589,7 @@ -

Confidence Level: 1

+

Confidence Level: NaN

NOTES:added for BiomassUpdate (PR #174)

 @@ -192611,7 +192611,7 @@ -

Confidence Level: 0

+

Confidence Level: 1

NOTES:added for BiomassUpdate (PR #174)

 @@ -192645,7 +192645,7 @@ -

Confidence Level: 0

+

Confidence Level: 1

NOTES:added for BiomassUpdate (PR #174)

 @@ -192679,7 +192679,7 @@ -

Confidence Level: 1

+

Confidence Level: NaN

NOTES:added for BiomassUpdate (PR #174)

 diff --git a/ModelFiles/yml/yeastGEM.yml b/ModelFiles/yml/yeastGEM.yml index 80c1dfc5..66e65ad7 100644 --- a/ModelFiles/yml/yeastGEM.yml +++ b/ModelFiles/yml/yeastGEM.yml @@ -93915,7 +93915,6 @@ - upper_bound: 1000 - annotation: !!omap - sbo: SBO:0000627 - - confidence_score: 1 - !!omap - id: r_4594 - name: Cu2(+) exchange @@ -93925,7 +93924,6 @@ - upper_bound: 1000 - annotation: !!omap - sbo: SBO:0000627 - - confidence_score: 1 - !!omap - id: r_4595 - name: Mn(2+) exchange @@ -93935,7 +93933,6 @@ - upper_bound: 1000 - annotation: !!omap - sbo: SBO:0000627 - - confidence_score: 1 - !!omap - id: r_4596 - name: Zn(2+) exchange @@ -93945,7 +93942,6 @@ - upper_bound: 1000 - annotation: !!omap - sbo: SBO:0000627 - - confidence_score: 1 - !!omap - id: r_4597 - name: Mg(2+) exchange @@ -93955,7 +93951,6 @@ - upper_bound: 1000 - annotation: !!omap - sbo: SBO:0000627 - - confidence_score: 1 - !!omap - id: r_4598 - name: cofactor pseudoreaction @@ -93975,7 +93970,7 @@ - upper_bound: 1000 - annotation: !!omap - sbo: SBO:0000395 - - confidence_score: 0 + - confidence_score: 1 - !!omap - id: r_4599 - name: ion pseudoreaction @@ -93995,7 +93990,7 @@ - upper_bound: 1000 - annotation: !!omap - sbo: SBO:0000395 - - confidence_score: 0 + - confidence_score: 1 - !!omap - id: r_4600 - name: Ca(2+) exchange @@ -94005,7 +94000,6 @@ - upper_bound: 1000 - annotation: !!omap - sbo: SBO:0000627 - - confidence_score: 1 - genes: - !!omap - id: GR191W diff --git a/README.md b/README.md index f44b6b24..a5edbb25 100644 --- a/README.md +++ b/README.md @@ -10,7 +10,7 @@ This repository contains the current consensus genome-scale metabolic model of _ **GEM Category:** species; **Utilisation:** experimental data reconstruction, multi-omics integrative analysis, _in silico_ strain design, model template; **Field:** metabolic-network reconstruction; **Type of Model:** reconstruction, curated; **Model Source:** YeastMetabolicNetwork; **Omic Source:** genomics, metabolomics; **Taxonomy:** _Saccharomyces cerevisiae_; **Metabolic System:** general metabolism; **Bioreactor**; **Strain:** S288C; **Condition:** aerobic, glucose-limited, defined media; -* Last update: 2018-12-04 +* Last update: 2018-12-05 * Main Model Descriptors: