From e4a3d59b28f69fea0f262894ea48b67dad088094 Mon Sep 17 00:00:00 2001 From: Eduard Kerkhoven Date: Sat, 23 Nov 2024 16:05:13 +0100 Subject: [PATCH] chore: round of model I/O --- README.md | 2 +- model/dependencies.txt | 2 +- model/yeast-GEM.txt | 4 ++-- model/yeast-GEM.xml | 8 ++++---- model/yeast-GEM.yml | 2 +- 5 files changed, 9 insertions(+), 9 deletions(-) diff --git a/README.md b/README.md index 0e5c140e..0d1ea942 100644 --- a/README.md +++ b/README.md @@ -39,7 +39,7 @@ This repository contains the current consensus genome-scale metabolic model of _ | Taxonomy | Latest update | Version | Reactions | Metabolites | Genes | |:-------|:--------------|:------|:------|:----------|:-----| -| _Saccharomyces cerevisiae_ | 14-Nov-2024 | develop | 4131 | 2806 | 1161 | +| _Saccharomyces cerevisiae_ | 23-Nov-2024 | develop | 4131 | 2806 | 1161 | # Installation & usage diff --git a/model/dependencies.txt b/model/dependencies.txt index 521bd83c..e7ad180d 100644 --- a/model/dependencies.txt +++ b/model/dependencies.txt @@ -1,4 +1,4 @@ MATLAB 24.1.0.2568132 (R2024a) Update 1 libSBML 5.20.2 -RAVEN_toolbox commit c90390e +RAVEN_toolbox 2.10.2 COBRA_toolbox 3.4 diff --git a/model/yeast-GEM.txt b/model/yeast-GEM.txt index 2fcfc84c..08be6e37 100755 --- a/model/yeast-GEM.txt +++ b/model/yeast-GEM.txt @@ -653,7 +653,7 @@ r_0810 GDP[g] + H2O[g] => GMP[g] + H+[g] + phosphate[g] YEL042W 0.00 1000.00 r_0811 ATP[c] + UDP[c] => ADP[c] + UTP[c] YKL067W 0.00 1000.00 0.00 r_0812 methanethiol[c] + O-acetyl-L-homoserine[c] => acetate[c] + H+[c] + L-methionine[c] YLR303W 0.00 1000.00 0.00 r_0813 hydrogen sulfide[c] + O-acetyl-L-homoserine[c] => acetate[c] + L-homocysteine[c] YLR303W 0.00 1000.00 0.00 -r_0815 L-cysteine[c] + O-succinyl-L-homoserine[c] <=> H+[c] + L-cystathionine[c] + succinate[c] YLL058W or YML082W or YAL012W 0.00 1000.00 0.00 +r_0815 L-cysteine[c] + O-succinyl-L-homoserine[c] => H+[c] + L-cystathionine[c] + succinate[c] YLL058W or YML082W or YAL012W 0.00 1000.00 0.00 r_0816 carbamoyl phosphate[c] + ornithine[c] => H+[c] + L-citrulline[c] + phosphate[c] YJL088W 0.00 1000.00 0.00 r_0817 H+[c] + ornithine[c] => carbon dioxide[c] + putrescine[c] YKL184W 0.00 1000.00 0.00 r_0818 L-glutamate[m] + N(2)-acetyl-L-ornithine[m] => N-acetyl-L-glutamate[m] + ornithine[m] YMR062C 0.00 1000.00 0.00 @@ -4050,7 +4050,7 @@ r_4699 ethyl propionate[e] => 0.00 1000.00 0.00 r_4700 hydrogen sulfide[c] => hydrogen sulfide[e] YIL166C 0.00 1000.00 0.00 r_4701 H2O[m] + L-cysteine[m] <=> ammonium[m] + pyruvate[m] + hydrogen sulfide[m] YFR055W -1000.00 1000.00 0.00 r_4702 2-oxoglutarate[c] + L-cysteine[c] <=> L-glutamate[c] + 3-mercaptopyruvate[c] -1000.00 1000.00 0.00 -r_4703 TRX1[c] + 3-mercaptopyruvate[c] <=> hydrogen sulfide[c] + pyruvate[c] + TRX1 disulphide[c] YOR251C 0.00 1000.00 0.00 +r_4703 TRX1[c] + 3-mercaptopyruvate[c] => hydrogen sulfide[c] + pyruvate[c] + TRX1 disulphide[c] YOR251C 0.00 1000.00 0.00 r_4704 alkanesulfonate[e] => alkanesulfonate[c] YIL166C 0.00 1000.00 0.00 r_4705 taurocholate[e] => taurocholate[c] YIL166C 0.00 1000.00 0.00 r_4706 2-oxoglutarate[c] + oxygen[c] + alkanesulfonate[c] <=> aminoacetaldehyde[c] + carbon dioxide[c] + succinate[c] + sulphite[c] YLL057C -1000.00 1000.00 0.00 diff --git a/model/yeast-GEM.xml b/model/yeast-GEM.xml index bb1efd89..c664e445 100644 --- a/model/yeast-GEM.xml +++ b/model/yeast-GEM.xml @@ -24,10 +24,10 @@ - 2024-11-14T21:12:33Z + 2024-11-23T16:03:25Z - 2024-11-14T21:12:33Z + 2024-11-23T16:03:25Z @@ -65955,7 +65955,7 @@ - +

Confidence Level: 3

@@ -166516,7 +166516,7 @@ - +

AUTHORS: 10.1093/femsyr/foy046

diff --git a/model/yeast-GEM.yml b/model/yeast-GEM.yml index 5d669ce6..fb81ec00 100755 --- a/model/yeast-GEM.yml +++ b/model/yeast-GEM.yml @@ -4,7 +4,7 @@ id: "yeastGEM_develop" name: "The Consensus Genome-Scale Metabolic Model of Yeast" version: "" - date: "2024-11-14" + date: "2024-11-23" defaultLB: "-1000" defaultUB: "1000" givenName: "Eduard"