From 034d763e9c00a9c2e842e30d38aa061f2a7a0794 Mon Sep 17 00:00:00 2001 From: KennetLindquist Date: Wed, 4 Feb 2026 16:28:19 +0100 Subject: [PATCH 1/2] fix: make succt1pp irreversible in the forward direction fix: make succt1pp irreversible in the forward direction according to issue #37. --- model/Ecoli-GEM.yml | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/model/Ecoli-GEM.yml b/model/Ecoli-GEM.yml index fa8683e..ac4027f 100644 --- a/model/Ecoli-GEM.yml +++ b/model/Ecoli-GEM.yml @@ -2,7 +2,7 @@ - metaData: id: "Ecoli-GEM" name: "The Consensus Genome-Scale Metabolic Model of Escherichia coli" - date: "2025-10-30" + date: "2026-02-04" version: "" github: "https://github.com/SysBioChalmers/Ecoli-GEM" - metabolites: @@ -79112,8 +79112,8 @@ - hom__L_c: 1.0 - nadp_c: 1.0 - nadph_c: -1.0 - - lower_bound: 0 - - upper_bound: 1000 + - lower_bound: 0.0 + - upper_bound: 1000.0 - gene_reaction_rule: b3940 or b0002 - subsystem: Threonine and Lysine Metabolism - annotation: !!omap @@ -100346,10 +100346,10 @@ - id: SUCCt1pp - name: Succinate transport via diffusion in (periplasm) - metabolites: !!omap - - succ_c: 1.0 - - succ_p: -1.0 - - lower_bound: 0.0 - - upper_bound: 1000.0 + - succ_c: -1.0 + - succ_p: 1.0 + - lower_bound: 0 + - upper_bound: 1000 - gene_reaction_rule: b1206 - subsystem: Transport, Inner Membrane - annotation: !!omap From 4fc2c459da90d287f6d70da1b5aed7d0a6ee6507 Mon Sep 17 00:00:00 2001 From: KennetLindquist Date: Wed, 4 Feb 2026 15:32:06 +0000 Subject: [PATCH 2/2] chore: add macaw test result --- data/testResults/macaw_results.csv | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/data/testResults/macaw_results.csv b/data/testResults/macaw_results.csv index e0a32bc..74f060f 100644 --- a/data/testResults/macaw_results.csv +++ b/data/testResults/macaw_results.csv @@ -2500,7 +2500,7 @@ SSALy,h2o_c + nadp_c + sucsal_c --> 2.0 h_c + nadph_c + succ_c,ok,ok,ok,ok,N/A SUCASPtpp,asp__L_p + succ_c <=> asp__L_c + succ_p,ok,ok,ok,ok,N/A SUCBZL,atp_c + coa_c + sucbz_c --> amp_c + ppi_c + sbzcoa_c,ok,ok,ok,ok,N/A SUCBZS,2shchc_c --> h2o_c + sucbz_c,ok,ok,ok,ok,N/A -SUCCt1pp,succ_p --> succ_c,ok,ok,ok,ok,N/A +SUCCt1pp,succ_c --> succ_p,ok,ok,ok,ok,N/A SUCCt2_2pp,2.0 h_p + succ_p --> 2.0 h_c + succ_c,ok,ok,ok,SUCCt2_3pp,N/A SUCCt2_3pp,3.0 h_p + succ_p --> 3.0 h_c + succ_c,ok,ok,ok,SUCCt2_2pp,N/A SUCCtex,succ_e <=> succ_p,only when going forwards,ok,ok,ok,N/A