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* fix: remove non-metabolic genes * fix: remove the actual genes from the model
* Wrong subsystems > Peptide metabolism * Set all rxns irreversible in Peptide metabolism
fix: heneicosanoic acid in metabolicTasks_Full.txt
* feat: PR template specify merge type * feat: clarify location of deprecated IDs lists
* feat: first macaw test scripts * fix: set python version to 3.10 * fix: path to human-GEM repo * fix: correct path to macaw-tests.py * feat: store macaw results * fix: prepare output for comment post * test: storing of output file in new commit * chore: add macaw test result * fix: reorganize macaw output file * fix: write macaw results to correct location * chore: add macaw test result * fix: reset when different workflow are run * chore: add macaw test result * test: reset macaw_results to test workflow commit * chore: add macaw test result * fix: no need to specify action on PR, as push already has the same effect * fix: but run macaw only in PR as output is tracked with PR number, which would not exist with every push * fix: remove link to macaw_results in comment * fix: reference to PR # in README.md --------- Co-authored-by: edkerk <edkerk@users.noreply.github.com>
* fix: removed MAR07799 for being a less-accurate version of MAR00080 * fix: added ATP6AP1 to GPR of MAR00080 so it was still associated with at least one reaction * feat: adds new reference for MAR00080 * chore: add macaw test result * fix: stoichiometry of V-ATPase * chore: add macaw test result --------- Co-authored-by: Eduard Kerkhoven <eduardk@chalmers.se> Co-authored-by: edkerk <edkerk@users.noreply.github.com>
* feat: gene essentiality workflow with pr comment * chore: expand workflow targets * fix: add to matlab path * fix: style of macaw summary output * feat: post and store gene essentiality results * fix: model path and allow 2 workflow comments * chore: add macaw test result * fix: use recent RAVEN and gurobi * fix: avoid Penr statistic calculation * fix: missing ) in gene-essentiality.yml * chore: add gene essentiality test result * fix: gene-essentiality.yml output format * fix: location of data/testResults/README.md * chore: add macaw test result * fix: test workflow including branch update * fix: correct git-auto-commit-action@v5 * chore: add gene essentiality test result * fix: run all Hart et al. 2015 tests * fix: missing ) * chore: add gene essentiality test result * fix: only git stash pop if stash exist * fix gene-essentiality ' not " --------- Co-authored-by: Eduard Kerkhoven <eduardk@chalmers.se> Co-authored-by: edkerk <edkerk@users.noreply.github.com>
# Conflicts: # .github/workflows/macaw-tests.yml # data/testResults/README.md
feat: store summary macaw results
fix-GPR curation for Xenobiotics metabolism
Fix: GPR curation for Sulfur metabolism
…amino_acid Fix: GPR curation for subsystems related with amino acid
…tabolism Fix: GPR curation for starch and sucrose metabolism
…genes Fix: remove nonassociated genes
…of_MAR02041_MAR02036 Fix: change the reversibility of MAR02041 and MAR02036
…of-MAR04644 Fix: change the bounds of MAR04644
…for_FN_FP_genes Fix: Curate the GPRs for FN and FP genes
…nsistent_compartments- Fix: curate GPRs with inconsistent compartments
…4387_MAR04386 Fix: curate GPRs of MAR09802, MAR04387 and MAR04386
Fix: curate the GPR of MAR06474
…ene_associated Fix remove rxns without gene associated with them
mihai-sysbio
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Jul 4, 2025
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All looks good, very minor formatting issue in the TSV files.
| mead acid[c] 1 | ||
| 149 Henicosanoic acid de novo synthesis (minimal substrates, physiological excretion) O2[e];glucose[e];isoleucine[c] CO2[e];H2O[e];urate[e] | ||
| henicosanoic acid[c] 1 | ||
| 149 heneicosanoic acid de novo synthesis (minimal substrates, physiological excretion) O2[e];glucose[e];isoleucine[c] CO2[e];H2O[e];urate[e] |
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I'd suggest capitalising here and in 3 other instances below.
| "MAR04205" "" "" "RT0084" "" "" "HMR_4205" "" "HMR_4205" "RCR20258" "" 0 "" "" "HMR_4205" | ||
| "MAR08745" "" "THMMPtm" "" "" "" "" "MNXR104822" "HMR_8745" "RCR20669" "" 0 "" "" "HMR_8745" | ||
| "MAR08747" "" "THMPPtm" "" "" "" "" "MNXR104824" "HMR_8747" "RCR20670" "" 0 "" "" "HMR_8747" | ||
| MAR01459 HSD17B7r HSD17B7r MNXR100715 0 HSD17B7r |
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metabolites.tsv in the model/ folder is using quotation marks, even on the header line, but reactions.tsv does not.
In this file quotesa are removed.
For consistency, the same style should be used in both instances.
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Main improvements in this PR:
MAR07799and changes the GPR ofMAR00080as discussed in A few reactions that look fishy #348Peptide metabolismto irreversible;Peptide metabolism: MAR11413, MAR11414, MAR11411, MAR06898, MAR06861, MAR06915, MAR07149, MAR07193, MAR08979metabolicTasks_Full.txtas discussed in Update name of heneicosanoic acid in full metabolic task file #828ENSG00000175592) and EGFR (ENSG00000146648)data/macawResults/macawSummary.mdreadYAMLmodel,writeYAMLmodelandexportForGitto load and export Human-GEM;increaseHumanGEMVersionHuman-GEM.txtto showmetNames[comps];getGenesFromGrRulesfunction;README.mdto reflect changes in model I/O functions.developbranch #938developbranch #963MAR05769,MAR05891,MAR05856,MAR05821,MAR05756,MAR05757,MAR05818,MAR05813,MAR05816,MAR05758,MAR05805, MAR05759, MAR05761, MAR05804, MAR05770, MAR05771, MAR05773, MAR05774, MAR05775, MAR05786, MAR05789, MAR05467, MAR06383, MAR06379, MAR05901, MAR05886, MAR05831, MAR05811, MAR05809, MAR05806, MAR05803, MAR05802, MAR05801, MAR05799, MAR05798, MAR05794
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developas a target branch