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Human 1.17 #700
Human 1.17 #700
Commits on Sep 15, 2022
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Commits on Jun 7, 2023
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fix: remove ubiquinone-dependent versions of all duplicated reactions…
… but remove the FAD-dependent version of the SDH reaction
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Commits on Jun 8, 2023
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fix: change subsystems for MAR07672 and MAR07673 to Fatty acid biosyn…
…thesis (even-chain)
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fix: moved MAR11651 from reactions.tsv to deprecatedReactions.tsv, wh…
…ich I apparently forgot to do earlier
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Commits on Jun 9, 2023
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fix: merge annotations from deleted reactions into annotations for ke…
…pt reactions in model/reactions.tsv
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Commits on Jun 13, 2023
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- This commit includes fixing typos, and reverting back to original way of extracting subsystem values
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Commits on Jun 14, 2023
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fix: swap products and reactants of PPi <-> -PP reactions then make t…
…hem irreversible
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Commits on Jun 18, 2023
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Commits on Jun 19, 2023
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Merge pull request #625 from Devlin-Moyer/fix/merge_irrev_trans_pairs
Merge Pairs Of Irreversible Transport Reactions
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Commits on Jun 20, 2023
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fix: removes MAR05310 for being duplicate of MAR06380 with wrong stoi…
…ch & merges annotations for MAR05310 into annotations for MAR06380
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fix: remove MAR02358 for being duplicate of MAR08482, merged annotati…
…ons in reactions.tsv, and made MAR08482 reversible
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Commits on Jun 21, 2023
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Merge pull request #613 from Devlin-Moyer/fix/FAD_ubiquinone_duplicates
Fix FAD/Ubiquinone Duplicates
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fix: replace inaccurate GPR of MAR01527 and add new gene entries for …
…several sodium channels
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Commits on Jun 22, 2023
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Merge pull request #494 from SysBioChalmers/fix/simplifyGrRules
fix: adapt simplifyGrRules to updates in Matlab children function
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Commits on Jun 23, 2023
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Commits on Jun 25, 2023
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Merge pull request #663 from JHL-452b/fix-HMDB
Fix duplicate metabolites identified by HMDB IDs
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Merge pull request #661 from JHL-452b/fix-KEGG(2)
Fix duplicate metabolites identified by KEGG IDs(2)
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Merge pull request #667 from JHL-452b/fix-ChEBI(2)
Fix duplicate metabolites identified by ChEBI IDs(2)
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Merge pull request #666 from SysBioChalmers/feat/logDeprecatedIDsIn#613
feat: log duplicated ids to the column of rxnRetired
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Commits on Jun 26, 2023
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Merge pull request #662 from JHL-452b/fix-PubChem(2)
Fix duplicate metabolites identified by PubChem IDs(2)
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Merge pull request #646 from JHL-452b/fix-BiGG
Fix duplicate metabolites identified by BiGG IDs
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Merge pull request #649 from JHL-452b/fix-EHMN
Fix duplicate metabolites identified by EHMN IDs
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Merge pull request #660 from SysBioChalmers/fix/remove_MAR03767
Remove MAR03767
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Commits on Jun 27, 2023
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fix: added MAR04156 to retiredRxn column for MAR07672 and MAR07673 in…
… model/reactions.tsv
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Merge pull request #624 from Devlin-Moyer/fix/acCoA_carboxylase_rxns
Fix Acetyl-CoA Carboxylase Reactions
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test: re-introduce bug to Yaml file
- Test if GH action really work
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fix: remove MAR01458 and merge annotations (except wrong EC number) i…
…nto MAR01642 and MAR01646
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fix: replaced O2 with FAD and H2O2 with FADH2 in all peroxisomal reac…
…tions that contained O2 and H2O2
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Commits on Jun 28, 2023
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Merge pull request #650 from JHL-452b/fix-LipidMaps
Fix duplicate metabolites identified by LipidMaps IDs
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Merge pull request #641 from Devlin-Moyer/fix/ppi_rxns_round_2
Make Reversible PPi Reactions Irreversible, Part 2
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Commits on Jul 2, 2023
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Merge pull request #658 from SysBioChalmers/fix/remove_lipid_droplet_…
…loop Remove lipid droplet breakdown reaction MAR00032
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Commits on Jul 3, 2023
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Commits on Jul 4, 2023
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Commits on Jul 5, 2023
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Merge pull request #672 from SysBioChalmers/fix/yaml-test-bug
feat: add basic memote tests
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Commits on Jul 6, 2023
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Merge pull request #655 from SysBioChalmers/fix/sodium_cotransport_gprs
Fix Sodium Cotransport GPRs
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fix: retain MAR08482 in its original form
- keep MAR08482 irreversible - keep compartment specific genes for MAR08482 and MAR03931
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Merge pull request #657 from SysBioChalmers/fix/same_stoich_diff_gpr_…
…dupes Merge Reactions With Same Stoichiometry But Different Genes
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Commits on Jul 7, 2023
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Merge pull request #635 from SysBioChalmers/fix/importExportCycle
fix: GH workflow test
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Commits on Jul 10, 2023
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Commits on Jul 16, 2023
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Commits on Jul 19, 2023
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Merge pull request #676 from SysBioChalmers/fix/citrate_synthase
Make Citrate Synthase Irreversible
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Commits on Jul 21, 2023
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Merge pull request #677 from SysBioChalmers/fix/ammonium-ammonia_dupl…
…icates Merge Ammonium/Ammonia Duplicates Into Single Reactions
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Commits on Jul 28, 2023
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Commits on Aug 1, 2023
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Merge pull request #678 from SysBioChalmers/fix/remove_ppara_rxns
Remove PPARA Reactions
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Commits on Aug 2, 2023
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Commits on Aug 3, 2023
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Merge pull request #664 from SysBioChalmers/fix/sodium_channel_genes
add Alpha subunits of sodium channel genes to MAR01527
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Commits on Aug 16, 2023
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fix: sync geneShortNames field with genes field
- These gene names are now padded with empty elements, this is fine but not a decent way
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feat: enable the option to reset biomass equation or not
- Previously, the only option is to set biomass to MAR00021, now the option of reusing MAR13082 from HumanGEM is provided
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Commits on Aug 17, 2023
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Co-authored-by: Mihail Anton <mihail.anton@chalmers.se>
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Commits on Aug 18, 2023
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fix: ensure b field in single column
- This is to resolve recurring issue reported in #511
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Commits on Aug 21, 2023
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Merge pull request #692 from SysBioChalmers/fix/refineAnimalGemPipeline
fix: refine animal GEM updating pipeline
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Merge pull request #669 from SysBioChalmers/fix/remove_mito_bile_acid…
…_synth Remove Mitochondrial Bile Acid Synthesis Pathway
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Commits on Aug 29, 2023
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Merge pull request #696 from exaexa/mk-fix-gap
fix: update name for GAP in CellfieConsensus metabolic tasks
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Commits on Sep 20, 2023
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fix: re-remove deprecated reactions from "reactions.tsv"
remove rows 'MAR01639', 'MAR01635', 'MAR01637', 'MAR01653', 'MAR01656' from "reactions.tsv"
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Commits on Sep 21, 2023
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Commits on Sep 24, 2023
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Merge pull request #670 from SysBioChalmers/fix/FAD_O2_dupes
Fix FAD/Oxygen-Peroxide Duplicate Reactions
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