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Human 1.17 #700

Merged
merged 211 commits into from
Sep 30, 2023
Merged

Human 1.17 #700

merged 211 commits into from
Sep 30, 2023

Commits on Sep 15, 2022

  1. fix: adapt simplifyGrRules to updates in Matlab children function

    @JonathanRob
    JonathanRob committed Sep 15, 2022
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Commits on Jun 7, 2023

  1. fix: remove ubiquinone-dependent versions of all duplicated reactions… 

    … but remove the FAD-dependent version of the SDH reaction
    @Devlin-Moyer
    Devlin-Moyer committed Jun 7, 2023
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  2. fix: update reactions data files

    @Devlin-Moyer
    Devlin-Moyer committed Jun 7, 2023
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  3. fix: deleted extra omap line that I missed when removing reactions ea… 

    …rlier
    @Devlin-Moyer
    Devlin-Moyer committed Jun 7, 2023
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Commits on Jun 8, 2023

  1. fix: correct spelling errors in names of MAM00185c and MAM00185m

    @Devlin-Moyer
    Devlin-Moyer committed Jun 8, 2023
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  2. fix: remove mitochondrial ACACB from GPRs of cytosolic MAR07672 and M… 

    …AR07673
    @Devlin-Moyer
    Devlin-Moyer committed Jun 8, 2023
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  3. fix: change subsystems for MAR07672 and MAR07673 to Fatty acid biosyn… 

    …thesis (even-chain)
    @Devlin-Moyer
    Devlin-Moyer committed Jun 8, 2023
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  4. fix: remove MAR04156 for being redundant with MAR07672+MAR07673

    @Devlin-Moyer
    Devlin-Moyer committed Jun 8, 2023
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  5. fix: add new metabolite MAM01422m

    @Devlin-Moyer
    Devlin-Moyer committed Jun 8, 2023
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  6. fix: edited MAR04295 to become mitochondrial version of MAR07673

    @Devlin-Moyer
    Devlin-Moyer committed Jun 8, 2023
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  7. fix: made new reaction MAR20112 to represent mitochondrial version of… 

    … MAR07672
    @Devlin-Moyer
    Devlin-Moyer committed Jun 8, 2023
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  8. fix: made new reaction MAR20113 to transport MAM00185 between [c] and… 

    … [m]
    @Devlin-Moyer
    Devlin-Moyer committed Jun 8, 2023
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  9. fix: resolved merge conflict in deprecatedReactions.tsv

    @Devlin-Moyer
    Devlin-Moyer committed Jun 8, 2023
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  10. fix: fixed typo in MAR20111 that was causing automated YAML validatio… 

    …n to fail
    @Devlin-Moyer
    Devlin-Moyer committed Jun 8, 2023
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  11. fix: typo in model/reactions.tsv

    @Devlin-Moyer
    Devlin-Moyer committed Jun 8, 2023
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  12. fix: merge reactions

    @Devlin-Moyer
    Devlin-Moyer committed Jun 8, 2023
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  13. fix: add IVD to GPR of MAR03770

    @Devlin-Moyer
    Devlin-Moyer committed Jun 8, 2023
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  14. fix: remove MAR11652, which I apparently forgot to do earlier

    @Devlin-Moyer
    Devlin-Moyer committed Jun 8, 2023
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  15. fix: moved MAR11651 from reactions.tsv to deprecatedReactions.tsv, wh… 

    …ich I apparently forgot to do earlier
    @Devlin-Moyer
    Devlin-Moyer committed Jun 8, 2023
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Commits on Jun 9, 2023

  1. fix: add references and EC codes from deleted reactions to duplicate … 

    …kept reactions
    @Devlin-Moyer
    Devlin-Moyer committed Jun 9, 2023
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  2. fix: merge annotations from deleted reactions into annotations for ke… 

    …pt reactions in model/reactions.tsv
    @Devlin-Moyer
    Devlin-Moyer committed Jun 9, 2023
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  3. fix: remove MAR02369 for being redundant with MAR03149

    @Devlin-Moyer
    Devlin-Moyer committed Jun 9, 2023
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  4. fix: merged references, EC codes, and GPRs of deleted reactions into … 

    …kept ones
    @Devlin-Moyer
    Devlin-Moyer committed Jun 9, 2023
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  5. fix: merged annotations of removed reactions with kept ones in reacti… 

    …ons.tsv
    @Devlin-Moyer
    Devlin-Moyer committed Jun 9, 2023
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  6. feat: improve test output for unused entities

    @mihai-sysbio
    mihai-sysbio committed Jun 9, 2023
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Commits on Jun 13, 2023

  1. test: introduce a bug to see if it is picked up by the workflow

    @mihai-sysbio
    mihai-sysbio authored Jun 13, 2023
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  2. fix: typos introduced in #606 

    - This commit includes fixing typos, and reverting back to original way of extracting subsystem values
    @haowang-bioinfo
    haowang-bioinfo committed Jun 13, 2023
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  3. test: revert back testYamlConversion to the original

    @haowang-bioinfo
    haowang-bioinfo committed Jun 13, 2023
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Commits on Jun 14, 2023

  1. refactor: test yaml conversion

    @mihai-sysbio
    mihai-sysbio committed Jun 14, 2023
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  2. fix: make reversible NTP <-> PPi reactions irreversible in PPi-produc… 

    …tion direction
    @Devlin-Moyer
    Devlin-Moyer committed Jun 14, 2023
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  3. fix: swap products and reactants of PPi <-> -PP reactions then make t… 

    …hem irreversible
    @Devlin-Moyer
    Devlin-Moyer committed Jun 14, 2023
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Commits on Jun 18, 2023

  1. fix-remove mets and rxns

    @JHL-452b
    JHL-452b committed Jun 18, 2023
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  2. fix-change BiGG ID annotations

    @JHL-452b
    JHL-452b committed Jun 18, 2023
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  3. fix-replace mets

    @JHL-452b
    JHL-452b committed Jun 18, 2023
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  4. fix-remove mets and rxns

    @JHL-452b
    JHL-452b committed Jun 18, 2023
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  5. fix-change EHMN ID annotations

    @JHL-452b
    JHL-452b committed Jun 18, 2023
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  6. fix-change HMDB ID annotations

    @JHL-452b
    JHL-452b committed Jun 18, 2023
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  7. fix-change LipidMaps ID annotations

    @JHL-452b
    JHL-452b committed Jun 18, 2023
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  8. fix-replace mets

    @JHL-452b
    JHL-452b committed Jun 18, 2023
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Commits on Jun 19, 2023

  1. fix-replace mets

    @JHL-452b
    JHL-452b committed Jun 19, 2023
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  2. fix-remove mets and rxns

    @JHL-452b
    JHL-452b committed Jun 19, 2023
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  3. fix-replace mets

    @JHL-452b
    JHL-452b committed Jun 19, 2023
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  4. Merge branch 'develop' into fix/merge_irrev_trans_pairs

    @haowang-bioinfo
    haowang-bioinfo authored Jun 19, 2023
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  5. feat: fail action based on matlab exit code

    @mihai-sysbio
    mihai-sysbio committed Jun 19, 2023
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  6. revert: remove purposeful error

    @mihai-sysbio
    mihai-sysbio authored Jun 19, 2023
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  7. feat:add duplicated rxn and mets to the annotation list for further u… 

    …sage
    @feiranl
    feiranl committed Jun 19, 2023
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  8. fix: metabolic tasks fail visibly

    @mihai-sysbio
    mihai-sysbio committed Jun 19, 2023
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  9. revert: purposeful error in metabolic tasks test

    @mihai-sysbio
    mihai-sysbio authored Jun 19, 2023
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  10. Merge pull request #625 from Devlin-Moyer/fix/merge_irrev_trans_pairs 

    Merge Pairs Of Irreversible Transport Reactions
    @haowang-bioinfo
    haowang-bioinfo authored Jun 19, 2023
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Commits on Jun 20, 2023

  1. fix: merge in latest develop branch

    @Devlin-Moyer
    Devlin-Moyer committed Jun 20, 2023
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  2. fix: resolve merge conflicts with latest develop branch

    @Devlin-Moyer
    Devlin-Moyer committed Jun 20, 2023
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  3. fix: removes MAR05310 for being duplicate of MAR06380 with wrong stoi… 

    …ch & merges annotations for MAR05310 into annotations for MAR06380
    @Devlin-Moyer
    Devlin-Moyer committed Jun 20, 2023
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  4. fix: replaces inaccurate GPRs of MAR06380 and MAR09887 with accurate … 

    …ones
    @Devlin-Moyer
    Devlin-Moyer committed Jun 20, 2023
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  5. fix: remove MAR02358 for being duplicate of MAR08482, merged annotati… 

    …ons in reactions.tsv, and made MAR08482 reversible
    @Devlin-Moyer
    Devlin-Moyer committed Jun 20, 2023
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  6. fix: remove MAR20066 for being duplicate of MAR03984 and merged their… 

    … annotations
    @Devlin-Moyer
    Devlin-Moyer committed Jun 20, 2023
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  7. fix: remove MAR20020 for being duplicate of MAR04521 and merged their… 

    … annotations
    @Devlin-Moyer
    Devlin-Moyer committed Jun 20, 2023
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  8. fix: remove MAR20002 for being duplicate of MAR06631 and merged their… 

    … annotations
    @Devlin-Moyer
    Devlin-Moyer committed Jun 20, 2023
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  9. fix: remove MAR00030 for being duplicate of MAR00025 and merged their… 

    … annotations
    @Devlin-Moyer
    Devlin-Moyer committed Jun 20, 2023
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  10. fix: remove MAR00032

    @Devlin-Moyer
    Devlin-Moyer committed Jun 20, 2023
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  11. fix: removed MAR03767 and merged all annotations into MAR06421 and MA… 

    …R06422
    @Devlin-Moyer
    Devlin-Moyer committed Jun 20, 2023
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Commits on Jun 21, 2023

  1. feat-add MAM00853c to replace MAM00902c

    @JHL-452b
    JHL-452b committed Jun 21, 2023
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  2. fix-remove mets and rxns ID to 'Retired'

    @JHL-452b
    JHL-452b committed Jun 21, 2023
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  3. fix-remove mets ID to 'Retired'

    @JHL-452b
    JHL-452b committed Jun 21, 2023
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  4. fix-remove mets and rxns

    @JHL-452b
    JHL-452b committed Jun 21, 2023
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  5. fix-change KEGG ID annotations

    @JHL-452b
    JHL-452b committed Jun 21, 2023
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  6. fix-remove mets and rxns ID to 'Retired'

    @JHL-452b
    JHL-452b committed Jun 21, 2023
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  7. fix-remove rxn

    @JHL-452b
    JHL-452b committed Jun 21, 2023
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  8. feat-add MAM01729e to replace MAM03540e

    @JHL-452b
    JHL-452b committed Jun 21, 2023
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  9. fix-replace mets

    @JHL-452b
    JHL-452b committed Jun 21, 2023
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  10. fix-change PubChem ID annotations

    @JHL-452b
    JHL-452b committed Jun 21, 2023
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  11. fix-remove mets and rxns ID to 'Retired'

    @JHL-452b
    JHL-452b committed Jun 21, 2023
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  12. feat-add MAM01435m to replace MAM03318m

    @JHL-452b
    JHL-452b committed Jun 21, 2023
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  13. fix-remove mets and rxns ID to 'Retired'

    @JHL-452b
    JHL-452b committed Jun 21, 2023
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  14. Merge pull request #613 from Devlin-Moyer/fix/FAD_ubiquinone_duplicates 

    Fix FAD/Ubiquinone Duplicates
    @haowang-bioinfo
    haowang-bioinfo authored Jun 21, 2023
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  15. fix: replace inaccurate GPR of MAR01527 and add new gene entries for … 

    …several sodium channels
    @Devlin-Moyer
    Devlin-Moyer committed Jun 21, 2023
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  16. fix: added new rows to genes.tsv for new genes

    @Devlin-Moyer
    Devlin-Moyer committed Jun 21, 2023
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  17. fix: added info for new genes to genes.tsv

    @Devlin-Moyer
    Devlin-Moyer committed Jun 21, 2023
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Commits on Jun 22, 2023

  1. Merge pull request #494 from SysBioChalmers/fix/simplifyGrRules 

    fix: adapt simplifyGrRules to updates in Matlab children function
    @mihai-sysbio
    mihai-sysbio authored Jun 22, 2023
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Commits on Jun 23, 2023

  1. feat: log duplicated ids to the column of rxnRetired

    @haowang-bioinfo
    haowang-bioinfo committed Jun 23, 2023
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  2. fix: correct misplaced retired reaction ID

    @haowang-bioinfo
    haowang-bioinfo committed Jun 23, 2023
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  3. fix: add MAR03783 as a duplicate for MAR03784

    @haowang-bioinfo
    haowang-bioinfo committed Jun 23, 2023
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Commits on Jun 25, 2023

  1. fix-change ChEBI ID annotations

    @JHL-452b
    JHL-452b committed Jun 25, 2023
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  2. Merge pull request #663 from JHL-452b/fix-HMDB 

    Fix duplicate metabolites identified by HMDB IDs
    @feiranl
    feiranl authored Jun 25, 2023
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  3. fix-replace mets

    @JHL-452b
    JHL-452b committed Jun 25, 2023
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  4. Merge branch 'develop' into pr/661

    @feiranl
    feiranl committed Jun 25, 2023
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  5. fix-bug with the space

    @feiranl
    feiranl committed Jun 25, 2023
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  6. fix-bug: removing the empty line

    @feiranl
    feiranl committed Jun 25, 2023
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  7. fix-bug: introduced in the merge develop branch

    @feiranl
    feiranl committed Jun 25, 2023
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  8. Merge branch 'develop' into feat/logDeprecatedIDsIn#613

    @haowang-bioinfo
    haowang-bioinfo committed Jun 25, 2023
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  9. Merge pull request #661 from JHL-452b/fix-KEGG(2) 

    Fix duplicate metabolites identified by KEGG IDs(2)
    @feiranl
    feiranl authored Jun 25, 2023
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  10. Merge branch 'develop' into feat/logDeprecatedIDsIn#613

    @haowang-bioinfo
    haowang-bioinfo committed Jun 25, 2023
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  11. Merge branch 'develop' into pr/667

    @feiranl
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  12. Merge pull request #667 from JHL-452b/fix-ChEBI(2) 

    Fix duplicate metabolites identified by ChEBI IDs(2)
    @feiranl
    feiranl authored Jun 25, 2023
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  13. Merge pull request #666 from SysBioChalmers/feat/logDeprecatedIDsIn#613 

    feat: log duplicated ids to the column of rxnRetired
    @haowang-bioinfo
    haowang-bioinfo authored Jun 25, 2023
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  14. Merge branch 'develop' into fix/remove_MAR03767

    @haowang-bioinfo
    haowang-bioinfo committed Jun 25, 2023
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  15. fix: re-remove MAR03767

    @haowang-bioinfo
    haowang-bioinfo committed Jun 25, 2023
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  16. log: update duplication info to rxnRetired column

    @haowang-bioinfo
    haowang-bioinfo committed Jun 25, 2023
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Commits on Jun 26, 2023

  1. Merge branch 'develop' into pr/662

    @feiranl
    feiranl committed Jun 26, 2023
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  2. Merge pull request #662 from JHL-452b/fix-PubChem(2) 

    Fix duplicate metabolites identified by PubChem IDs(2)
    @feiranl
    feiranl authored Jun 26, 2023
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  3. Merge branch 'develop' into pr/646

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  4. Merge branch 'develop' into fix-BiGG

    @feiranl
    feiranl authored Jun 26, 2023
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  5. Merge pull request #646 from JHL-452b/fix-BiGG 

    Fix duplicate metabolites identified by BiGG IDs
    @feiranl
    feiranl authored Jun 26, 2023
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  6. Merge branch 'develop' into fix-EHMN

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  7. fix-metabolites for model load

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  8. fix-metabolites for model load(2)

    @JHL-452b
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  9. Merge branch 'develop' into fix-LipidMaps

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  10. fix-update annotation of ‘MAM00131r’

    @JHL-452b
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  11. Merge pull request #649 from JHL-452b/fix-EHMN 

    Fix duplicate metabolites identified by EHMN IDs
    @haowang-bioinfo
    haowang-bioinfo authored Jun 26, 2023
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  12. Merge branch 'develop' into fix/remove_MAR03767

    @haowang-bioinfo
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  13. Merge pull request #660 from SysBioChalmers/fix/remove_MAR03767 

    Remove MAR03767
    @haowang-bioinfo
    haowang-bioinfo authored Jun 26, 2023
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Commits on Jun 27, 2023

  1. Merge branch 'develop' into fix-LipidMaps

    @JHL-452b
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  2. fix: merge in latest develop branch

    @Devlin-Moyer
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  3. fix: added MAR04156 to retiredRxn column for MAR07672 and MAR07673 in… 

    … model/reactions.tsv
    @Devlin-Moyer
    Devlin-Moyer committed Jun 27, 2023
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  4. fix: merge in latest develop branch

    @Devlin-Moyer
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  5. fix: remove genes that were only associated with MAR00032 and no othe… 

    …r reactions
    @Devlin-Moyer
    Devlin-Moyer committed Jun 27, 2023
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  6. fix: remove MAR01630 and merge annotations with MAR01629

    @Devlin-Moyer
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  7. fix: remove MAR01635 and merge annotations with MAR01632

    @Devlin-Moyer
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  8. fix: remove MAR01637 and merge annotations with MAR01639 and MAR01638

    @Devlin-Moyer
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  9. fix: remove MAR01644 and merge annotations with MAR01642

    @Devlin-Moyer
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  10. fix: add BiGG id to MAM01422m

    @haowang-bioinfo
    haowang-bioinfo authored Jun 27, 2023
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  11. fix: remove MAR01651 and merge annotations into MAR01646

    @Devlin-Moyer
    Devlin-Moyer committed Jun 27, 2023
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  12. fix: remove MAR01653 and merge annotations into MAR01652

    @Devlin-Moyer
    Devlin-Moyer committed Jun 27, 2023
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  13. fix: remove MAR03754 and merge annotations into MAR03756

    @Devlin-Moyer
    Devlin-Moyer committed Jun 27, 2023
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  14. fix: remove MAR03760 and merge annotations into MAR03764

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  15. Merge pull request #624 from Devlin-Moyer/fix/acCoA_carboxylase_rxns 

    Fix Acetyl-CoA Carboxylase Reactions
    @haowang-bioinfo
    haowang-bioinfo authored Jun 27, 2023
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  16. test: re-introduce bug to Yaml file 

    - Test if GH action really work
    @haowang-bioinfo
    haowang-bioinfo committed Jun 27, 2023
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  17. fix: remove MAR07785

    @Devlin-Moyer
    Devlin-Moyer committed Jun 27, 2023
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  18. fix: remove MAR01662 and merge annotations into MAR01663

    @Devlin-Moyer
    Devlin-Moyer committed Jun 27, 2023
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  19. fix: remove MAR01666 and merge annotations into MAR01665

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    Devlin-Moyer committed Jun 27, 2023
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  20. fix: remove MAR01458 and merge annotations (except wrong EC number) i… 

    …nto MAR01642 and MAR01646
    @Devlin-Moyer
    Devlin-Moyer committed Jun 27, 2023
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  21. fix: remove now-isolated metabolites

    @Devlin-Moyer
    Devlin-Moyer committed Jun 27, 2023
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  22. merge in latest develop branch

    @Devlin-Moyer
    Devlin-Moyer committed Jun 27, 2023
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  23. fix: removed more isolated metabolites I missed the first time

    @Devlin-Moyer
    Devlin-Moyer committed Jun 27, 2023
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  24. merge in latest develop branch

    @Devlin-Moyer
    Devlin-Moyer committed Jun 27, 2023
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  25. fix: removed genes that were only associated with MAR00030

    @Devlin-Moyer
    Devlin-Moyer committed Jun 27, 2023
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  26. merge in latest develop branch

    @Devlin-Moyer
    Devlin-Moyer committed Jun 27, 2023
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  27. fix: add MAR05310 to rxnRetired column for MAR06380 in model/reaction… 

    …s.tsv
    @Devlin-Moyer
    Devlin-Moyer committed Jun 27, 2023
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  28. fix: removed MAR01639 and merged annotations into MAR01638

    @Devlin-Moyer
    Devlin-Moyer committed Jun 27, 2023
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  29. fix: removed MAR03301 and merged annotations into MAR02804

    @Devlin-Moyer
    Devlin-Moyer committed Jun 27, 2023
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  30. fix: removed MAR03306 and merged annotations into MAR02808

    @Devlin-Moyer
    Devlin-Moyer committed Jun 27, 2023
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  31. fix: removed MAR03311 and merged annotations into MAR02810

    @Devlin-Moyer
    Devlin-Moyer committed Jun 27, 2023
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  32. fix: removed MAR04966 and merged annotations into MAR02818

    @Devlin-Moyer
    Devlin-Moyer committed Jun 27, 2023
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  33. fix: removed MAR03364 and merged annotations into MAR03276

    @Devlin-Moyer
    Devlin-Moyer committed Jun 27, 2023
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  34. fix: removed MAR03369 and merged annotations into MAR03289

    @Devlin-Moyer
    Devlin-Moyer committed Jun 27, 2023
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  35. fix: reversed MAR00059 and removed the 0.5 O2 that shouldn't've been … 

    …there
    @Devlin-Moyer
    Devlin-Moyer committed Jun 27, 2023
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  36. feat: added MAR20114 to represent reduction of O2 by FADH2 in peroxis… 

    …omes
    @Devlin-Moyer
    Devlin-Moyer committed Jun 27, 2023
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  37. fix: replaced O2 with FAD and H2O2 with FADH2 in all peroxisomal reac… 

    …tions that contained O2 and H2O2
    @Devlin-Moyer
    Devlin-Moyer committed Jun 27, 2023
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Commits on Jun 28, 2023

  1. Merge pull request #650 from JHL-452b/fix-LipidMaps 

    Fix duplicate metabolites identified by LipidMaps IDs
    @feiranl
    feiranl authored Jun 28, 2023
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  2. Merge pull request #641 from Devlin-Moyer/fix/ppi_rxns_round_2 

    Make Reversible PPi Reactions Irreversible, Part 2
    @feiranl
    feiranl authored Jun 28, 2023
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  3. fix: catch all potential errors in yaml conversion workflow

    @mihai-sysbio
    mihai-sysbio committed Jun 28, 2023
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Commits on Jul 2, 2023

  1. Merge pull request #658 from SysBioChalmers/fix/remove_lipid_droplet_… 

    …loop

Remove lipid droplet breakdown reaction MAR00032
    @haowang-bioinfo
    haowang-bioinfo authored Jul 2, 2023
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Commits on Jul 3, 2023

  1. test: replicate Yaml bug reported in #6286

    @haowang-bioinfo
    haowang-bioinfo committed Jul 3, 2023
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Commits on Jul 4, 2023

  1. feat: add basic memote test

    @mihai-sysbio
    mihai-sysbio committed Jul 4, 2023
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Commits on Jul 5, 2023

  1. Merge pull request #672 from SysBioChalmers/fix/yaml-test-bug 

    feat: add basic memote tests
    @mihai-sysbio
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  2. make MAR06380 reversible

    @Devlin-Moyer
    Devlin-Moyer committed Jul 5, 2023
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  3. fix: remove MAR09887 and merge annotations into MAR06896

    @Devlin-Moyer
    Devlin-Moyer committed Jul 5, 2023
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  4. fix: merge in latest develop branch

    @Devlin-Moyer
    Devlin-Moyer committed Jul 5, 2023
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  5. fix: typos & mistakes pointed out by reviewers

    @Devlin-Moyer
    Devlin-Moyer committed Jul 5, 2023
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  6. chore: merge in latest develop branch

    @Devlin-Moyer
    Devlin-Moyer committed Jul 5, 2023
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  7. fix: only keep most accurate EC numbers for MAR04521 and MAR03984

    @Devlin-Moyer
    Devlin-Moyer committed Jul 5, 2023
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  8. chore: merge in latest develop branch

    @Devlin-Moyer
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Commits on Jul 6, 2023

  1. Merge pull request #655 from SysBioChalmers/fix/sodium_cotransport_gprs 

    Fix Sodium Cotransport GPRs
    @haowang-bioinfo
    haowang-bioinfo authored Jul 6, 2023
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  2. refactor: use warning instead of disp in matlab tests

    @mihai-sysbio
    mihai-sysbio authored Jul 6, 2023
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  3. fix: retain MAR08482 in its original form 

    - keep MAR08482 irreversible
- keep compartment specific genes for MAR08482 and MAR03931
    @haowang-bioinfo
    haowang-bioinfo committed Jul 6, 2023
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  4. Merge branch 'develop' into fix/same_stoich_diff_gpr_dupes

    @haowang-bioinfo
    haowang-bioinfo authored Jul 6, 2023
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  5. log: update retired duplicate reaction ids

    @haowang-bioinfo
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  6. Merge pull request #657 from SysBioChalmers/fix/same_stoich_diff_gpr_… 

    …dupes

Merge Reactions With Same Stoichiometry But Different Genes
    @haowang-bioinfo
    haowang-bioinfo authored Jul 6, 2023
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Commits on Jul 7, 2023

  1. test: revert typo purposely introduced to the "metabolites" key

    @haowang-bioinfo
    haowang-bioinfo committed Jul 7, 2023
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  2. test: revert typo purposely introduced to id MAM01261m

    @haowang-bioinfo
    haowang-bioinfo committed Jul 7, 2023
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  3. Merge pull request #635 from SysBioChalmers/fix/importExportCycle 

    fix: GH workflow test
    @mihai-sysbio
    mihai-sysbio authored Jul 7, 2023
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  4. Merge branch 'develop' into fix/sodium_channel_genes

    @mihai-sysbio
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Commits on Jul 10, 2023

  1. refactor: improve test output in test workflow

    @mihai-sysbio
    mihai-sysbio committed Jul 10, 2023
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Commits on Jul 16, 2023

  1. fix: made MAR04145 irreversible and added textbook reference to rxnNotes

    @Devlin-Moyer
    Devlin-Moyer committed Jul 16, 2023
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  2. fix: merged MAR01515 into MAR08529

    @Devlin-Moyer
    Devlin-Moyer committed Jul 16, 2023
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  3. fix: merged MAR00039 into MAR07992

    @Devlin-Moyer
    Devlin-Moyer committed Jul 16, 2023
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  4. fix: merged MAR00096 into MAR04819

    @Devlin-Moyer
    Devlin-Moyer committed Jul 16, 2023
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  5. fix: merged MAR02027 into MAR0302

    @Devlin-Moyer
    Devlin-Moyer committed Jul 16, 2023
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  6. fix: merged MAR02006 into MAR03873

    @Devlin-Moyer
    Devlin-Moyer committed Jul 16, 2023
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  7. fix: remove all reactions involving MAM01268 or MAR02757 in all compa… 

    …rtments
    @Devlin-Moyer
    Devlin-Moyer committed Jul 16, 2023
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  8. fix: remove now-isolated MAM01816n

    @Devlin-Moyer
    Devlin-Moyer committed Jul 16, 2023
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  9. fix: remove all genes that were only associated with PPARA reactions

    @Devlin-Moyer
    Devlin-Moyer committed Jul 16, 2023
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Commits on Jul 19, 2023

  1. Merge pull request #676 from SysBioChalmers/fix/citrate_synthase 

    Make Citrate Synthase Irreversible
    @feiranl
    feiranl authored Jul 19, 2023
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  2. chore: merge in latest develop branch

    @Devlin-Moyer
    Devlin-Moyer committed Jul 19, 2023
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  3. chore: merge in latest develop branch

    @Devlin-Moyer
    Devlin-Moyer committed Jul 19, 2023
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Commits on Jul 21, 2023

  1. Merge pull request #677 from SysBioChalmers/fix/ammonium-ammonia_dupl… 

    …icates

Merge Ammonium/Ammonia Duplicates Into Single Reactions
    @feiranl
    feiranl authored Jul 21, 2023
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Commits on Jul 28, 2023

  1. chore: merge in latest develop branch

    @Devlin-Moyer
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  2. chore: merge in latest develop branch

    @Devlin-Moyer
    Devlin-Moyer committed Jul 28, 2023
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Commits on Aug 1, 2023

  1. Merge pull request #678 from SysBioChalmers/fix/remove_ppara_rxns 

    Remove PPARA Reactions
    @haowang-bioinfo
    haowang-bioinfo authored Aug 1, 2023
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  2. Merge branch 'develop' into fix/sodium_channel_genes

    @Devlin-Moyer
    Devlin-Moyer committed Aug 1, 2023
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  3. fix: added in some genes I missed the first time

    @Devlin-Moyer
    Devlin-Moyer committed Aug 1, 2023
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  4. fix: add new gene entries for new genes

    @Devlin-Moyer
    Devlin-Moyer committed Aug 1, 2023
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  5. fix: update model/genes.tsv

    @Devlin-Moyer
    Devlin-Moyer committed Aug 1, 2023
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Commits on Aug 2, 2023

  1. fix: AND together SCNN1A, SCNN1B, and SCNN1G since they form a trimer

    @Devlin-Moyer
    Devlin-Moyer committed Aug 2, 2023
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  2. feat: added refs for SCNN1A/B/G/D complex/isozyme situation

    @Devlin-Moyer
    Devlin-Moyer committed Aug 2, 2023
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Commits on Aug 3, 2023

  1. Merge pull request #664 from SysBioChalmers/fix/sodium_channel_genes 

    add Alpha subunits of sodium channel genes to MAR01527
    @haowang-bioinfo
    haowang-bioinfo authored Aug 3, 2023
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Commits on Aug 16, 2023

  1. fix: sync geneShortNames field with genes field 

    - These gene names are now padded with empty elements, this is fine but not a decent way
    @haowang-bioinfo
    haowang-bioinfo committed Aug 16, 2023
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  2. 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
    @haowang-bioinfo
    haowang-bioinfo committed Aug 16, 2023
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Commits on Aug 17, 2023

  1. Update code/updateAnimalGEM.m 

    Co-authored-by: Mihail Anton <mihail.anton@chalmers.se>
    @haowang-bioinfo @mihai-sysbio
    haowang-bioinfo and mihai-sysbio authored Aug 17, 2023
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Commits on Aug 18, 2023

  1. fix: ensure b field in single column 

    - This is to resolve recurring issue reported in #511
    @haowang-bioinfo
    haowang-bioinfo committed Aug 18, 2023
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Commits on Aug 21, 2023

  1. Merge pull request #692 from SysBioChalmers/fix/refineAnimalGemPipeline 

    fix: refine animal GEM updating pipeline
    @haowang-bioinfo
    haowang-bioinfo authored Aug 21, 2023
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  2. doc: do not treat mito-version rxns as duplicates to peroxisome ones

    @haowang-bioinfo
    haowang-bioinfo committed Aug 21, 2023
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  3. Merge pull request #669 from SysBioChalmers/fix/remove_mito_bile_acid… 

    …_synth

Remove Mitochondrial Bile Acid Synthesis Pathway
    @haowang-bioinfo
    haowang-bioinfo authored Aug 21, 2023
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Commits on Aug 29, 2023

  1. fix: update name for GAP

    @exaexa
    exaexa committed Aug 29, 2023
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  2. Merge pull request #696 from exaexa/mk-fix-gap 

    fix: update name for GAP in CellfieConsensus metabolic tasks
    @haowang-bioinfo
    haowang-bioinfo authored Aug 29, 2023
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Commits on Sep 20, 2023

  1. Merge branch 'develop' into fix/FAD_O2_dupes

    @haowang-bioinfo
    haowang-bioinfo committed Sep 20, 2023
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  2. fix: re-remove duplicated reaction MAR01639

    @haowang-bioinfo
    haowang-bioinfo committed Sep 20, 2023
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  3. fix: re-remove deprecated reactions from "reactions.tsv" 

    remove rows 'MAR01639', 'MAR01635', 'MAR01637', 'MAR01653', 'MAR01656' from "reactions.tsv"
    @haowang-bioinfo
    haowang-bioinfo committed Sep 20, 2023
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Commits on Sep 21, 2023

  1. fix: removed MAR00059 for being less accurate version of MAR01706

    @Devlin-Moyer
    Devlin-Moyer committed Sep 21, 2023
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  2. Fixed GPR of MAR01706 and added reference

    @Devlin-Moyer
    Devlin-Moyer committed Sep 21, 2023
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  3. chore: resolve merge conflicts

    @Devlin-Moyer
    Devlin-Moyer committed Sep 21, 2023
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Commits on Sep 24, 2023

  1. Merge pull request #670 from SysBioChalmers/fix/FAD_O2_dupes 

    Fix FAD/Oxygen-Peroxide Duplicate Reactions
    @haowang-bioinfo
    haowang-bioinfo authored Sep 24, 2023
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