Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Human 1.15 #554

Merged
merged 137 commits into from
May 9, 2023
Merged

Human 1.15 #554

merged 137 commits into from
May 9, 2023

Commits on Feb 28, 2023

  1. fix: update GPRs for OXPHOS complexes II, IV, V 

    -Update GPRs for OXPHOS complexes II, IV, V according to Complex Portal annotation
    @haowang-bioinfo
    haowang-bioinfo committed Feb 28, 2023
    Configuration menu
    Copy the full SHA
    a77d9a0 View commit details
    Browse the repository at this point in the history

  2. fix-gene: update added genes to genes.tsv

    @haowang-bioinfo
    haowang-bioinfo committed Feb 28, 2023
    Configuration menu
    Copy the full SHA
    c3faf5b View commit details
    Browse the repository at this point in the history

Commits on Mar 2, 2023

  1. refactor: gh workflow

    @mihai-sysbio
    mihai-sysbio committed Mar 2, 2023
    Configuration menu
    Copy the full SHA
    62404cb View commit details
    Browse the repository at this point in the history

  2. chore: update workflow dependency

    @mihai-sysbio
    mihai-sysbio committed Mar 2, 2023
    Configuration menu
    Copy the full SHA
    0780660 View commit details
    Browse the repository at this point in the history

  3. chore: typo

    @mihai-sysbio
    mihai-sysbio committed Mar 2, 2023
    Configuration menu
    Copy the full SHA
    73ace80 View commit details
    Browse the repository at this point in the history

  4. fix: worklow needs repo checkout for every job

    @mihai-sysbio
    mihai-sysbio committed Mar 2, 2023
    Configuration menu
    Copy the full SHA
    63d2bcb View commit details
    Browse the repository at this point in the history

Commits on Mar 3, 2023

  1. Merge pull request #489 from SysBioChalmers/fix/modifyMitoComplexGPR 

    fix: modify GPR rules of mitochondrial complexes II, IV, and V
    @haowang-bioinfo
    haowang-bioinfo authored Mar 3, 2023
    Configuration menu
    Copy the full SHA
    d6f92a3 View commit details
    Browse the repository at this point in the history

  2. fix: consolidate subsystem of coenzyme A metabolism

    @haowang-bioinfo
    haowang-bioinfo committed Mar 3, 2023
    Configuration menu
    Copy the full SHA
    be85db2 View commit details
    Browse the repository at this point in the history

Commits on Mar 6, 2023

  1. fix: correct ARG1 and ARG2 GPRs 

    - This is to address the issue reported in #495
    @haowang-bioinfo
    haowang-bioinfo committed Mar 6, 2023
    Configuration menu
    Copy the full SHA
    d42f065 View commit details
    Browse the repository at this point in the history

  2. feat: update Rhea ids for MAR03816 and MAR08426

    @haowang-bioinfo
    haowang-bioinfo committed Mar 6, 2023
    Configuration menu
    Copy the full SHA
    5dee342 View commit details
    Browse the repository at this point in the history

  3. chore: update Docker image of Memote

    @mihai-sysbio
    mihai-sysbio committed Mar 6, 2023
    Configuration menu
    Copy the full SHA
    e77cd7d View commit details
    Browse the repository at this point in the history

Commits on Mar 7, 2023

  1. fix: correct TYMP and PNP GPRs

    @juliette-cooke
    juliette-cooke committed Mar 7, 2023
    Configuration menu
    Copy the full SHA
    2058020 View commit details
    Browse the repository at this point in the history

  2. Merge pull request #499 from juliette-cooke/fix/correctTYMPgprs 

    fix: correct TYMP and PNP GPRs
    @haowang-bioinfo
    haowang-bioinfo authored Mar 7, 2023
    Configuration menu
    Copy the full SHA
    a4c4b96 View commit details
    Browse the repository at this point in the history

  3. Merge branch 'develop' into fix/correctARGgprs

    @haowang-bioinfo
    haowang-bioinfo committed Mar 7, 2023
    Configuration menu
    Copy the full SHA
    67ec9e5 View commit details
    Browse the repository at this point in the history

  4. feat: update Rhea ids for reactions catalyzed by TYMP and PNP 

    - add Rhea ids to MAR04603, MAR04651, MAR04709, MAR04485, MAR04754
    @haowang-bioinfo
    haowang-bioinfo committed Mar 7, 2023
    Configuration menu
    Copy the full SHA
    4248562 View commit details
    Browse the repository at this point in the history

  5. Merge pull request #496 from SysBioChalmers/fix/correctARGgprs 

    fix: correct ARG GPRs
    @haowang-bioinfo
    haowang-bioinfo authored Mar 7, 2023
    Configuration menu
    Copy the full SHA
    ca5dc94 View commit details
    Browse the repository at this point in the history

  6. Merge branch 'develop' into chore/update-memote-image

    @haowang-bioinfo
    haowang-bioinfo committed Mar 7, 2023
    Configuration menu
    Copy the full SHA
    f88437b View commit details
    Browse the repository at this point in the history

  7. Merge pull request #497 from SysBioChalmers/chore/update-memote-image 

    chore: update Docker image of Memote
    @mihai-sysbio
    mihai-sysbio authored Mar 7, 2023
    Configuration menu
    Copy the full SHA
    6a57017 View commit details
    Browse the repository at this point in the history

Commits on Mar 8, 2023

  1. Merge branch 'develop' into fix/mergeCoAmetabolism

    @haowang-bioinfo
    haowang-bioinfo committed Mar 8, 2023
    Configuration menu
    Copy the full SHA
    63a66c3 View commit details
    Browse the repository at this point in the history

  2. refactor: combine jobs in workflow

    @mihai-sysbio
    mihai-sysbio committed Mar 8, 2023
    Configuration menu
    Copy the full SHA
    62259e2 View commit details
    Browse the repository at this point in the history

  3. Merge branch 'develop' into refactor/gh-workflow

    @mihai-sysbio
    mihai-sysbio committed Mar 8, 2023
    Configuration menu
    Copy the full SHA
    dd51152 View commit details
    Browse the repository at this point in the history

  4. feat: update memote image from metabolicatlas

    @mihai-sysbio
    mihai-sysbio committed Mar 8, 2023
    Configuration menu
    Copy the full SHA
    8f736ad View commit details
    Browse the repository at this point in the history

  5. fix: typo

    @mihai-sysbio
    mihai-sysbio committed Mar 8, 2023
    Configuration menu
    Copy the full SHA
    98d2793 View commit details
    Browse the repository at this point in the history

  6. Merge branch 'develop' into refactor/gh-workflow

    @mihai-sysbio
    mihai-sysbio authored Mar 8, 2023
    Configuration menu
    Copy the full SHA
    f9cc433 View commit details
    Browse the repository at this point in the history

  7. Merge pull request #490 from SysBioChalmers/refactor/gh-workflow 

    refactor: gh workflow
    @mihai-sysbio
    mihai-sysbio authored Mar 8, 2023
    Configuration menu
    Copy the full SHA
    a742f25 View commit details
    Browse the repository at this point in the history

Commits on Mar 9, 2023

  1. Merge remote-tracking branch 'origin/develop' into fix/mergeCoAmetabo… 

    …lism
    @haowang-bioinfo
    haowang-bioinfo committed Mar 9, 2023
    Configuration menu
    Copy the full SHA
    48ad302 View commit details
    Browse the repository at this point in the history

  2. Merge pull request #492 from SysBioChalmers/fix/mergeCoAmetabolism 

    fix: consolidate subsystem of coenzyme A metabolism
    @haowang-bioinfo
    haowang-bioinfo authored Mar 9, 2023
    Configuration menu
    Copy the full SHA
    59d45a4 View commit details
    Browse the repository at this point in the history

Commits on Mar 17, 2023

  1. fix: refine NADK GPRs 

    - assign only NADK2 to MAR04268
- assign only NADK to MAR04269
- empty GPR to MAR04279
    @haowang-bioinfo
    haowang-bioinfo committed Mar 17, 2023
    Configuration menu
    Copy the full SHA
    baa413e View commit details
    Browse the repository at this point in the history

Commits on Mar 19, 2023

  1. fix-rxn: remove remove MAR04279 from HumanGEM

    @haowang-bioinfo
    haowang-bioinfo committed Mar 19, 2023
    Configuration menu
    Copy the full SHA
    6719328 View commit details
    Browse the repository at this point in the history

  2. doc: update removed rxn to deprecated identifiers

    @haowang-bioinfo
    haowang-bioinfo committed Mar 19, 2023
    Configuration menu
    Copy the full SHA
    334451b View commit details
    Browse the repository at this point in the history

Commits on Mar 20, 2023

  1. feat: update Rhea master IDs 

    -  get Rhea master IDs from KEGG ids via www.rhea-db.org/mapping
    @haowang-bioinfo
    haowang-bioinfo committed Mar 20, 2023
    Configuration menu
    Copy the full SHA
    c64c632 View commit details
    Browse the repository at this point in the history

  2. fix: correct Rhea ids for MAR07745

    @haowang-bioinfo
    haowang-bioinfo committed Mar 20, 2023
    Configuration menu
    Copy the full SHA
    a151b3d View commit details
    Browse the repository at this point in the history

  3. fix: correct Rhea ids for MAR00478

    @haowang-bioinfo
    haowang-bioinfo committed Mar 20, 2023
    Configuration menu
    Copy the full SHA
    708c7ee View commit details
    Browse the repository at this point in the history

  4. fix: correct Rhea ids for MAR03208

    @haowang-bioinfo
    haowang-bioinfo committed Mar 20, 2023
    Configuration menu
    Copy the full SHA
    1f5dc26 View commit details
    Browse the repository at this point in the history

  5. fix: correct Rhea ids for MAR01589

    @haowang-bioinfo
    haowang-bioinfo committed Mar 20, 2023
    Configuration menu
    Copy the full SHA
    aa63b30 View commit details
    Browse the repository at this point in the history

Commits on Mar 21, 2023

  1. Merge pull request #506 from SysBioChalmers/feat/updateRheaIDs 

    feat: update Rhea ids
    @haowang-bioinfo
    haowang-bioinfo authored Mar 21, 2023
    Configuration menu
    Copy the full SHA
    edf973f View commit details
    Browse the repository at this point in the history

  2. feat: add new Rhea master IDs 

    -  map new Rhea IDs from Reactome ids via rhea-db.org/mapping
    @haowang-bioinfo
    haowang-bioinfo committed Mar 21, 2023
    Configuration menu
    Copy the full SHA
    7377b0f View commit details
    Browse the repository at this point in the history

  3. fix: correct Rhea ids for MAR01784, MAR01785, MAR01786

    @haowang-bioinfo
    haowang-bioinfo committed Mar 21, 2023
    Configuration menu
    Copy the full SHA
    aa8ab76 View commit details
    Browse the repository at this point in the history

  4. fix: correct Rhea ids for MAR01467, MAR02147

    @haowang-bioinfo
    haowang-bioinfo committed Mar 21, 2023
    Configuration menu
    Copy the full SHA
    be01c34 View commit details
    Browse the repository at this point in the history

Commits on Mar 22, 2023

  1. Merge pull request #508 from SysBioChalmers/feat/addRheaIDsViaReactome 

    feat: update Rhea IDs associated from Reactome IDs
    @haowang-bioinfo
    haowang-bioinfo authored Mar 22, 2023
    Configuration menu
    Copy the full SHA
    c5ed1ad View commit details
    Browse the repository at this point in the history

  2. fix: refine GPRs for Pyrroline-5-carboxylate reductase

    @haowang-bioinfo
    haowang-bioinfo committed Mar 22, 2023
    Configuration menu
    Copy the full SHA
    9d3818b View commit details
    Browse the repository at this point in the history

  3. fix-met: rename MAM01939 from G3P to D-glyceraldehyde 3-phosphate 

    - rename metabolite as discussed in #500
    @haowang-bioinfo
    haowang-bioinfo committed Mar 22, 2023
    Configuration menu
    Copy the full SHA
    96a672e View commit details
    Browse the repository at this point in the history

Commits on Mar 23, 2023

  1. Merge pull request #509 from SysBioChalmers/fix/refineP5CGPRs 

    fix: refine GPRs for Pyrroline-5-carboxylate reductase
    @haowang-bioinfo
    haowang-bioinfo authored Mar 23, 2023
    Configuration menu
    Copy the full SHA
    aa37637 View commit details
    Browse the repository at this point in the history

Commits on Mar 25, 2023

  1. fix: remove pseudogenes, read through, and ones with predicted function

    @haowang-bioinfo
    haowang-bioinfo committed Mar 25, 2023
    Configuration menu
    Copy the full SHA
    a3b8752 View commit details
    Browse the repository at this point in the history

  2. fix-gene: remove readthrough ENSG00000282301 and sync genes.tsv to model

    @haowang-bioinfo
    haowang-bioinfo committed Mar 25, 2023
    Configuration menu
    Copy the full SHA
    bcf006c View commit details
    Browse the repository at this point in the history

Commits on Mar 26, 2023

  1. fix-GPR: refine GPRs in Pentose phosphate pathway as proposed in #501

    @haowang-bioinfo
    haowang-bioinfo committed Mar 26, 2023
    Configuration menu
    Copy the full SHA
    19c0d58 View commit details
    Browse the repository at this point in the history

  2. feat: add comp info to ENSG00000148057

    @haowang-bioinfo
    haowang-bioinfo committed Mar 26, 2023
    Configuration menu
    Copy the full SHA
    ab84543 View commit details
    Browse the repository at this point in the history

Commits on Mar 27, 2023

  1. fix-GPR: add gene ENSG00000171174 back to MAR08074

    @haowang-bioinfo
    haowang-bioinfo committed Mar 27, 2023
    Configuration menu
    Copy the full SHA
    be86919 View commit details
    Browse the repository at this point in the history

Commits on Mar 28, 2023

  1. fix: resume upper bound

    @haowang-bioinfo
    haowang-bioinfo committed Mar 28, 2023
    Configuration menu
    Copy the full SHA
    699893a View commit details
    Browse the repository at this point in the history

  2. Merge pull request #515 from SysBioChalmers/fix/refineGPRs4PPP 

    fix: refine GPRs in Pentose phosphate pathway
    @haowang-bioinfo
    haowang-bioinfo authored Mar 28, 2023
    Configuration menu
    Copy the full SHA
    0d82fe6 View commit details
    Browse the repository at this point in the history

  3. Merge branch 'develop' into fix/removeGenesIssue510

    @haowang-bioinfo
    haowang-bioinfo committed Mar 28, 2023
    Configuration menu
    Copy the full SHA
    ecd2d3b View commit details
    Browse the repository at this point in the history

  4. feat-refine GPR for glycolysis pathway

    @feiranl
    feiranl committed Mar 28, 2023
    Configuration menu
    Copy the full SHA
    1c8eacf View commit details
    Browse the repository at this point in the history

  5. Merge pull request #513 from SysBioChalmers/fix/removeGenesIssue510 

    fix: remove pseudogenes, read through genes, and ones with only predicted functions
    @haowang-bioinfo
    haowang-bioinfo authored Mar 28, 2023
    Configuration menu
    Copy the full SHA
    5edef01 View commit details
    Browse the repository at this point in the history

Commits on Mar 29, 2023

  1. fix the GPR for lactate dehydrogenase

    @feiranl
    feiranl committed Mar 29, 2023
    Configuration menu
    Copy the full SHA
    0bdb653 View commit details
    Browse the repository at this point in the history

  2. Fixed the name of MAM02053

    @pranasag
    pranasag committed Mar 29, 2023
    Configuration menu
    Copy the full SHA
    d7779bc View commit details
    Browse the repository at this point in the history

  3. Merge pull request #518 from SysBioChalmers/fix/typoMAM02053 

    Fixed the name of MAM02053
    @haowang-bioinfo
    haowang-bioinfo authored Mar 29, 2023
    Configuration menu
    Copy the full SHA
    37430b1 View commit details
    Browse the repository at this point in the history

  4. Merge branch develop into refine-gly

    @haowang-bioinfo
    haowang-bioinfo committed Mar 29, 2023
    Configuration menu
    Copy the full SHA
    0796938 View commit details
    Browse the repository at this point in the history

  5. fix: re-delete previously removed gene

    @haowang-bioinfo
    haowang-bioinfo committed Mar 29, 2023
    Configuration menu
    Copy the full SHA
    f4e3b95 View commit details
    Browse the repository at this point in the history

  6. Merge pull request #517 from SysBioChalmers/refine-gly 

    Remove wrongly annotated genes for glycolysis pathway and lactate dehydrogenase
    @haowang-bioinfo
    haowang-bioinfo authored Mar 29, 2023
    Configuration menu
    Copy the full SHA
    0b1bd42 View commit details
    Browse the repository at this point in the history

Commits on Apr 2, 2023

  1. fix: refine GPRs in CoA metabolism

    @haowang-bioinfo
    haowang-bioinfo committed Apr 2, 2023
    Configuration menu
    Copy the full SHA
    8066838 View commit details
    Browse the repository at this point in the history

  2. doc: sync removed reaction identifier

    @haowang-bioinfo
    haowang-bioinfo committed Apr 2, 2023
    Configuration menu
    Copy the full SHA
    40e2ac7 View commit details
    Browse the repository at this point in the history

Commits on Apr 5, 2023

  1. fix: refine GPRs of Isocitrate Dehydrogenase Reactions 

    - remove rxns: MAR04111, MAR04112, MAR04113, MAR04585, MAR04586, MAR04587, MAR04588 
- modify GPRs for MAR0710, MAR0712, MAR03957, MAR03958
    @haowang-bioinfo
    haowang-bioinfo committed Apr 5, 2023
    Configuration menu
    Copy the full SHA
    1c0e8fd View commit details
    Browse the repository at this point in the history

  2. fix: change MAR00710, MAR00712, and MAR03958 to reversible

    @haowang-bioinfo
    haowang-bioinfo committed Apr 5, 2023
    Configuration menu
    Copy the full SHA
    3e0464a View commit details
    Browse the repository at this point in the history

  3. doc: sync removed rxns t o deprecatedReactions.tsv

    @haowang-bioinfo
    haowang-bioinfo committed Apr 5, 2023
    Configuration menu
    Copy the full SHA
    b9ed58c View commit details
    Browse the repository at this point in the history

  4. feat: update Rhea ids

    @haowang-bioinfo
    haowang-bioinfo committed Apr 5, 2023
    Configuration menu
    Copy the full SHA
    bab19bb View commit details
    Browse the repository at this point in the history

Commits on Apr 6, 2023

  1. Merge pull request #525 from SysBioChalmers/fix/modifyIDHgprs 

    fix: refine reactions, reversibility, and GPRs of Isocitrate Dehydrogenase metabolism
    @haowang-bioinfo
    haowang-bioinfo authored Apr 6, 2023
    Configuration menu
    Copy the full SHA
    be8998b View commit details
    Browse the repository at this point in the history

Commits on Apr 13, 2023

  1. Merge branch 'develop' into fix/refineCoAMetabolismGPR

    @haowang-bioinfo
    haowang-bioinfo committed Apr 13, 2023
    Configuration menu
    Copy the full SHA
    a2f2eea View commit details
    Browse the repository at this point in the history

  2. Merge pull request #520 from SysBioChalmers/fix/refineCoAMetabolismGPR 

    fix: refine GPRs in Coenzyme A metabolism
    @haowang-bioinfo
    haowang-bioinfo authored Apr 13, 2023
    Configuration menu
    Copy the full SHA
    b5a8a3e View commit details
    Browse the repository at this point in the history

Commits on Apr 14, 2023

  1. fix: update GPRs for Cytochrome C Oxidoreductase, as proposed in #526

    @haowang-bioinfo
    haowang-bioinfo committed Apr 14, 2023
    Configuration menu
    Copy the full SHA
    84b3cbd View commit details
    Browse the repository at this point in the history

  2. Modified peptide reaction names tyr -> Tyr

    @pranasag
    pranasag committed Apr 14, 2023
    Configuration menu
    Copy the full SHA
    f1151b5 View commit details
    Browse the repository at this point in the history

  3. Changed name Argtyrval

    @pranasag
    pranasag committed Apr 14, 2023
    Configuration menu
    Copy the full SHA
    5fe6ddc View commit details
    Browse the repository at this point in the history

  4. fix: remove MAR04456 that's duplicate to MAR04458+MAR04589

    @haowang-bioinfo
    haowang-bioinfo committed Apr 14, 2023
    Configuration menu
    Copy the full SHA
    8e4f2d2 View commit details
    Browse the repository at this point in the history

  5. data: sync deleted rxn to deprecatedReactions.tsv

    @haowang-bioinfo
    haowang-bioinfo committed Apr 14, 2023
    Configuration menu
    Copy the full SHA
    c94e0c6 View commit details
    Browse the repository at this point in the history

  6. Merge pull request #533 from SysBioChalmers/fix/peptideRxnNameCuration 

    Curated names of peptide reactions
    @haowang-bioinfo
    haowang-bioinfo authored Apr 14, 2023
    Configuration menu
    Copy the full SHA
    c6ce423 View commit details
    Browse the repository at this point in the history

  7. fix-remove the duplicate mets and corresponding rxns

    @feiranl
    feiranl committed Apr 14, 2023
    Configuration menu
    Copy the full SHA
    e629d36 View commit details
    Browse the repository at this point in the history

  8. fix-met: move GPR from MAR03488 to MAR03386

    @haowang-bioinfo
    haowang-bioinfo committed Apr 14, 2023
    Configuration menu
    Copy the full SHA
    ffeca7f View commit details
    Browse the repository at this point in the history

  9. Merge remote-tracking branch 'origin/develop' into rm-duplicate

    @haowang-bioinfo
    haowang-bioinfo committed Apr 14, 2023
    Configuration menu
    Copy the full SHA
    e7a8f78 View commit details
    Browse the repository at this point in the history

  10. Merge pull request #534 from SysBioChalmers/rm-duplicate 

    fix-remove the duplicate met MAM00077x  and corresponding rxns
    @haowang-bioinfo
    haowang-bioinfo authored Apr 14, 2023
    Configuration menu
    Copy the full SHA
    359a000 View commit details
    Browse the repository at this point in the history

  11. fix: assign comp-specific GPR to MAR04454, MAR04458, MAR04589

    @haowang-bioinfo
    haowang-bioinfo committed Apr 14, 2023
    Configuration menu
    Copy the full SHA
    62a9e89 View commit details
    Browse the repository at this point in the history

  12. fix-gene: remove ENSG00000136381 from MAR04454

    @haowang-bioinfo
    haowang-bioinfo committed Apr 14, 2023
    Configuration menu
    Copy the full SHA
    f8f6706 View commit details
    Browse the repository at this point in the history

Commits on Apr 15, 2023

  1. addRawData for Glycolysis new rxn

    @feiranl
    feiranl committed Apr 15, 2023
    Configuration menu
    Copy the full SHA
    106e1e4 View commit details
    Browse the repository at this point in the history

  2. feat-add code and model change

    @feiranl
    feiranl committed Apr 15, 2023
    Configuration menu
    Copy the full SHA
    6e7836a View commit details
    Browse the repository at this point in the history

  3. fix-confidence score

    @feiranl
    feiranl committed Apr 15, 2023
    Configuration menu
    Copy the full SHA
    12bac20 View commit details
    Browse the repository at this point in the history

  4. fix-the order of the metAnnotation

    @feiranl
    feiranl committed Apr 15, 2023
    Configuration menu
    Copy the full SHA
    1ee3c2b View commit details
    Browse the repository at this point in the history

Commits on Apr 16, 2023

  1. add subsystem and extra annotation for new rxn

    @feiranl
    feiranl committed Apr 16, 2023
    Configuration menu
    Copy the full SHA
    ab41b3e View commit details
    Browse the repository at this point in the history

  2. feat-update reaction.tsv

    @feiranl
    feiranl committed Apr 16, 2023
    Configuration menu
    Copy the full SHA
    973081f View commit details
    Browse the repository at this point in the history

  3. fix-rxn: block MAR13081 ub=lb=0 

    - avoid ROX version complex IV from carrying flux
- remove COX8C (ENSG00000187581)
    @haowang-bioinfo
    haowang-bioinfo committed Apr 16, 2023
    Configuration menu
    Copy the full SHA
    d73f951 View commit details
    Browse the repository at this point in the history

Commits on Apr 17, 2023

  1. fix-bug in the code for metabolite annotation file

    @feiranl
    feiranl committed Apr 17, 2023
    Configuration menu
    Copy the full SHA
    c73db68 View commit details
    Browse the repository at this point in the history

Commits on Apr 18, 2023

  1. doc: log the purpose and blocking of MAR13081

    @haowang-bioinfo
    haowang-bioinfo committed Apr 18, 2023
    Configuration menu
    Copy the full SHA
    e9b0f73 View commit details
    Browse the repository at this point in the history

  2. Merge pull request #535 from SysBioChalmers/addGlyRxn 

    feat: Add new reactions annotated for genes related to Glycolysis pathway
    @haowang-bioinfo
    haowang-bioinfo authored Apr 18, 2023
    Configuration menu
    Copy the full SHA
    885c9a6 View commit details
    Browse the repository at this point in the history

  3. Merge remote-tracking branch 'origin/develop' into fix/updateComplexI… 

    …Vgprs
    @haowang-bioinfo
    haowang-bioinfo committed Apr 18, 2023
    Configuration menu
    Copy the full SHA
    f06c144 View commit details
    Browse the repository at this point in the history

  4. Merge pull request #532 from SysBioChalmers/fix/updateComplexIVgprs 

    fix: update GPRs for Cytochrome C Oxidoreductase
    @haowang-bioinfo
    haowang-bioinfo authored Apr 18, 2023
    Configuration menu
    Copy the full SHA
    4908d07 View commit details
    Browse the repository at this point in the history

  5. fix: modify GPRs 

    - replace ENSG00000137700 with ENSG00000281500, as proposed in #510
- remove other GCS genes from GPR of MAR06409, as discussed in #529
    @haowang-bioinfo
    haowang-bioinfo committed Apr 18, 2023
    Configuration menu
    Copy the full SHA
    c7a28df View commit details
    Browse the repository at this point in the history

Commits on Apr 19, 2023

  1. feat: complete association to Uniprot in genes.tsv

    @haowang-bioinfo
    haowang-bioinfo committed Apr 19, 2023
    Configuration menu
    Copy the full SHA
    d6b291c View commit details
    Browse the repository at this point in the history

Commits on Apr 20, 2023

  1. fix-rxn: remove reactions MAR08435, MAR08436, and MAR08437

    @haowang-bioinfo
    haowang-bioinfo committed Apr 20, 2023
    Configuration menu
    Copy the full SHA
    c679b77 View commit details
    Browse the repository at this point in the history

  2. fix-met: remove unused metabolites

    @haowang-bioinfo
    haowang-bioinfo committed Apr 20, 2023
    Configuration menu
    Copy the full SHA
    6c8e6be View commit details
    Browse the repository at this point in the history

  3. fix-rxn: remove low resolution GCS reaction MAR03923

    @haowang-bioinfo
    haowang-bioinfo committed Apr 20, 2023
    Configuration menu
    Copy the full SHA
    96b9697 View commit details
    Browse the repository at this point in the history

  4. data: sync removed rxns and mets to deprecated identifiers

    @haowang-bioinfo
    haowang-bioinfo committed Apr 20, 2023
    Configuration menu
    Copy the full SHA
    4093ae8 View commit details
    Browse the repository at this point in the history

  5. feat: update Rhea ids

    @haowang-bioinfo
    haowang-bioinfo committed Apr 20, 2023
    Configuration menu
    Copy the full SHA
    8215f7d View commit details
    Browse the repository at this point in the history

Commits on Apr 21, 2023

  1. doc: add PMID to MAR06409

    @haowang-bioinfo
    haowang-bioinfo committed Apr 21, 2023
    Configuration menu
    Copy the full SHA
    c042f34 View commit details
    Browse the repository at this point in the history

  2. Merge pull request #537 from SysBioChalmers/fix/modifyGPRs 

    fix: modify GPRs
    @haowang-bioinfo
    haowang-bioinfo authored Apr 21, 2023
    Configuration menu
    Copy the full SHA
    95fc00d View commit details
    Browse the repository at this point in the history

  3. fix-gpr: reduce MAR08433 and MAR08434 GPRs to specific components 

    - MAR08433: ENSG00000178445 and ENSG00000140905
- MAR08434: ENSG00000140905 and ENSG00000145020
    @haowang-bioinfo
    haowang-bioinfo committed Apr 21, 2023
    Configuration menu
    Copy the full SHA
    20961d5 View commit details
    Browse the repository at this point in the history

  4. Merge branch 'develop' into fix/resolveDuplicateGCSreactions

    @haowang-bioinfo
    haowang-bioinfo committed Apr 21, 2023
    Configuration menu
    Copy the full SHA
    3918b12 View commit details
    Browse the repository at this point in the history

  5. style: reformat PMID

    @haowang-bioinfo
    haowang-bioinfo committed Apr 21, 2023
    Configuration menu
    Copy the full SHA
    9168d17 View commit details
    Browse the repository at this point in the history

Commits on Apr 23, 2023

  1. fix-bug: bug in GPR

    @feiranl
    feiranl committed Apr 23, 2023
    Configuration menu
    Copy the full SHA
    6405dcf View commit details
    Browse the repository at this point in the history

  2. Merge pull request #538 from SysBioChalmers/fix/resolveDuplicateGCSre… 

    …actions

fix: resolve duplicated GCS reactions
    @haowang-bioinfo
    haowang-bioinfo authored Apr 23, 2023
    Configuration menu
    Copy the full SHA
    981b6fc View commit details
    Browse the repository at this point in the history

  3. Merge branch 'develop' into fix-LDH

    @haowang-bioinfo
    haowang-bioinfo committed Apr 23, 2023
    Configuration menu
    Copy the full SHA
    1a44fc6 View commit details
    Browse the repository at this point in the history

Commits on Apr 24, 2023

  1. Merge pull request #540 from SysBioChalmers/fix-LDH 

    fix-bug: bug in GPR in #528
    @haowang-bioinfo
    haowang-bioinfo authored Apr 24, 2023
    Configuration menu
    Copy the full SHA
    17f67c0 View commit details
    Browse the repository at this point in the history

  2. fix-rxn: remove duplicated reactions MAR04137 and MAR05297

    @haowang-bioinfo
    haowang-bioinfo committed Apr 24, 2023
    Configuration menu
    Copy the full SHA
    9514724 View commit details
    Browse the repository at this point in the history

  3. fix-rxn: remove medium resolution version of PDH and OGDH 

    - remove reactions MAR06410 and MAR06411, and retain the high-resolution version
    @haowang-bioinfo
    haowang-bioinfo committed Apr 24, 2023
    Configuration menu
    Copy the full SHA
    60e7db5 View commit details
    Browse the repository at this point in the history

  4. fix: convert MAR08746 and MAM00561 from [c] to [m]

    @haowang-bioinfo
    haowang-bioinfo committed Apr 24, 2023
    Configuration menu
    Copy the full SHA
    b158eaf View commit details
    Browse the repository at this point in the history

  5. fix: add new reaction MAM00561m + MAM02393m -> MAM02869m + MAM02984m 

    - this new reaction converts mitochondrial 2-(alpha-hydroxyethyl)thiamine-diphosphate and lipoamide into S-acetyldihydrolipoamide and thiamin-PP
    @haowang-bioinfo
    haowang-bioinfo committed Apr 24, 2023
    Configuration menu
    Copy the full SHA
    e2868bc View commit details
    Browse the repository at this point in the history

Commits on Apr 25, 2023

  1. data: sync remove rxns to deprecated ids

    @haowang-bioinfo
    haowang-bioinfo committed Apr 25, 2023
    Configuration menu
    Copy the full SHA
    9db0059 View commit details
    Browse the repository at this point in the history

  2. fix-gpr: modify GPRs for PDH reactions 

    MAR20069: (ENSG00000131828 and ENSG00000168291) or (ENSG00000163114 and ENSG00000168291)
MAR06412: ENSG00000110435 and ENSG00000150768
    @haowang-bioinfo
    haowang-bioinfo committed Apr 25, 2023
    Configuration menu
    Copy the full SHA
    952ca0c View commit details
    Browse the repository at this point in the history

  3. fix-gpr: add E2 (DLAT) as subunit

    @haowang-bioinfo
    haowang-bioinfo committed Apr 25, 2023
    Configuration menu
    Copy the full SHA
    d095d98 View commit details
    Browse the repository at this point in the history

Commits on Apr 28, 2023

  1. Merge pull request #541 from SysBioChalmers/fix/removeDuplicateKrebsC… 

    …ycleRxns

fix: remove duplicate krebs cycle rxns of PDH and OGDH
    @haowang-bioinfo
    haowang-bioinfo authored Apr 28, 2023
    Configuration menu
    Copy the full SHA
    3fd17f4 View commit details
    Browse the repository at this point in the history

  2. style: move forward to community curation 

    - use GitHub to count contributors and empty author line in Yaml
    @haowang-bioinfo
    haowang-bioinfo committed Apr 28, 2023
    Configuration menu
    Copy the full SHA
    4fcfeae View commit details
    Browse the repository at this point in the history

Commits on Apr 30, 2023

  1. style: removed fields authors, email, and organization 

    - removed these fields from Yaml file
- disabled them in `importYaml` and `exportYaml` functions
    @haowang-bioinfo
    haowang-bioinfo committed Apr 30, 2023
    Configuration menu
    Copy the full SHA
    14695c9 View commit details
    Browse the repository at this point in the history

Commits on May 3, 2023

  1. Update code/io/importYaml.m 

    Co-authored-by: Mihail Anton <mihail.anton@chalmers.se>
    @haowang-bioinfo @mihai-sysbio
    haowang-bioinfo and mihai-sysbio authored May 3, 2023
    Configuration menu
    Copy the full SHA
    a52c2d5 View commit details
    Browse the repository at this point in the history

  2. Update code/io/exportYaml.m 

    Co-authored-by: Mihail Anton <mihail.anton@chalmers.se>
    @haowang-bioinfo @mihai-sysbio
    haowang-bioinfo and mihai-sysbio authored May 3, 2023
    Configuration menu
    Copy the full SHA
    41d9e44 View commit details
    Browse the repository at this point in the history

  3. Merge pull request #546 from SysBioChalmers/style/migrateToCommunityC… 

    …uration

style: move from lab-based development to community curation
    @haowang-bioinfo
    haowang-bioinfo authored May 3, 2023
    Configuration menu
    Copy the full SHA
    2df1146 View commit details
    Browse the repository at this point in the history

Commits on May 4, 2023

  1. feat: add gene symbols to model 

    - extract gene symbols from genes.tsv and include to Human-GEM
    @haowang-bioinfo
    haowang-bioinfo committed May 4, 2023
    Configuration menu
    Copy the full SHA
    efe35d9 View commit details
    Browse the repository at this point in the history

  2. feat: enable geneShortNames field for gene symbols

    @haowang-bioinfo
    haowang-bioinfo committed May 4, 2023
    Configuration menu
    Copy the full SHA
    23e088f View commit details
    Browse the repository at this point in the history

Commits on May 5, 2023

  1. fix: remove MAR04568

    @Devlin-Moyer
    Devlin-Moyer committed May 5, 2023
    Configuration menu
    Copy the full SHA
    8141d9d View commit details
    Browse the repository at this point in the history

  2. fix: make MAR04567 irreversible and switch products & reactants

    @Devlin-Moyer
    Devlin-Moyer committed May 5, 2023
    Configuration menu
    Copy the full SHA
    2d1a950 View commit details
    Browse the repository at this point in the history

  3. fix: add new reaction MAM02883c + MAM02040c -> MAM02884c + MAM02751c

    @Devlin-Moyer
    Devlin-Moyer committed May 5, 2023
    Configuration menu
    Copy the full SHA
    45c8364 View commit details
    Browse the repository at this point in the history

  4. fix: indentation errors in new entry for MAR20070

    @Devlin-Moyer
    Devlin-Moyer committed May 5, 2023
    Configuration menu
    Copy the full SHA
    e146780 View commit details
    Browse the repository at this point in the history

  5. Fix: remove empty line at end of deprecatedReactions.tsv 

    Co-authored-by: Mihail Anton <mihail.anton@chalmers.se>
    @Devlin-Moyer @mihai-sysbio
    Devlin-Moyer and mihai-sysbio authored May 5, 2023
    Configuration menu
    Copy the full SHA
    9ed8d58 View commit details
    Browse the repository at this point in the history

Commits on May 6, 2023

  1. Merge pull request #551 from Devlin-Moyer/develop 

    fix: sedoheptulose kinase/phosphatase reactions
    @haowang-bioinfo
    haowang-bioinfo authored May 6, 2023
    Configuration menu
    Copy the full SHA
    757585f View commit details
    Browse the repository at this point in the history

  2. Merge branch 'develop' into feat/addGeneSymbols

    @haowang-bioinfo
    haowang-bioinfo committed May 6, 2023
    Configuration menu
    Copy the full SHA
    79b628d View commit details
    Browse the repository at this point in the history

Commits on May 7, 2023

  1. chore: add Devlin-Moyer as a contributor (#542)

    @haowang-bioinfo
    haowang-bioinfo committed May 7, 2023
    Configuration menu
    Copy the full SHA
    9396e4c View commit details
    Browse the repository at this point in the history

  2. chore: expand .gitignore

    @mihai-sysbio @haowang-bioinfo
    mihai-sysbio authored and haowang-bioinfo committed May 7, 2023
    Configuration menu
    Copy the full SHA
    6073f0d View commit details
    Browse the repository at this point in the history

  3. docs: add manas-kohli as contrib

    @mihai-sysbio @haowang-bioinfo
    mihai-sysbio authored and haowang-bioinfo committed May 7, 2023
    Configuration menu
    Copy the full SHA
    5bf841d View commit details
    Browse the repository at this point in the history

  4. docs: add juliette-cooke as contrib

    @mihai-sysbio @haowang-bioinfo
    mihai-sysbio authored and haowang-bioinfo committed May 7, 2023
    Configuration menu
    Copy the full SHA
    b760c18 View commit details
    Browse the repository at this point in the history

  5. Merge pull request #549 from SysBioChalmers/feat/addGeneSymbols 

    feat: add gene symbols to model
    @haowang-bioinfo
    haowang-bioinfo authored May 7, 2023
    Configuration menu
    Copy the full SHA
    06ea460 View commit details
    Browse the repository at this point in the history

Commits on May 8, 2023

  1. fix: remove orphan mets MAM02662c, MAM02662m, MAM02662x

    @haowang-bioinfo
    haowang-bioinfo committed May 8, 2023
    Configuration menu
    Copy the full SHA
    38fde13 View commit details
    Browse the repository at this point in the history

  2. Merge pull request #555 from SysBioChalmers/fix/removeMAM02662 

    fix: remove orphan mets MAM02662c, MAM02662m,  MAM02662x
    @haowang-bioinfo
    haowang-bioinfo authored May 8, 2023
    Configuration menu
    Copy the full SHA
    0162a45 View commit details
    Browse the repository at this point in the history