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Human 1.12#396

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haowang-bioinfo merged 59 commits intomainSysBioChalmers/Human-GEM:mainfrom developSysBioChalmers/Human-GEM:developCopy head branch name to clipboardJun 21, 2022

+2,584-2,814

Commits

Commits on Jan 21, 2022

• changing chebi xref of MAM00097s

  ANiknejad

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  6d1a33b

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• removing xref hmdb:HMDB0006248 from MAM00097s

  ANiknejad

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• removing xref 'gluala' from MAM00097s

  ANiknejad

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Commits on Jan 26, 2022

• reverting to previous state of the metabolites.tsv file without modification on MAM00097

  ANiknejad

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• removing xref C03740 from MAM00097, will then avoid conflict during conversion to MNXref

  ANiknejad

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Commits on Feb 3, 2022

• MAM01656 dehydrodolichol mapped to CHEBI:136960

  ANiknejad

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• correction, MAM01657 dehydrodolichol_diphosphate mapped to CHEBI:136960 (instead of previous erroneous MAM01656 dehydrodolichol)

  ANiknejad

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Commits on Feb 10, 2022

• MAM00813p (3-ketopristanoyl-CoA) remapped to CHEBI:57291 (was mapped to CHEBI:28542 (2-deoxy-D-ribofuranose 1-phosphate)

  ANiknejad

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Commits on Feb 17, 2022

• fix: remove gpr for MAR04840 resolves #342

  mihai-sysbio

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• fix: mark MAR04840 as spontaneous

  mihai-sysbio

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• Merge pull request #362 from SysBioChalmers/fix/remove-gpr-MAR04840

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  mihai-sysbio

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• refactor: DNA production/consumption in cytoplasm (#352)

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  PkiwiBird

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Commits on Feb 18, 2022

• refactor: merge MAR08973 into MAR04474 resolves #346

  mihai-sysbio

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Commits on Feb 24, 2022

• refactor: RNA formation, issue #354 (#364)

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  PkiwiBird

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Commits on Feb 25, 2022

• Update metabolites.tsv

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  ANiknejad

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• Update metabolites.tsv

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  ANiknejad

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• Update metabolites.tsv

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  ANiknejad

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Commits on Feb 28, 2022

• Merge branch 'develop' into develop

  mihai-sysbio

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Commits on Mar 1, 2022

• Merge pull request #358 from ANiknejad/develop

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  JonathanRob

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Commits on Mar 4, 2022

• fix: reconcile conflict with deprecatedReactions on develop branch

  JonathanRob

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• fix: add empty line at end of file for consistency

  JonathanRob

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• Merge branch 'develop' into refactor/merge-MAR08973-into-MAR04474

  JonathanRob

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• Merge pull request #365 from SysBioChalmers/refactor/merge-MAR08973-into-MAR04474

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  JonathanRob

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Commits on Mar 15, 2022

• doc: reference exchange metabolites as boundary metabolites

  JonathanRob

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Commits on Mar 18, 2022

• Merge pull request #374 from SysBioChalmers/doc/tINIT_messages

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  haowang-bioinfo

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Commits on Mar 20, 2022

• feat: replace empty reaction names with those from KEGG

  mihai-sysbio

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Commits on Mar 21, 2022

• Merge pull request #367 from SysBioChalmers/feat/reaction-names

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  mihai-sysbio

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Commits on Mar 22, 2022

• fix: change to txt format metabolic task file

  haowang-bioinfo

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Commits on Mar 25, 2022

• fix: flag rxns MAR05127, MAR08749, MAR08750 as spontaneous

  JonathanRob

  committed
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• Merge pull request #379 from SysBioChalmers/fix/issue349

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  JonathanRob

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Commits on Mar 28, 2022

• fix: Inactivate human biomass reaction (MAR13082) by default

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  haowang-bioinfo

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• fix: add proper LB and UB to generated draft model

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  haowang-bioinfo

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Commits on Mar 30, 2022

• feat: turn into a more generic function by adding annPath argument

  haowang-bioinfo

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• fix: minor bugs

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  haowang-bioinfo

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Commits on Apr 3, 2022

• Merge pull request #382 from SysBioChalmers/fix/animalGEM-code

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  haowang-bioinfo

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Commits on May 5, 2022

• refactor: Moved removeLowScoreGenes.m and scoreComplexModel.m from Human-GEM to RAVEN - these are used by ftINIT.

  johan-gson

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• style: commented getINITModel2 as deprecated

  johan-gson

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Commits on May 13, 2022

• feat: Added Human-GEM related files for ftINIT. Also adapted the previous tINIT since the RAVEN function has been tagged with '_legacy'.

  johan-gson

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• fix: Changed back the getINITModel - it no longer calls something named legacy. This makes the pull requests in RAVEN and Human-GEM independent. Let's fix this at some later point.

  johan-gson

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Commits on May 21, 2022

• style: Removed the word "deprecated" from the description of the previous version of tINIT.

  johan-gson

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Commits on May 26, 2022

• fix: skip adding metabolites step if none are to be added

  JonathanRob

  committed
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Commits on Jun 3, 2022

• refactor: read subsystem in a more generic way

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  haowang-bioinfo

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• fix: remove redundant code

  haowang-bioinfo

  committed
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• refactor: enable the option of retaining genes in the original order

  haowang-bioinfo

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• refactor: stop sorting the original gene list

  haowang-bioinfo

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Commits on Jun 6, 2022

• style: Removed some commented out code

  johan-gson

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• Merge branch 'ftINITHelpers' of https://github.com/SysBioChalmers/Human-GEM into ftINITHelpers

  johan-gson

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Commits on Jun 14, 2022

• Merge pull request #388 from SysBioChalmers/ftINITHelpers

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  haowang-bioinfo

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• refactor: speed up writing model fields

  edkerk

  committed
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• refactor: speed-up other model fields

  edkerk

  committed
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• chore: yml file after importYaml & exportYaml

  edkerk

  committed
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• refactor: another ~6 sec saved by faster concat

  edkerk

  committed
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• refactor: avoid conversion str->num->str

  edkerk

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• refactor: importYaml first reads whole file

  edkerk

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Commits on Jun 15, 2022

• Update code/io/importYaml.m

  edkerk

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• Update code/io/importYaml.m

  edkerk

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• Merge pull request #392 from SysBioChalmers/refactor/importYaml

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  haowang-bioinfo

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• Merge remote-tracking branch 'origin/develop' into refactor/importYamlSpeed

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  edkerk

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Commits on Jun 17, 2022

• Merge pull request #393 from SysBioChalmers/refactor/importYamlSpeed

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  mihai-sysbio

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