Code

Sco-GEM 1.3.0#122

Code

Merged

sulheim merged 77 commits intomasterSysBioChalmers/Sco-GEM:masterfrom develSysBioChalmers/Sco-GEM:develCopy head branch name to clipboardMar 7, 2021

+41,355-455,952

Commits

Commits on Nov 15, 2020

• Merge branch 'devel' of https://github.com/SysBioChalmers/Sco-GEM into devel

  sulheim

  committed
  c518535

• Merge branch 'devel' of https://github.com/SysBioChalmers/Sco-GEM into devel

  sulheim

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  3c323a6

• Add reference and pubmed link (#113)

  sulheim

  authored
  5033ffa

Commits on Jan 18, 2021

• fix: annotations

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  edkerk

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  540f36c

• fix: correct KEGG compound IDs

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  edkerk

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  693523c

• fix: remove reaction GND2

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  edkerk

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  edcaf13

• fix: duplicate reactions

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  edkerk

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  834563e

Commits on Jan 19, 2021

• refactor: reorganize scripts

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  edkerk

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  91c893e

• refactor: reorganize data

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  edkerk

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  bfd3c86

• fix: /code instead of /script

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• refactor: reorganize model files

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  3eb9462

• refactor: README.md

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• style: README.md headings

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• doc: README.md link to releases

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• style: README.md fix

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• chore: git and memote settings

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• doc: zenodo batch

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• Merge pull request #115 from SysBioChalmers/refactor/standardGEM

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  edkerk

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• Merge remote-tracking branch 'origin/devel' into fix/misc

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• chore: rerun export.py

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  edkerk

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  70296dc

• Merge pull request #116 from SysBioChalmers/chore/rerunExport

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  edkerk

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  3379bfa

• Merge remote-tracking branch 'origin/devel' into fix/misc

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  926f17e

• fix: closes #33 #87 #90

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  5096b32

• fix: correct biocyc IDs, append META: prefix

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  edkerk

  committed
  ebe2ad8

Commits on Jan 20, 2021

• fix: correct pubmed ID annotations

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  edkerk

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  f323ff0

• fix: remove multiple annotations when not suitable

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  edkerk

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  fe36d32

• fix: remove incomplete and correct faulty annotation

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  c1f60e6

Commits on Jan 21, 2021

• Merge pull request #117 from SysBioChalmers/fix/misc

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  edkerk

  authored
  1b698f4

Commits on Jan 24, 2021

• fix: remove unused genes

  edkerk

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  5a35e26

• feat: gene annotation data from uniprot

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  edkerk

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  da8d704

• fix: correct gene annotation (fixes #44)

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  f8b319b

Commits on Jan 25, 2021

• feat: include GO term annotations for genes

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  e2e71b6

• fix: remove G6PDH1b wrong co-factor

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  edkerk

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  669bab3

• fix: consistent NOTES fields in SBML

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  edkerk

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  f54c54f

• feat: specify grRule for XYLabc

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• Merge branch 'fix/geneAnnotation' into chore/standardGEM

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• refactor: abolish model type subfolders

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  edkerk

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  11123ea

• fix: consistent annotations (#119)

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  edkerk

  authored
  c92db2b

• fix: remove incorrect gene CAT reaction

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  edkerk

  committed
  5db44c5

Commits on Jan 26, 2021

• Merge remote-tracking branch 'origin/devel' into chore/standardGEM

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  3055d14

• fix: remove unnecessary anomers of carbohydrates

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  edkerk

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  dd9362d

• fix: uncomment change related to v1.2.1 -> v1.3.0

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  e63f663

• chore: rename script to match version number

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• Merge remote-tracking branch 'origin/chore/standardGEM' into fix/miscCurations

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  b8fe63f

• chore: standard-GEM model folder (#120)

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  edkerk

  authored
  71ca07f

• Merge remote-tracking branch 'origin/devel' into fix/miscCurations

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  d029e40

• Merge pull request #121 from SysBioChalmers/fix/miscCurations

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  edkerk

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  2b3af66

• Update issue templates

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  sulheim

  committed
  41a255b

• Merge branch 'devel' into doc/move_discussions_from_gitter

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• doc/remove_gitter_badge

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• chore/remove_old_issue_template

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• Merge pull request #125 from SysBioChalmers/doc/move_discussions_from_gitter

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  edkerk

  authored
  3393f06

• fix: remove remaining glucose anomer reactions

  edkerk

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  f0e2fd5

Commits on Jan 27, 2021

• doc: increase readability

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  sulheim

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  333dd23

• Fix: replace and delete accoa_res

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  3dcd0db

• Fix: delete metabolite accoa_res

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• Chore: Add model ID

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• Merge pull request #130 from SysBioChalmers/chore/model_id

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  edkerk

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  78fee57

• Merge pull request #129 from SysBioChalmers/fix/acetyl_coa_rewiring

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  edkerk

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  5097394

Commits on Jan 28, 2021

• feat: get latest master model for use in devel (#131)

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  edkerk

  and

  sulheim

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  5141d75

• Merge branch 'devel' into fix/anomers

  sulheim

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  f2bbbeb

• Merge pull request #126 from SysBioChalmers/fix/anomers

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  edkerk

  authored
  821a958

Commits on Feb 1, 2021

• fix: block redox pseudorxns by default (#135)

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  edkerk

  authored
  390f68e

• refactor: separate requirements.txt for sulheim2020 (#134)

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  edkerk

  authored
  603087c

• doc: update contributing guidelines and README.md (#133)

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  edkerk

  and

  sulheim

  authored
  8843bdb

• feat: simplify curation scripts (#132)

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  edkerk

  and

  sulheim

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  6718f24

• Merge remote-tracking branch 'origin/master' into devel

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  edkerk

  committed
  de7382a

Commits on Mar 5, 2021

• fix: memote Travis and custom tests (#137)

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  edkerk

  authored
  d8a02e6

• fix: travis.yml prevent timeout

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  edkerk

  authored
  c150715

• trav

  edkerk

  authored
  19c42ba

• fix: use travis_wait and remove unnecessary memote run

  edkerk

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  6661a22

• Merge pull request #138 from SysBioChalmers/fix/travisTimeout

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  edkerk

  authored
  026a3ce

• refactor: travis prevent time-out

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  edkerk

  committed
  1da470d

• Merge pull request #139 from SysBioChalmers/fix/travisTimeout

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  edkerk

  authored
  386e7a7

• fix: revert travis time-out, skip memote test

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  edkerk

  committed
  5da0f83

• Merge pull request #140 from SysBioChalmers/fix/travisTimeout

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  edkerk

  authored
  bea50ee

Commits on Mar 6, 2021

• refactor: increaseVersion.py --skipMemote flag

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  edkerk

  authored
  b39f6b2