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yeast 8.4.0 #229

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merged 79 commits into from
Jun 15, 2020
Merged

yeast 8.4.0 #229

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3b83df2
feat-met.BiGGID: add BiGG identifiers for metabolites and reactions
snmendoz Mar 15, 2019
52c24ab
test: model properly loaded by cobrapy
BenjaSanchez Apr 21, 2020
434d240
fix: replace proteins with geneNames
BenjaSanchez Apr 21, 2020
4722c45
Merge pull request #216 from SysBioChalmers/fix/gene-names
BenjaSanchez Apr 24, 2020
325be62
Revert "feat-met.BiGGID: add BiGG identifiers for metabolites and rea…
BenjaSanchez Apr 24, 2020
0a8150a
Merge branch 'devel' into feat/bigg_compliance
BenjaSanchez Apr 27, 2020
ff435cb
fix-met.annot: KEGG id
BenjaSanchez Apr 27, 2020
4785040
fix-rxn: remove duplicated rxns
BenjaSanchez Apr 28, 2020
93d99ca
feat: BiGG dictionaries
BenjaSanchez Apr 29, 2020
6f593ef
fix-rxn.annot: correct reaction IDs and add new reaction IDs (MetaNet…
eiden309 May 16, 2020
48df2c6
fix-met.annot: correct metabolite IDs and add new metabolite IDs (Met…
eiden309 May 16, 2020
001c5a5
feat-rxn.annot: added new rxnKEGGIDs into model via ID mapping
eiden309 May 16, 2020
22eab97
feat-met.annot: added new metKEGGIDs into model via ID mapping
eiden309 May 16, 2020
ce55eeb
feat-met.annot: added new metMetaNetXID into model via ID mapping
eiden309 May 16, 2020
b3418ad
fix-met.annot: remove metabolite ID with modifyID.m and correct modif…
eiden309 May 16, 2020
76846e1
style: change notes annotation in modifyID.m to PR (#220)
eiden309 May 16, 2020
f0687d8
Update README.md
edkerk May 16, 2020
b3deb51
style-rxn.prop: shorten rxnNotes added in modifyID.m
eiden309 May 17, 2020
859e2ab
fix-rxn.annot: correct rxnName
eiden309 May 17, 2020
daa5737
style-met.prop: shorten metNotes added in modifyID.tsv
eiden309 May 17, 2020
029b34d
feat: add .gitattributes for unified line endings
eiden309 May 18, 2020
77906f8
fix: update .gitattributes
eiden309 May 19, 2020
682263d
fix: normalize all line endings
eiden309 May 19, 2020
b8a5d32
feat: add checks for MetaCyc/modelSEED data import in mapKEGGID.m
eiden309 May 19, 2020
80ff31a
fix: improve indexing in mapMNXMID.m
eiden309 May 19, 2020
f28c99f
Revert line endings commits
edkerk May 19, 2020
67a5b4e
feat: specify EOL behaviour in gitattributes
edkerk May 19, 2020
248d2be
Merge pull request #221 from SysBioChalmers/fix/normalizeLineEndings
edkerk May 19, 2020
eadc9f8
Merge remote-tracking branch 'origin/devel' into fix/update_IDs
edkerk May 19, 2020
24570ce
Merge branch 'devel' into feat/bigg_compliance
BenjaSanchez May 19, 2020
d21cae3
fix-data: split BiGG files in two separate lists
BenjaSanchez May 19, 2020
5132b88
fix-data: remove helper lists
BenjaSanchez May 19, 2020
cdbd689
fix-data: remove compartment info from met BiGG dict
BenjaSanchez May 19, 2020
e533f93
fix-data: keep original compartment abbreviations
BenjaSanchez May 19, 2020
ef49b1e
fix-data: automatic lipid id generation
BenjaSanchez May 19, 2020
71f8217
fix-data: manual lipid id curation
BenjaSanchez May 19, 2020
1987a59
fix-data: remove copy suffix from rxn BiGG dict
BenjaSanchez May 19, 2020
2d09bc9
style: minor formatting changes in mapKEGGID.m and mapMNXMID.m
eiden309 May 19, 2020
c41e0ec
fix: resolve issue with shortening rxnNotes and metNotes
eiden309 May 19, 2020
dc4ecc2
fix-data: redefine BiGG ids for SLIME rxns
BenjaSanchez May 20, 2020
5784e29
fix-data: exchange rxn notation in BiGG dict with new ids
BenjaSanchez May 20, 2020
d98fa22
fix-data: pseudo-mets & pseudo-rxns in both BiGG dicts
BenjaSanchez May 20, 2020
6290b49
fix: cd back to the original filefolder at the end
feiranl May 20, 2020
14a3b7b
Merge pull request #220 from SysBioChalmers/fix/update_IDs
BenjaSanchez May 20, 2020
0f2a766
fix-data: ER membrane notation in rxns
BenjaSanchez May 20, 2020
219203e
fix: changes to .gitignore
BenjaSanchez May 20, 2020
d35822e
fix-data: simple transport notation for rxn BiGG ids
BenjaSanchez May 20, 2020
87785e3
Merge branch 'devel' into feat/bigg_compliance
BenjaSanchez May 21, 2020
037c93f
fix-data: rename compartments in new rxn ids in BiGG dict
BenjaSanchez May 21, 2020
59b6d88
fix-data: misc manual fixes in new rxn BiGG dict
BenjaSanchez May 21, 2020
8a51b6f
fix-data: remove redundant chain position in new rxn BiGG dict
BenjaSanchez May 21, 2020
8ed678f
chore: update cobratoolbox/RAVEN
BenjaSanchez May 21, 2020
5ffdb0d
feat: met+rxn BiGG ids
BenjaSanchez May 25, 2020
7f72dea
feat: automatic curation of reactions via MetaNetX reac_prop.tsv
eiden309 May 26, 2020
89fb8a3
fix-rxn: balance reaction via modification of metabolite formula and …
eiden309 May 27, 2020
cd8a356
fix-rxn: balance reaction via modification of model.S
eiden309 May 27, 2020
35600d9
fix: remove requirement of coenzyme A in biomass equation for anaerob…
eiden309 May 27, 2020
8444355
Merge pull request #188 from SysBioChalmers/feat/bigg_compliance
BenjaSanchez May 27, 2020
1f7c113
Merge branch 'devel' into fix/unbalanced_rxns
BenjaSanchez May 27, 2020
e1d1945
feat: better python io functions
BenjaSanchez May 27, 2020
3963759
test: check if model changes with cobrapy
BenjaSanchez May 27, 2020
9469493
fix: cd to the right filefolder
feiranl May 27, 2020
a81a2cf
style: remove repetitive codes
feiranl May 27, 2020
8ccaa3e
feat: BiGG compliance flag in read_yeast_model
BenjaSanchez May 28, 2020
9b0ec0a
feat: load missing ids from bigg dicts
BenjaSanchez May 28, 2020
32e3391
fix: add exception for repeated BiGG ids
BenjaSanchez May 28, 2020
eb459aa
fix: revert back to original matlab-compliant model
BenjaSanchez May 28, 2020
60342ad
doc: add description for output
eiden309 May 29, 2020
53c81d9
fix: indexing issues when updating model.S
eiden309 May 29, 2020
17d84c9
fix: -R4 in TRX1
edkerk May 28, 2020
1979871
fix: resolve unbalanced rxns due to H+/H2O
eiden309 Jun 1, 2020
57e0cab
fix-bug for wrong mets in the readme
feiranl Jun 5, 2020
afcb9fe
chore-cd to the right folder
feiranl Jun 5, 2020
e6205e9
feat-update the model with the balance of H+/H2O
feiranl Jun 5, 2020
15e6ccb
doc: rename to avoid conflict with COBRA function
eiden309 Jun 7, 2020
2ef9281
feat: display_rxnMetInfo.m to facilitate curation of reaction balance
eiden309 Jun 7, 2020
984dca1
Merge pull request #224 from SysBioChalmers/feat/python-compatibility
BenjaSanchez Jun 10, 2020
39ada1b
Merge pull request #222 from SysBioChalmers/fix/unbalanced_rxns
BenjaSanchez Jun 12, 2020
9e36261
chore: update dependencies
BenjaSanchez Jun 12, 2020
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5 changes: 5 additions & 0 deletions .gitattributes
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Original file line number Diff line number Diff line change
@@ -0,0 +1,5 @@
* text=auto
*.m text diff=matlab
.gitattributes export-ignore
.gitignore export-ignore
.github export-ignore
6 changes: 6 additions & 0 deletions .gitignore
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Expand Up @@ -46,6 +46,12 @@ Thumbs.db
*.mat
helpsearch*/

# Python-related things #
#########################
*.ipynb_checkpoints/
*.pyc
*.env

# Non-complying tables #
########################
*.xls
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