Human 1.4 #180
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Human 1.4 #180
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- The Yaml file is updated by exporting with the new writeHumanYaml function.
- this optional feature allows to mute the notification messages while running the function
1. Enable automatic loading of yaml file from default location; 2. Mute notification messages while running the test.
fix: systematically add double quote to string elements in Yaml file
HMR_3851 is the only reaction in the "Nitrogen metabolism" subsystem, so this change also effectively removes this subsystem from the model.
Subsystem was duplicated with different capitalization
Evidence does not support the existence of this reaction in humans.
- Since the addition of `spontaneous` field, there could be non-string elements in array. This adjustment allows the recognition of last element regardless of its type.
The change of this commit is made through following command: `rxnAssoc.rxnMAID = regexprep(rxnAssoc.rxns,'^HMR_','MA_');`
1. Remove ids that do not start with `MA_` prefix; 2. Pad in zero to digital part to ensure the elements with identical length.
feat: add `rxnMAID`field to JSON file
feat: yaml worflow
command: git merge -Xtheirs devel
Co-authored-by: Ronan Fleming, Thomas Pfau
Fix: subsystem changes and reaction deletion
- Modify rxn JSON file by removing the id that had been deleted in #171
chore: sync JSON file content with model
previously the leftEquation and rightEquation fields became unequal in size
style: cleauthorship and timestamps
- Since the boundary mets had been removed from model, it is no longer necessary to load them into `unconstrained` field.
feat: remove the boundary compartment
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It's not really obvious to me if it should be a |
mihai-sysbio
approved these changes
Jun 12, 2020
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The removal of the boundary compartment is a pretty substantial change. Not necessarily in terms of work, but in terms of model changes (>1000 metabolites deleted). |
JonathanRob
approved these changes
Jun 12, 2020
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Main improvements in this PR:
Human-GEM, given the built-inGithub blamefeaturerxnMAIDfield to JSON file #175):rxnMAIDfield to reaction annotation JSON file, as discussed in feat: new sets of id for reactions and metabolites #174yamllintandcobrapymodel import as GitHub actionsHMR_5407,RN0001R,RN0002NandRN0002R, as addressed in Remove Nitrogen metabolism subsystem #129HMR_4362from model and reaction annotation JSON file, as proposed in Remove HMR_4362 from the model #153Yaml, as reported in YAML format issues in modelFiles/yml/HumanGEM.yml #169