yeast 8.3.5 #213
Merged
yeast 8.3.5 #213
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Contributor
BenjaSanchez
commented
Apr 1, 2020
BenjaSanchez
commented
- Fixes:
- Closes fix: remove genes not found in S288C annotation #129: Removed non-S288C genes (PR fix: remove non-S288C genes #211).
- Closes fix: zero-growth in anaerobic conditions #198: Fixes function for converting model to anaerobic (PR feat/anaerobicgrowth&Nitrogen-limited growth #199).
- Tests:
- Added growth tests for carbon & nitrogen limitation (feat/anaerobicgrowth&Nitrogen-limited growth #199).
- Added test for computing gene essentiality (PR feat-add a function to test essential genes #200).
- Documentation/Others:
- Clarified with README's the purpose of each script/data folder (chore: move deprecated scripts #209).
- Closes Cite yeast 8 #206: Updated citation guidelines (PR Doc/update guidelines #210).
- Updated contribution guidelines + issue/PR templates (PR Doc/update guidelines #210).
- Created folders with deprecated scripts (PR chore: move deprecated scripts #209).
so to not rely on added paths
* avoid initializing cobra for speed-up * linted all files * some typo fixes
to avoid undesired changes
* isolate rescalePseudoReaction * move sumBioMass & fitGAM
MW data is now loaded at the beginning of the function
* scaleBioMass is now a function for scaling any component in the biomass pseudoreaction * called by anaerobicModel.m and growth.m * old scaleBioMass is now renamed "fixBiomassComp", to avoid confusion
if lipid is chosen, 2 pseudoreactions need to be rescaled
feat/anaerobicgrowth&Nitrogen-limited growth
to match devel structure/standards
compliant documentation + misc formatting
to guide users on what can and cannot be used
avoid redundancy in documentation
feat-add a function to test essential genes
…ipts chore: move deprecated scripts
remove description lines for checklist, as it lead to mispells by users (e.g. "[ X]") and it is anyways more intuitive to check the boxes later
as there is now a paper
* clarified that greek letters should be avoided * added a new release step: reviewing the Zenodo release
Doc/update guidelines
As discussed in #129, YAR069W-A and YHR214W-F are not from the s288c strain and therefore are here removed
fix: remove non-S288C genes
BenjaSanchez
added
the
new release
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.