Ecosyste.ms: Timeline
Browse the timeline of events for every public repo on GitHub. Data updated hourly from GH Archive.
Unaimend opened an issue on Porthmeus/MeMoMe
Refactor html output of annotator test to use websockets
Unaimend created a comment on an issue on Porthmeus/MeMoMe
- [ ] Reimplement vmh tests (We have the same weird bug as before)
Unaimend opened an issue on Porthmeus/MeMoMe
Implement data repository
For know I would implement a git hub repo that contains the databases and the necessary scripts
Unaimend created a comment on a pull request on Porthmeus/MeMoMe
@Porthmeus What is your take on this?
Unaimend pushed 1 commit to thomas/dev/annotation_refactor2.0 Porthmeus/MeMoMe
- Refactored annotateModelSEED Keep in mind that several features were removed * Inchi annotation, * identifier trans... 86f5e48
Unaimend pushed 6 commits to thomas/dev/annotation_refactor2.0 Porthmeus/MeMoMe
- . d247405
- Refactored extractModelSEEDAnnotationsFromAlias 0e0b26c
- Refactored annotateModelSEED_entry 503fea2
- Refactored annotateModelSEED_id 8b4731b
- Added modelSeed test Added a new test for ModelSeed that tests the main annotation function 42cb4b8
- Added __repr__ to AnnotationResult Apparently, unittest now uses __repr__ for printing, not __str__. da89549
Unaimend created a comment on an issue on Porthmeus/MeMoMe
VMH uses `seed` for ModelSeed while, ModelSeed uses `seed.compound` Jan did the translation already for ModelSeed, but we should do this for all Dbs
Unaimend created a comment on an issue on Porthmeus/MeMoMe
``` # get the inchi strings smiles = mseed.loc[mseed["id"] == met._id, "smiles"] smiles = smiles.loc[~pd.isna(smiles)] inchi_strings = [] # ther...
Unaimend created a comment on an issue on Porthmeus/MeMoMe
I assume this code in the modelSEED code does sth. to solve the aobce mentioned problem. @Porthmeus ? ``` # load the prefixes for the identifies.org list that is needed for the correction of the ...
Unaimend created a comment on an issue on Porthmeus/MeMoMe
Bigg for example uses ` 'kegg.compound'` and modelSEED uses just `'kegg'`
Unaimend pushed 1 commit to thomas/dev/annotation_refactor2.0 Porthmeus/MeMoMe
- Refactored HMDB and VMH into common structure 4881a6b
Unaimend created a branch on Porthmeus/MeMoMe
thomas/dev/annotation_refactor2.0 - Metabolic Model Merging - a semiautomated way to merge genome scale metabolic models
Unaimend opened an issue on Porthmeus/MeMoMe
We need more/better tests for annotation performance
We have quite a few dbs that are not properly tested on their annotation performace
Unaimend created a comment on an issue on Porthmeus/MeMoMe
I guess it would be best to collect all of them in one place and visually inspect them.
Unaimend opened an issue on Porthmeus/MeMoMe
Clean up unused branches
@SteFlor and @Porthmeus please get rid of old branches. Thanks
Unaimend opened a pull request on Porthmeus/MeMoMe
Feature/153
This is a super old old branch. That requires detailed review. It implements: * #165 (At least the thresholding part) * And also relates to #186
Unaimend created a review comment on a pull request on Porthmeus/MeMoMe
This line requires internet connection? I think it would be better to just download the fire and load it locally
Unaimend created a comment on a pull request on Porthmeus/MeMoMe
- [] Fix the required internet connection by download chart.js
Unaimend created a comment on an issue on Porthmeus/MeMoMe
8379b127d3158c3b852b5dbbd624909d07c7432d Fixes this
Unaimend opened an issue on Porthmeus/MeMoMe
Inter-database linking
What if the model has chebi key A but no Inchi, Now VMH contains a model that has chebi key in some columns and an inch as well. I though we handle this, but I am not so sure anymore. Please make ...