chemical_checker issueshttps://gitlabsbnb.irbbarcelona.org/packages/chemical_checker/-/issues2022-05-19T15:39:05Zhttps://gitlabsbnb.irbbarcelona.org/packages/chemical_checker/-/issues/154Verify Chemical Checker API2022-05-19T15:39:05ZMartina LocatelliVerify Chemical Checker APIStress test CC API:
https://chemicalchecker.com/api/db/getSignature/<CC SPACE e.g. A1>/<INCHIKEYS SEPARATED BY COMMA>
Possible memory leak which causes the web server to get down.Stress test CC API:
https://chemicalchecker.com/api/db/getSignature/<CC SPACE e.g. A1>/<INCHIKEYS SEPARATED BY COMMA>
Possible memory leak which causes the web server to get down.Martina LocatelliMartina Locatellihttps://gitlabsbnb.irbbarcelona.org/packages/chemical_checker/-/issues/88Install lxml python module into the cc image2019-04-24T17:34:26ZMiquel Duran-Frigolamiquel.duran@irbbarcelona.orgInstall lxml python module into the cc imageI would like to learn how you guys do it.I would like to learn how you guys do it.Oriol GuitartOriol Guitarthttps://gitlabsbnb.irbbarcelona.org/packages/chemical_checker/-/issues/85adanet utilities2019-05-06T08:08:16ZMartino Bertoniadanet utilities* Add dropout-based confidence (add predict_proba function)
* In case of classification pass predicted probabilities
* Add unit-tests* Add dropout-based confidence (add predict_proba function)
* In case of classification pass predicted probabilities
* Add unit-testsMartino BertoniMartino Bertonihttps://gitlabsbnb.irbbarcelona.org/packages/chemical_checker/-/issues/71evaluate() functions2019-07-24T08:41:40ZMartino Bertonievaluate() functionsCurrently sign2 and sign3 'fit' functions served the purpose of evaluating the performances (i.e. train-test split of data).
In production we want the 'fit' function to make use of all data available and hence I'm going to refactor 'fit'...Currently sign2 and sign3 'fit' functions served the purpose of evaluating the performances (i.e. train-test split of data).
In production we want the 'fit' function to make use of all data available and hence I'm going to refactor 'fit' to 'evaluate' and create a new 'fit' function where no split and no evaluation is performed.Martino BertoniMartino Bertonihttps://gitlabsbnb.irbbarcelona.org/packages/chemical_checker/-/issues/59Add method of the dataset2022-02-15T17:39:38ZMiquel Duran-Frigolamiquel.duran@irbbarcelona.orgAdd method of the datasetWhen adding a new dataset into the database, as agreed today in the group meeting, we need to put some controls. I will fill this thread when I have time.When adding a new dataset into the database, as agreed today in the group meeting, we need to put some controls. I will fill this thread when I have time.Oriol GuitartOriol Guitarthttps://gitlabsbnb.irbbarcelona.org/packages/chemical_checker/-/issues/58Suggested notebooks2022-02-15T17:40:55ZMiquel Duran-Frigolamiquel.duran@irbbarcelona.orgSuggested notebooksI like the idea of having notebooks to illustrate use cases.
Here I list some possible notebooks:
* [ ] Loading a new chemical library (as illustrated by ChemistriX).
* [ ] Signature reversion of Alzheimer's-related traits.
* [ ] 2D pr...I like the idea of having notebooks to illustrate use cases.
Here I list some possible notebooks:
* [ ] Loading a new chemical library (as illustrated by ChemistriX).
* [ ] Signature reversion of Alzheimer's-related traits.
* [ ] 2D projections of small compound collections, and straightforward characterization
* [ ] Signature mimicking of bio-drugs
* [ ] Supervised learning inspired by MoleculeNet.
@oguitart please let me know when you are ready for this and we will try to do this together. As an inspiration, the deepchem library has some excellent notebooks.Oriol GuitartOriol Guitarthttps://gitlabsbnb.irbbarcelona.org/packages/chemical_checker/-/issues/49IPython / Jupyter notebooks within singularity...2019-01-31T10:22:38ZMiquel Duran-Frigolamiquel.duran@irbbarcelona.orgIPython / Jupyter notebooks within singularity...Would be nice to have Ipython notebooks work with the singularity images.Would be nice to have Ipython notebooks work with the singularity images.Oriol GuitartOriol Guitarthttps://gitlabsbnb.irbbarcelona.org/packages/chemical_checker/-/issues/48Incorporation of the ChemistriX / BIUR library2019-01-31T10:23:24ZMiquel Duran-Frigolamiquel.duran@irbbarcelona.orgIncorporation of the ChemistriX / BIUR libraryHi @oguitart,
in `/aloy/home/mduran/myscripts/chemistrix/` you can find a `parse.ipynb` that exemplifies how to parse the BIUR "real" and "virtual" libraries.
These libraries could be incorporated into the CC repository as "private" li...Hi @oguitart,
in `/aloy/home/mduran/myscripts/chemistrix/` you can find a `parse.ipynb` that exemplifies how to parse the BIUR "real" and "virtual" libraries.
These libraries could be incorporated into the CC repository as "private" libraries. Again, let's discuss these issues as soon as we can.
Thanks!Oriol GuitartOriol Guitarthttps://gitlabsbnb.irbbarcelona.org/packages/chemical_checker/-/issues/31CC paper TO-DO list2018-11-23T12:33:14ZMiquel Duran-Frigolamiquel.duran@irbbarcelona.orgCC paper TO-DO list* [ ] Projections and libraries figure
* [ ] Main figures
* [ ] Inference script
* [ ] Inference script validation
* [ ] Toxicity prediction
* [ ] Target prediction* [ ] Projections and libraries figure
* [ ] Main figures
* [ ] Inference script
* [ ] Inference script validation
* [ ] Toxicity prediction
* [ ] Target predictionMiquel Duran-Frigolamiquel.duran@irbbarcelona.orgMiquel Duran-Frigolamiquel.duran@irbbarcelona.org2018-11-26https://gitlabsbnb.irbbarcelona.org/packages/chemical_checker/-/issues/26Write wiki kick-off version2018-11-09T13:40:10ZMiquel Duran-Frigolamiquel.duran@irbbarcelona.orgWrite wiki kick-off versionIn the wiki, do the following:
* [x] Access to data
* [x] Connectivity
* [x] Data
* [x] Database
* [x] Dataset correlation
* [x] Datasets
* [X] Home
* [x] Libraries
* [x] Manifesto
* [X] Production phase
* [x] Publications
* [x] Signatu...In the wiki, do the following:
* [x] Access to data
* [x] Connectivity
* [x] Data
* [x] Database
* [x] Dataset correlation
* [x] Datasets
* [X] Home
* [x] Libraries
* [x] Manifesto
* [X] Production phase
* [x] Publications
* [x] Signaturization
It is not necessary that, in this first version, everything is finished. This is just a running version to interact with Oriol and Martino.Miquel Duran-Frigolamiquel.duran@irbbarcelona.orgMiquel Duran-Frigolamiquel.duran@irbbarcelona.org2018-11-04https://gitlabsbnb.irbbarcelona.org/packages/chemical_checker/-/issues/21Do the projections, finally, so that they look nice on node2vec embeddings2018-11-04T10:51:03ZMiquel Duran-Frigolamiquel.duran@irbbarcelona.orgDo the projections, finally, so that they look nice on node2vec embeddingsMiquel Duran-Frigolamiquel.duran@irbbarcelona.orgMiquel Duran-Frigolamiquel.duran@irbbarcelona.org