The TOXicogenomic sIgNature (TOXsIgN) is a user-friendly and cross-species resource that supports online submission, storage, and retrieval of TOXicogenomic sIgNatures. TOXsIgN aims at complementing existing resources by acting as a distribution hub for the community. One of its unique features is its ability to archive heterogeneous data. TOXsIgN thus allows users to upload lists of genes positively (overexpressed for transcriptomic assays) affected and negatively (underexpressed) affected from distinct –omics experiments (e.g., transcriptomics, proteomics, or epigenomics). It also provides users with a working environment containing a powerful search engine as well as bioinformatics/biostatistics modules that enable cross-species and cross-technology signature comparisons or enrichment analyses. TOXsIgN is thus intended to serve as a warehouse for toxicogenomics and predictive toxicology tools simultaneously based on and able to analyze the overall set of signatures deposited by the community.
| License: | MIT |
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Currently, 8 ontologies types are available : Biological, Cell, CellLine, Chemical, Disease, Experiment, Species, Tissue There is an autmated script that will download and add a list of ontologies in the database.
A TOXsIgN_ontologies.csv.example in available in loading_data/ontologies. It need to be filled out and copied to loading_data/ontologies/TOXsIgN_ontologies.csv
Columns are :
- Name of the ontology
- Url where the ontology can be downloaded if remote. The data must be available with a get request, so the access key must be included in the url (url?apikey=XXXXXX)
- Ontology type (needs to be in [biological, cell, cellline, chemical, disease, experiment, species, tissue])
- Format (only owl and obo are supported for now)
- Local path : Path where the file will be downloaded, or where the local file can be found. Must be a path visible from inside the docker (so /app/*/*)
- Where the file can be found (remote or local). If set to remote, and there are no file on the specified path, the script will attempt to download it using the url column.
Moved to settings.
To create a normal user account, just go to Sign Up and fill out the form. Once you submit it, you'll see a "Verify Your E-mail Address" page. Go to your console to see a simulated email verification message. Copy the link into your browser. Now the user's email should be verified and ready to go.
To create an superuser account, use this command:
$ python manage.py createsuperuser
For convenience, you can keep your normal user logged in on Chrome and your superuser logged in on Firefox (or similar), so that you can see how the site behaves for both kinds of users.
Running type checks with mypy:
$ mypy toxsign
To run the tests, check your test coverage, and generate an HTML coverage report:
$ coverage run -m pytest $ coverage html $ open htmlcov/index.html
$ pytest
Moved to Live reloading and SASS compilation.
This app comes with Celery.
To run a celery worker:
cd toxsign
celery -A toxsign.taskapp worker -l infoPlease note: For Celery's import magic to work, it is important where the celery commands are run. If you are in the same folder with manage.py, you should be right.
In development, it is often nice to be able to see emails that are being sent from your application. For that reason local SMTP server MailHog with a web interface is available as docker container.
Container mailhog will start automatically when you will run all docker containers. Please check cookiecutter-django Docker documentation for more details how to start all containers.
With MailHog running, to view messages that are sent by your application, open your browser and go to http://127.0.0.1:8025
Sentry is an error logging aggregator service. You can sign up for a free account at https://sentry.io/signup/?code=cookiecutter or download and host it yourself. The system is setup with reasonable defaults, including 404 logging and integration with the WSGI application.
You must set the DSN url in production.
The following details how to deploy this application.
See detailed cookiecutter-django Docker documentation.
