PharmacoDB allows scientists to search across publicly available datasets to find instances where a drug or cell line of interest has been profiled, and to view and compare the dose-response data for a specific cell line - drug pair from any of the studies included in the database.
We are providing full access to the contents of PharmacoDB and are distributing the database as a docker image. Making our research fully reproducible is part of the mission of the Haibe-Kains laboratory.
1.1.1(see release notes: https://pharmacodb.pmgenomics.ca/news?v=1.1.1-stable)
1.1.0(see release notes: https://pharmacodb.pmgenomics.ca/news?v=1.1.0-stable)
1.0.0(see release notes: https://pharmacodb.pmgenomics.ca/news?v=1.0.0-stable)
Instructions for deploying PharmacoDB are available below:
tag with a tag from
Supported tags above.
sudo docker pull bhklab/pharmacodb:tag
sudo docker run -d -p 3000:3000 -v ~:/home -it --name pharmacodb --entrypoint /bin/bash bhklab/pharmacodb:tag
sudo docker exec -it --user root pharmacodb /usr/src/app/prod
(The command above will take some time to run, please be patient)
The last command will deploy the web app and it should be accessible on
http://localhost:3000. Exiting through
Ctrl + C or
Ctrl + Z will cause PharmacoDB to shut down. If you want to have further interaction with the docker container please do so in a separate terminal.
MySQL Database Access
In a separate terminal interact with the database by accessing the shell like this:
docker exec -it pharmacodb bash
Once you have accessed the bash shell use the included mysql client to query the database (default password for user root is 'pass'):
mysql -uroot -ppass
mysql -u root -p (you will be prompted for password at which point please enter "pass")
PharmacoDB's contents are stored under the
pharmacodb_development database which can be accessed using standard SQL.
Create PostgreSQL Database Dump
In a separate terminal run the following command:
sudo docker exec -it --user root pharmacodb /usr/src/app/data/mysql_to_postgres
The dump should be available in your home directory:
All the data in the
bhklab/pharmacodb:1.1.1 Docker image corresponds to the following Zenodo dataset: 10.5281/zenodo.1143644
For more information, please visit https://pharmacodb.pmgenomics.ca