DREIMT - A tool for immune modulation drug prioritization (http://www.dreimt.org)
DREIMT is a bioinformatics tool for hypothesis generation and prioritization of drugs capable of modulating immune cell activity from transcriptomics data.
DREIMT integrates 4,694 drug profiles from The Library of Network-Based Cellular Signatures (LINCS) L1000 data set and 2,687 manually curated immune gene expression signatures from multiple resources to generate a drug-immune signature association database.
DREIMT can also prioritize drug associations from user-provided immune signatures.
The application has been configured to be easily run locally, by just invoking a Maven command.
To do so, Maven will download (if it is not already) a clean WildFly distribution to the target folder, configure it, start it and deploy the application on it.
This makes very easy and straightforward to manually test the application.
To execute the application you need a MySQL server running in localhost and using the default port (3306).
In this server you have to create a database named dreimt accessible for the dreimt user using the dreimtpass password.
This can be configured executing the follow SQL sentences in your MySQL:
CREATE DATABASE dreimt;
GRANT ALL ON dreimt.* TO dreimt@localhost IDENTIFIED BY 'dreimtpass';
FLUSH PRIVILEGES;Of course, this configuration can be changed in the POM file.
The additional-material/db contains several files related with the DREIMT db initialization. After creating a new database as described in the previous step, you can populate it with the following commands:
sudo mysql dreimt < additional-material/db/dreimt-db-initialization.sql
sudo mysql dreimt < additional-material/db/dreimt-schema.sql
zcat additional-material/db/dreimt-data.sql.gz | sudo mysql dreimt
sudo mysql dreimt < additional-material/db/fill_full_drug_signature_interaction_table.sql
The application can be built with the following Maven command:
mvn clean install
This will build the application launching the tests on a Wildfly 10.1.0 server.
The application can be started with the following Maven command:
mvn package wildfly:start wildfly:deploy-only -P wildfly-mysql-run
This will start a WildFly 10.1.0 serving the DREIMT application.
Once it is running, the application can be re-deployed with the following Maven command:
mvn package wildfly:deploy-only -P wildfly-mysql-run
The application can be stopped with the following Maven command:
mvn wildfly:shutdown
The REST API is documented using the Swagger framework. It can be browsed using the Swagger UI application to access the following URL:
http://localhost:8080/dreimt-backend/rest/api/swagger.json