DREIMT

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.

Development

Running the application

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.

Configure a local MySQL

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.

Development database initialization

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

Building the application

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.

Starting the application

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.

Redeploying the 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

Stopping the application

The application can be stopped with the following Maven command:

mvn wildfly:shutdown

REST API documentation

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