druglogics / drabme

Drug Response Analysis to Boolean Model Ensembles

drabme

Drabme is an acronym for Drug Response Analysis to Boolean Model Ensembles. This module performs a combinatorial drug response analysis using the boolean models generated by Gitsbe in order to evaluate and identify the synergistic drug combinations.

For a full documentation of this package check here.

Install

First, install gitsbe. Then:

git clone https://github.com/druglogics/drabme.git
cd drabme
mvn clean install

The above command creates a package <name>-jar-with-dependencies.jar file with all dependencies installed, in the target directory.

Alternatively, you could just use directly one of the released packages.

Run example

The recommended way to run Drabme is to use its Launcher. From the root directory of the repo run: (remember to change the {version} to the appropriate one, e.g. 1.2.0):

cd example_run_ags
java -cp ../target/drabme-{version}-jar-with-dependencies.jar eu.druglogics.drabme.Launcher --project=test --modelsDir=models --drugs=toy_ags_drugpanel.tab --perturbations=toy_ags_perturbations.tab --config=toy_ags_config.tab --modeloutputs=toy_ags_modeloutputs.tab

or run the mvn profile directly:

mvn compile -P runExampleAGS