gitsbe

Gitsbe is an acronym for Generic Interactions To Specific Boolean Equations. This module defines boolean models compliant with observed behavior (e.g. steady state or perturbation data) using an automated, model parameterization genetic algorithm.

For a full documentation of this package check here.

Install

git clone https://github.com/druglogics/gitsbe.git
cd gitsbe
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 Gitsbe is to use its Launcher. From the root directory of the repo run: (remember to change the {version} to the appropriate one, e.g. 1.3.0):

cd example_run_ags
java -cp ../target/gitsbe-{version}-jar-with-dependencies.jar eu.druglogics.gitsbe.Launcher --project=test --network=toy_ags_network.sif --trainingdata=toy_ags_training_data.tab --config=toy_ags_config.tab --modeloutputs=toy_ags_modeloutputs.tab

or run the mvn profile directly:

mvn compile -P runExampleAGS