Installation and Usage

Install

Prerequisites: maven 3.6.0 and Java 8.

Installation commands:

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 gitsbe packages.

Note that Gitsbe calculates attractors for the boolean models it generates using either the BNReduction tool (Veliz-Cuba et al. 2014), the BioLQM Java library (Naldi 2018) or the Most Permissive Boolean Networks framework (Paulevé et al. 2020). BioLQM is included by default in the code. The BNReduction and MPBN scripts have to be manually installed following the respective documentation.

Example

The recommended way to run Gitsbe is to use it’s Launcher. From the root directory of the repo run:

cd example_run_ags
java -cp ../target/gitsbe-1.3.1-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 (same input as the command above through the pom.xml):

mvn compile -P runExampleAGS

Inputs

Running the Gitsbe Launcher with no parameters, generates a usage message with the available options. The required parameters are:

• --network: a single-interactions network file (in Cytoscape’s .sif format, tab-delimited, with binary signed and directed interactions)
• --trainingdata: training data file
• --modeloutputs: model outputs file
• --config: configuration file

The non-required parameters are:

• --project: the project name which is used as the name of the directory where the outputs will be stored.
• --drugs: drug panel file: this is required only when the training data observations include either single or double drug perturbation conditions.

Outputs

The expected generated outputs of Gitsbe’s Launcher are:

• A models directory with files in .gitsbe format (or other formats as well if properly specified), which represent the boolean models that best fitted to the configuration and training data that the simulation of the genetic algorithm was based on.
• A summary file that includes the models’ fitness evolution throughout the genetic algorithm’s generations.
• The initial boolean model exported in many standard formats (e.g. .gitsbe, .sif, .ginml).

It is for the better that all input files are on the same directory as in the example above. In any case, the directory with all the output files when running the Launcher will be in the same path as the configuration file.