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The geneXplain platform Java API

The geneXplain platform is a software that, as a web service, provides a comprehensive environment to analyze biomedical and biological data. Its functionality includes, among other things, data storage, data management, data sharing, running bioinformatics and systems biology analysis tools, building and running analysis pipelines and workflows, building and visualizing molecular network models, or developing quantitative models and simulation. More details about the platform can be found here and in corresponding research articles.

This document describes the Java API for the geneXplain platform, which allows operation of platform functionality on a remote server using Java programs. Like user accounts for the platform, the API is freely available at GitHub.

You clone its GitHub repository with the following shell command or download a ZIP archive from the repository website.

git clone

A JAR package of the software can be built using the Gradle build tool.

cd genexplain-api
gradle build

There are two main ways to make use of genexplain-api. On one hand, the software can be used as a library to build Java programs that interact with the geneXplain platform. On the other hand, the JAR created by the build script is executable and offers several applicatons as well as a JSON interface that enables configuration and execution of individual analysis jobs up to complex workflows.

The core structure of the API is described in Java API. A number of examples in package show how to apply it, whereas the section named JAR applications and JSON interface describes the different applications that can be executed from the JAR file as well as how to use the JSON interface including a Hello world-tutorial.