Server Configuration


In order to install BioNetDB, the following packages are required:

  • Java 1.8.0_60+
  • Neo4j graph database
  • Apache Maven (when building BioNetDB from sources)

Installing Neo4j

In order to install Neo4j, follow the instructions from the Neo4j Operation Manual powered by the Neo4j Team. This describes how to install Neo4j in different deployment contexts, such as Linux, Mac OS, Windows, Debian, Docker.

Installing BioNetDB

In order to build BioNetDB from source code you must first get the source code of BioNetDB from GitHub, most of the dependencies - including OpenCB dependencies - will be fetched from Maven Central Repository, however in some scenarios OpenCB dependencies will need to be built from GitHub source code. Compiling and building processes are carried out by Apache Maven.

As mentioned, you get the BioNetDB source code from GitHub by downloading the tar ball or by cloning the git repository. Next sections describe both methods to get the source code. 

Downloading the tar ball

  1. Download the latest release from GitHub (tar.gz or zip file).

  2. Extract the contents of the archive using tar -xfz <filename> for the tar.gz file, or gunzip <filename> for the zip file.

Cloning the BioNetDB git repository

  1. Execute one of the following git commands:

    ## Latest stable version
    git clone -b master
    ## Develop branch, for this to work remember to clone and build BioNetDB dependencies (see below)
    git clone -b develop

Compiling BioNetDB source code

Once you get source the BioNetDB 

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