BioNetDB implements a storage engine to work with biological networks using a NoSQL graph database. BioNetDB integrates relevant biological networks information from well-known data sources such as Reactome. All this data can be queried through command line interface.
You can find BioNetDB documentation and tutorials at: https://github.com/opencb/bionetdb/wiki.
You can report bugs or request new features at GitHub issue tracking.
Releases notes are available at GitHub releases.
Roadmap is available at GitHub milestones.
BioNetDB is versioned following the rules from Semantic versioning.
We recommend to contact BioNetDB developers by writing to BioNetDB mailing list opencb@googlegroups.com. The main developers and maintainers are:
- Ignacio Medina (im411@cam.ac.uk) (Founder and Project Leader)
- Daniel Perez-Gil (daniel.perez@incliva.es)
- Pedro Furio-Tari (pfurio@cipf.es)
BioNetDB is an open-source and collaborative project. We appreciate any help and feedback from users, you can contribute in many different ways such as simple bug reporting and feature request. Depending on your skills you are more than welcome to develop client tools, new features or even fixing bugs.
BioNetDB is mainly developed in Java and it uses Apache Maven as building tool. BioNetDB requires Java 8+ and others OpenCB Java dependencies that can be found in Maven Central Repository.
Stable releases are merged and tagged at master branch. You are encouraged to use latest stable release for production. Current active development is carried out at develop branch, only compilation is guaranteed and bugs are expected, use this branch for development or for testing new functionalities. Only dependencies of master branch are ensured to be deployed at Maven Central Repository, develop branch may require users to download and install other active OpenCB repositories:
- biodata: https://github.com/opencb/biodata (branch 'develop')
- datastore: https://github.com/opencb/datastore (branch 'develop')
BioNetDB is an open-source and free project, you can download develop branch by executing:
$ git clone https://github.com/opencb/bionetdb.git
Latest stable release at master branch can be downloaded executing:
$ git clone -b master https://github.com/opencb/bionetdb.git
You can build BioNetDB by executing the following command from the root of the cloned repository:
$ mvn clean install -DskipTests
Remember that develop branch dependencies are not ensured to be deployed at Maven Central, you may need to clone and install develop branches from OpenCB biodata and datastore repositories.
You can run the unit tests using Maven or your favorite IDE.
If the build process has gone well you should get an integrated help by executing:
$ ./bin/bionetdb.sh --help
You can find more detailed documentation and tutorials at: https://github.com/opencb/bionetdb/wiki.