README.md


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[![DOI](https://zenodo.org/badge/5591/genenetwork/genenetwork2.svg)](https://zenodo.org/badge/latestdoi/5591/genenetwork/genenetwork2) [![JOSS](http://joss.theoj.org/papers/10.21105/joss.00025/status.svg)](http://joss.theoj.org/papers/10.21105/joss.00025)

# GeneNetwork

This repository contains the source code for the GeneNetwork (GN)
server http://gn2.genenetwork.org/ (version 2 aka GN2). GN is a Web
2.0 style framework with included tools for doing genetics online
using high-throughput data. GN is used for a wide range of studies. An
exhaustive list of publications mentioning GN and its previous
incarnation WebQTL can be found
[here](http://www.genenetwork.org/reference.html).

## Install

The recommended installation is with GNU Guix which allows you to
deploy GN2 and dependencies as a self contained unit on any machine.
The database can be run separately as well as the source tree (for
developers).  See the [installation docs](doc/README.org).

## Test

Once installed GN2 can be run online through a browser interface

```sh
./bin/genenetwork2
```

(default is http://localhost:5003/). For more examples, including running scripts and a Python REPL
see the startup script [./bin/genenetwork2](https://github.com/genenetwork/genenetwork2/blob/testing/bin/genenetwork2).


We are building up automated
testing using [mechanize](https://github.com/genenetwork/genenetwork2/tree/master/test/lib) which can be run with

```sh
./bin/test-website
```

## Documentation

User documentation can be found
[here](http://gn2.genenetwork.org/help).  The architecture of the
software stack is described [here](./doc/Architecture.org).  The
database schema is (still) shared with GN1 and currently described
[here](http://www.genenetwork.org/webqtl/main.py?FormID=schemaShowPage). Software
documentation is being expanded in the
[source code repository](https://github.com/genenetwork/genenetwork2/tree/master/doc).

## Contributing

Issues can be raised through
[github](https://github.com/genenetwork/genenetwork2/issues).

Contribute to GN2 source code by forking the
[github repository](https://github.com/genenetwork/genenetwork2/) with
git and sending us pull requests.

For development GN2 has a
[mailing list](http://listserv.uthsc.edu/mailman/listinfo/genenetwork-dev)
and an active IRC channel #genenetwork on freenode.net with a
[web interface](http://webchat.freenode.net/).

## License

The GeneNetwork2 source code is released under the Affero General
Public License 3 (AGPLv3). See [LICENSE.txt](LICENSE.txt).


## More information

For more information visit http://www.genenetwork.org/

## Cite

[![JOSS](http://joss.theoj.org/papers/10.21105/joss.00025/status.svg)](http://joss.theoj.org/papers/10.21105/joss.00025)

GeneNetwork was published in the Journal of Open Source Software as 'GeneNetwork: framework for web-based genetics' by Zachary Sloan, Danny Arends, Karl W. Broman, Arthur Centeno, Nicholas Furlotte, Harm Nijveen, Lei Yan, Xiang Zhou, Robert W. WIlliams and Pjotr Prins

You may also cite the software using

[![DOI](https://zenodo.org/badge/5591/genenetwork/genenetwork2.svg)](https://zenodo.org/badge/latestdoi/5591/genenetwork/genenetwork2).

## Contact

IRC on #genenetwork on irc.freenode.net.

Code and primary web service managed by Dr. Robert W. Williams and the
University of Tennessee Health Science Center, Memphis TN, USA.