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@@ -1,28 +1,85 @@ -genenetwork on github (May 7, 2012 by Lei Yan and Rob Williams) +[](https://zenodo.org/badge/latestdoi/5591/genenetwork/genenetwork2) [](http://joss.theoj.org/papers/10.21105/joss.00025) -www.genenetwork.org +# GeneNetwork -Released under Affero General Public License 3 (AGPLv3). See also -LICENSE.txt +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). -For background see: http://en.wikipedia.org/wiki/Genenetwork +## Install -WWW service initiated January, 1994 as The Portable Dictionary of the Mouse Genome and -June 15, 2001 as WebQTL. +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). -This code and the main web service is currently operated by Lei Yan, Zachary Sloan, -Arthur Centeno. Design and code by Xiaodong Zhou, Christian Fernandez, Sam Ockman, Ning Liu, Rudi Alberts, -Elissa Chesler, Jintao Wang, Kenneth Manly, Robert W. Williams, and colleagues. +## Test -Code and primary web service managed by Dr. Robert W. Williams and the University of Tennessee Health Science Center, -Memphis TN, USA. +Once installed GN2 can be run online through a browser interface -Email labwilliams@gmail.com or rwilliams@uthsc.edu +```sh +./bin/genenetwork2 +``` -Older version available on SourceForge http://sourceforge.net/projects/genenetwork/ +(default is http://localhost:5003/). We are building up automated +testing using [mechanize](https://github.com/genenetwork/genenetwork2/tree/master/test/lib) which can be run with -Funded by the National Institutes of Health and -University of Tennessee Center for Integrative and Translational Genomics +```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 + +[](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 + +[](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. -=========== |