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-genenetwork on github  (May 7, 2012 by Lei Yan and Rob Williams)
+[![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)
 
-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
+
+[![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. 
 
-===========