From e3fc8d16cff08ee9f42bf937121f7119d2670ded Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Thu, 2 Jun 2016 10:25:42 +0200
Subject: Paper: addressing JOSS requirements for contribution, where to find  
      documentation and testing materials

https://github.com/openjournals/joss-reviews/issues/25
---
 README.md | 47 +++++++++++++++++++++++++++++++++++++++++++++--
 1 file changed, 45 insertions(+), 2 deletions(-)

diff --git a/README.md b/README.md
index d814f090..85042e6a 100644
--- a/README.md
+++ b/README.md
@@ -2,8 +2,13 @@
 
 # GENENETWORK
 
-This repository contains the source code for the GeneNetwork server
-http://gn2.genenetwork.org/ (version 2 aka GN2).
+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
 
@@ -12,11 +17,49 @@ 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/). 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 database schema is
+shared with GN1 and 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/
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