Merge branch 'master' of github.com:genenetwork/genenetwork2

2 files changed, 59 insertions, 12 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/
diff --git a/doc/joss/2016/paper.md b/doc/joss/2016/paper.md
index 02fc6a65..9ac323d2 100644
--- a/doc/joss/2016/paper.md
+++ b/doc/joss/2016/paper.md
@@ -41,20 +41,24 @@ bibliography: paper.bib
 
 GeneNetwork (GN) is a free and open source (FOSS) framework for
 web-based genetics that can be deployed anywhere. GN allows biologists
-to upload experimental data and map phenotypes interactively against
-genotypes using tools, such as R/QTL [@Arends:2010] mapping, interval
-mapping for model organisms and pylmm; an implementation of FaST-LMM
-[@Lippert:2011] which is suitable for human populations and outbred
-crosses, such as the mouse diversity outcross. Interactive D3 graphics
-are included from R/qtlcharts and presentation-ready figures can be
-generated. Recently we have added functionality for phenotype
-correlation [@Wang:2016] and network analysis [@WGCNA:2008].
+to upload high-throughput experimental data, such as expression data
+from microarrays and RNA-seq, and also `classic' phenotypes, such as
+disease phenotypes.  These phenotypes can be mapped interactively
+against genotypes using embedded tools, such as R/QTL [@Arends:2010]
+mapping, interval mapping for model organisms and pylmm; an
+implementation of FaST-LMM [@Lippert:2011] which is more suitable for
+human populations and outbred crosses, such as the mouse diversity
+outcross. Interactive D3 graphics are included from R/qtlcharts and
+presentation-ready figures can be generated. Recently we have added
+functionality for phenotype correlation [@Wang:2016] and network
+analysis [@WGCNA:2008].
 
 -![Mouse LMM mapping example](qtl2.png)
 
 GN is written in python and javascript and contains a rich set of
 tools and libraries that can be written in any computer language. A
-full list of included software can be found in
+full list of included software can be found in the package named
+`genenetwork2' and defined in
 [guix-bioinformatics](https://github.com/genenetwork/guix-bioinformatics/blob/master/gn/packages/genenetwork.scm). To
 make it easy to install GN locally in a byte reproducible way,
 including all dependencies and a 2GB MySQL test database (the full
@@ -76,7 +80,7 @@ worked on, including GPU support.
 A REST interface is being added so that data can be uploaded to a
 server, analysis run remotely on high performance hardware, and
 results downloaded and used for further analysis. This feature will
-allow biologist-programmers to use R and python on their computer and
+allow biologist-programmers to use R and Python on their computer and
 execute computations on GN enabled servers.
 
 # References