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| -rw-r--r-- | README.md | 47 | ||||
| -rw-r--r-- | doc/joss/2016/paper.md | 24 |
2 files changed, 59 insertions, 12 deletions
@@ -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]. - 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 |