From e241d27ccd3302632fec52043fc8b42125f4cfd7 Mon Sep 17 00:00:00 2001 From: Pjotr Prins Date: Thu, 2 Jun 2016 09:40:22 +0200 Subject: Paper: addressing https://github.com/openjournals/joss-reviews/issues/25 1st par: "experimental data" could be fleshed out in 2-3 words for the biologist reader (is it SNPs, microarray data, NGS, Y2H or manually counted individuals?) --- doc/joss/2016/paper.md | 19 +++++++++++-------- 1 file changed, 11 insertions(+), 8 deletions(-) diff --git a/doc/joss/2016/paper.md b/doc/joss/2016/paper.md index 02fc6a65..a3eb4477 100644 --- a/doc/joss/2016/paper.md +++ b/doc/joss/2016/paper.md @@ -41,14 +41,17 @@ 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) -- cgit v1.2.3 From 9669b09bdd8885acae07e05cb878e575b1b2c6e1 Mon Sep 17 00:00:00 2001 From: Pjotr Prins Date: Thu, 2 Jun 2016 09:43:58 +0200 Subject: Paper: addressing https://github.com/openjournals/joss-reviews/issues/25 2nd par: "can be found in ___ guix-bioinformatics", please insert 'the article', 'the package', 'the lab fridge labeled'.. whichever is aproppriate ;-) --- doc/joss/2016/paper.md | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/doc/joss/2016/paper.md b/doc/joss/2016/paper.md index a3eb4477..62daf177 100644 --- a/doc/joss/2016/paper.md +++ b/doc/joss/2016/paper.md @@ -57,7 +57,8 @@ 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 -- cgit v1.2.3 From 3788a3ae75d8260c167818786aeeeb20b22fb305 Mon Sep 17 00:00:00 2001 From: Pjotr Prins Date: Thu, 2 Jun 2016 09:45:41 +0200 Subject: Paper: addressing https://github.com/openjournals/joss-reviews/issues/25 last par: "Python" is spelled with a capital 'P' --- doc/joss/2016/paper.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/joss/2016/paper.md b/doc/joss/2016/paper.md index 62daf177..9ac323d2 100644 --- a/doc/joss/2016/paper.md +++ b/doc/joss/2016/paper.md @@ -80,7 +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 -- cgit v1.2.3 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/ -- cgit v1.2.3