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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 |