diff options
Diffstat (limited to 'doc/joss/2016/paper.md')
| -rw-r--r-- | doc/joss/2016/paper.md | 84 |
1 files changed, 84 insertions, 0 deletions
diff --git a/doc/joss/2016/paper.md b/doc/joss/2016/paper.md new file mode 100644 index 00000000..42fcd500 --- /dev/null +++ b/doc/joss/2016/paper.md @@ -0,0 +1,84 @@ +--- +title: 'GeneNetwork: framework for web-based genetics' +tags: + - bioinformatics + - genetics + - genomics +authors: + - name: Zachary Sloan + orcid: 0000-0002-8099-1363 + affiliation: University of Tennessee Health Science Center, USA + - name: Danny Arends + orcid: 0000-0001-8738-0162 + affiliation: Humboldt Universityl, Berlin, Germany + - name: Karl W. Broman + orcid: 0000-0002-4914-6671 + affiliation: University of Wisconsin, USA + - name: Arthur Centeno + orcid: 0000-0003-3142-2081 + affiliation: University of Tennessee Health Science Center, USA + - name: Nick Furlotte + orcid: ? + - name: Harm Nijveen + orcid: 0000-0002-9167-4945 + affiliation: Wageningen University, The Netherlands + - name: Lei Yan + orcid: 0000-0001-5259-3379 + affiliation: University of Tennessee Health Science Center, USA + - name: Xiang Zhou + orcid: 0000-0002-4331-7599 + affiliation: University of Michigan + - name: Robert W. WIlliams + orcid: 0000-0001-8924-4447 + affiliation: University of Tennessee Health Science Center, USA + - name: Pjotr Prins + orcid: orcid.org/0000-0002-8021-9162 + affiliation: University Medical Center Utrecht, The Netherlands + affiliation: University of Tennessee Health Science Center, USA +date: 29 May 2016 +bibliography: paper.bib +--- + +# Summary + +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]. + +- + +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 +[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 +database is 160GB and growing), GN is packaged with +[GNU Guix](https://www.gnu.org/software/guix/), as described +[here](https://github.com/genenetwork/genenetwork2/blob/staging/doc/README.org). +GNU Guix deployment makes it feasible to deploy and rebrand GN +anywhere. + +# Future work + +More mapping tools will be added, including support for Genome-wide +Efficient Mixed Model Association (GEMMA). The +[Biodiallance genome browser](http://www.biodalliance.org/) is being +added as a Google Summer of Code project with special tracks related +to QTL mapping and network analysis. Faster LMM solutions are being +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 +execute computations on GN enabled servers. + +# References |