Merge branch 'rebase' into staging

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..81ec2b72
--- /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 [@mqm paper] 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].
+
+-![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
+[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