paper.md

title	tags	authors	date	bibliography
GeneNetwork: framework for web-based genetics	bioinformatics genetics genomics	name orcid affiliation Zachary Sloan 0000-0002-8099-1363 University of Tennessee Health Science Center, USA name orcid affiliation Danny Arends 0000-0001-8738-0162 Humboldt University, Berlin, Germany name orcid affiliation Karl W. Broman 0000-0002-4914-6671 University of Wisconsin, USA name orcid affiliation Arthur Centeno 0000-0003-3142-2081 University of Tennessee Health Science Center, USA name orcid Nicholas Furlotte 0000-0002-9096-6276 name orcid affiliation Harm Nijveen 0000-0002-9167-4945 Wageningen University, The Netherlands name orcid affiliation Lei Yan 0000-0001-5259-3379 University of Tennessee Health Science Center, USA name orcid affiliation Xiang Zhou 0000-0002-4331-7599 University of Michigan name orcid affiliation Robert W. Williams 0000-0001-8924-4447 University of Tennessee Health Science Center, USA name orcid affiliation Pjotr Prins 0000-0002-8021-9162 University Medical Center Utrecht, The Netherlands, University of Tennessee Health Science Center, USA	29 May 2016	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 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].

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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 the package named `genenetwork2' and defined in guix-bioinformatics. 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, as described here. 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 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