From 4ccb2411b78bcc5112316cef7192033d698b8b03 Mon Sep 17 00:00:00 2001 From: Pjotr Prins Date: Sun, 29 May 2016 16:51:45 +0000 Subject: Added JOSS paper --- doc/joss/2016/paper.md | 84 ++++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 84 insertions(+) create mode 100644 doc/joss/2016/paper.md (limited to 'doc/joss/2016/paper.md') 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 -- cgit v1.2.3 From 42f7955c8619ba43766a3b13626d554c2f3d8399 Mon Sep 17 00:00:00 2001 From: Pjotr Prins Date: Sun, 29 May 2016 16:57:28 +0000 Subject: JOSS: add MQM citation and fix typo --- doc/joss/2016/paper.bib | 14 ++++++++++++++ doc/joss/2016/paper.md | 8 ++++---- 2 files changed, 18 insertions(+), 4 deletions(-) (limited to 'doc/joss/2016/paper.md') diff --git a/doc/joss/2016/paper.bib b/doc/joss/2016/paper.bib index 73a88227..34c0fd05 100644 --- a/doc/joss/2016/paper.bib +++ b/doc/joss/2016/paper.bib @@ -34,3 +34,17 @@ url = {http://www.ncbi.nlm.nih.gov/pubmed/21892150}, abstract = {We describe factored spectrally transformed linear mixed models (FaST-LMM), an algorithm for genome-wide association studies (GWAS) that scales linearly with cohort size in both run time and memory use. On Wellcome Trust data for 15,000 individuals, FaST-LMM ran an order of magnitude faster than current efficient algorithms. Our algorithm can analyze data for 120,000 individuals in just a few hours, whereas current algorithms fail on data for even 20,000 individuals (http://mscompbio.codeplex.com/).} } + +@article{Arends:2010, + author = {Arends, D. and Prins, P. and Jansen, R. C. and Broman, K. W.}, + title = {{R/qtl: high-throughput multiple QTL mapping}}, + journal = {Bioinformatics}, + year = {2010}, + volume = {26}, + number = {23}, + pages = {2990-2992}, + doi = {10.1093/bioinformatics/btq565}, + url = {http://www.ncbi.nlm.nih.gov/pubmed/20966004}, + abstract = {MOTIVATION: R/qtl is free and powerful software for mapping and exploring quantitative trait loci (QTL). R/qtl provides a fully comprehensive range of methods for a wide range of experimental cross types. We recently added multiple QTL mapping (MQM) to R/qtl. MQM adds higher statistical power to detect and disentangle the effects of multiple linked and unlinked QTL compared with many other methods. MQM for R/qtl adds many new features including improved handling of missing data, analysis of 10,000 s of molecular traits, permutation for determining significance thresholds for QTL and QTL hot spots, and visualizations for cis-trans and QTL interaction effects. MQM for R/qtl is the first free and open source implementation of MQM that is multi-platform, scalable and suitable for automated procedures and large genetical genomics datasets. AVAILABILITY: R/qtl is free and open source multi-platform software for the statistical language R, and is made available under the GPLv3 license. R/qtl can be installed from http://www.rqtl.org/. R/qtl queries should be directed at the mailing list, see http://www.rqtl.org/list/. CONTACT: kbroman@biostat.wisc.edu.}, + +} diff --git a/doc/joss/2016/paper.md b/doc/joss/2016/paper.md index 81ec2b72..42fcd500 100644 --- a/doc/joss/2016/paper.md +++ b/doc/joss/2016/paper.md @@ -41,10 +41,10 @@ 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 +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 -- cgit v1.2.3