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 From 76a15627f15f9612702cc135747bb383c5a776b1 Mon Sep 17 00:00:00 2001 From: Arfon Smith Date: Sun, 29 May 2016 21:16:35 -0500 Subject: Fixing paper metadata --- doc/joss/2016/paper.md | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) (limited to 'doc/joss/2016/paper.md') diff --git a/doc/joss/2016/paper.md b/doc/joss/2016/paper.md index 42fcd500..38db3ca7 100644 --- a/doc/joss/2016/paper.md +++ b/doc/joss/2016/paper.md @@ -18,7 +18,6 @@ authors: 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 @@ -33,8 +32,7 @@ authors: 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 + affiliation: University Medical Center Utrecht, The Netherlands, University of Tennessee Health Science Center, USA date: 29 May 2016 bibliography: paper.bib --- -- cgit v1.2.3 From 7cc0899e46d2a5538b2646191daba6987d9ed16f Mon Sep 17 00:00:00 2001 From: DannyArends Date: Mon, 30 May 2016 09:39:00 +0200 Subject: Fixing my affiliation --- doc/joss/2016/paper.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'doc/joss/2016/paper.md') diff --git a/doc/joss/2016/paper.md b/doc/joss/2016/paper.md index 38db3ca7..bc63e835 100644 --- a/doc/joss/2016/paper.md +++ b/doc/joss/2016/paper.md @@ -10,7 +10,7 @@ authors: affiliation: University of Tennessee Health Science Center, USA - name: Danny Arends orcid: 0000-0001-8738-0162 - affiliation: Humboldt Universityl, Berlin, Germany + affiliation: Humboldt University, Berlin, Germany - name: Karl W. Broman orcid: 0000-0002-4914-6671 affiliation: University of Wisconsin, USA -- cgit v1.2.3 From 7e3e07c1e3fb150a2d37088a8b250ef028c162ba Mon Sep 17 00:00:00 2001 From: DannyArends Date: Mon, 30 May 2016 09:42:01 +0200 Subject: Consistency in the orchid IDs --- doc/joss/2016/paper.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'doc/joss/2016/paper.md') diff --git a/doc/joss/2016/paper.md b/doc/joss/2016/paper.md index bc63e835..02fc6a65 100644 --- a/doc/joss/2016/paper.md +++ b/doc/joss/2016/paper.md @@ -31,7 +31,7 @@ authors: orcid: 0000-0001-8924-4447 affiliation: University of Tennessee Health Science Center, USA - name: Pjotr Prins - orcid: orcid.org/0000-0002-8021-9162 + orcid: 0000-0002-8021-9162 affiliation: University Medical Center Utrecht, The Netherlands, University of Tennessee Health Science Center, USA date: 29 May 2016 bibliography: paper.bib -- cgit v1.2.3 From e241d27ccd3302632fec52043fc8b42125f4cfd7 Mon Sep 17 00:00:00 2001 From: Pjotr Prins Date: Thu, 2 Jun 2016 09:40:22 +0200 Subject: Paper: addressing https://github.com/openjournals/joss-reviews/issues/25 1st par: "experimental data" could be fleshed out in 2-3 words for the biologist reader (is it SNPs, microarray data, NGS, Y2H or manually counted individuals?) --- doc/joss/2016/paper.md | 19 +++++++++++-------- 1 file changed, 11 insertions(+), 8 deletions(-) (limited to 'doc/joss/2016/paper.md') diff --git a/doc/joss/2016/paper.md b/doc/joss/2016/paper.md index 02fc6a65..a3eb4477 100644 --- a/doc/joss/2016/paper.md +++ b/doc/joss/2016/paper.md @@ -41,14 +41,17 @@ 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]. -![Mouse LMM mapping example](qtl2.png) -- cgit v1.2.3 From 9669b09bdd8885acae07e05cb878e575b1b2c6e1 Mon Sep 17 00:00:00 2001 From: Pjotr Prins Date: Thu, 2 Jun 2016 09:43:58 +0200 Subject: Paper: addressing https://github.com/openjournals/joss-reviews/issues/25 2nd par: "can be found in ___ guix-bioinformatics", please insert 'the article', 'the package', 'the lab fridge labeled'.. whichever is aproppriate ;-) --- doc/joss/2016/paper.md | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) (limited to 'doc/joss/2016/paper.md') diff --git a/doc/joss/2016/paper.md b/doc/joss/2016/paper.md index a3eb4477..62daf177 100644 --- a/doc/joss/2016/paper.md +++ b/doc/joss/2016/paper.md @@ -57,7 +57,8 @@ 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 -- cgit v1.2.3 From 3788a3ae75d8260c167818786aeeeb20b22fb305 Mon Sep 17 00:00:00 2001 From: Pjotr Prins Date: Thu, 2 Jun 2016 09:45:41 +0200 Subject: Paper: addressing https://github.com/openjournals/joss-reviews/issues/25 last par: "Python" is spelled with a capital 'P' --- doc/joss/2016/paper.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'doc/joss/2016/paper.md') diff --git a/doc/joss/2016/paper.md b/doc/joss/2016/paper.md index 62daf177..9ac323d2 100644 --- a/doc/joss/2016/paper.md +++ b/doc/joss/2016/paper.md @@ -80,7 +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 -- cgit v1.2.3 From fbd60cd5fccdd6e664865a74fd1a4433fc1ec55d Mon Sep 17 00:00:00 2001 From: Pjotr Prins Date: Wed, 8 Jun 2016 10:23:53 +0000 Subject: JOSS: added orcid for Nick Furlotte --- doc/joss/2016/paper.md | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) (limited to 'doc/joss/2016/paper.md') diff --git a/doc/joss/2016/paper.md b/doc/joss/2016/paper.md index 9ac323d2..6b640836 100644 --- a/doc/joss/2016/paper.md +++ b/doc/joss/2016/paper.md @@ -17,7 +17,8 @@ authors: - name: Arthur Centeno orcid: 0000-0003-3142-2081 affiliation: University of Tennessee Health Science Center, USA - - name: Nick Furlotte + - name: Nicholas Furlotte + orcid: 0000-0002-9096-6276 - name: Harm Nijveen orcid: 0000-0002-9167-4945 affiliation: Wageningen University, The Netherlands -- cgit v1.2.3 From 47cf69f2f2fc8243b94f17387547c1fc12fb60ab Mon Sep 17 00:00:00 2001 From: Pjotr Prins Date: Thu, 9 Jun 2016 09:07:34 +0000 Subject: Docs: add SVG graph --- doc/README.org | 2 +- doc/joss/2016/paper.md | 2 ++ 2 files changed, 3 insertions(+), 1 deletion(-) (limited to 'doc/joss/2016/paper.md') diff --git a/doc/README.org b/doc/README.org index bcc8a65e..681357ef 100644 --- a/doc/README.org +++ b/doc/README.org @@ -24,7 +24,7 @@ * Introduction -Large system deployments can get very complex. In this document we +Large system deployments can get very [[http://biobeat.org/gn2.svg][complex]]. In this document we explain the GeneNetwork version 2 (GN2) reproducible deployment system which is based on GNU Guix (see also Pjotr's [[https://github.com/pjotrp/guix-notes/blob/master/README.md][Guix-notes]]). The Guix system can be used to install GN with all its files and dependencies. diff --git a/doc/joss/2016/paper.md b/doc/joss/2016/paper.md index 6b640836..7c6f76cc 100644 --- a/doc/joss/2016/paper.md +++ b/doc/joss/2016/paper.md @@ -69,6 +69,8 @@ database is 160GB and growing), GN is packaged with GNU Guix deployment makes it feasible to deploy and rebrand GN anywhere. +-![GN2 dependency graph](http://biobeat.org/gn2.svg) + # Future work More mapping tools will be added, including support for Genome-wide -- cgit v1.2.3 From ed482493f2fa907632bacffac7a1938e9656b0d5 Mon Sep 17 00:00:00 2001 From: Pjotr Prins Date: Thu, 9 Jun 2016 09:37:30 +0000 Subject: Doc: moved graph into README --- doc/README.org | 5 +++++ doc/joss/2016/paper.md | 2 -- 2 files changed, 5 insertions(+), 2 deletions(-) (limited to 'doc/joss/2016/paper.md') diff --git a/doc/README.org b/doc/README.org index 681357ef..a36d04bb 100644 --- a/doc/README.org +++ b/doc/README.org @@ -34,6 +34,11 @@ main Guix package tree and that of the Genenetwork package tree. Current supported versions can be found as the SHA values of 'gn-latest' branches of [[https://github.com/genenetwork/guix-bioinformatics/tree/gn-latest][Guix bioinformatics]] and [[https://github.com/genenetwork/guix/tree/gn-latest][GNU Guix main]]. +Graph of all runtime dependencies as installed by GNU Guix. + +-![GN2 dependency graph](http://biobeat.org/gn2.svg) + + * Quick installation recipe This is a recipe for quick and dirty installation of GN2. For diff --git a/doc/joss/2016/paper.md b/doc/joss/2016/paper.md index 7c6f76cc..6b640836 100644 --- a/doc/joss/2016/paper.md +++ b/doc/joss/2016/paper.md @@ -69,8 +69,6 @@ database is 160GB and growing), GN is packaged with GNU Guix deployment makes it feasible to deploy and rebrand GN anywhere. --![GN2 dependency graph](http://biobeat.org/gn2.svg) - # Future work More mapping tools will be added, including support for Genome-wide -- cgit v1.2.3 From 75c7a0828625e3aaf6326e91fadf20df96207fc3 Mon Sep 17 00:00:00 2001 From: Pjotr Prins Date: Thu, 16 Jun 2016 17:15:39 +0000 Subject: JOSS: fix typo and amend URL --- doc/joss/2016/paper.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'doc/joss/2016/paper.md') diff --git a/doc/joss/2016/paper.md b/doc/joss/2016/paper.md index 6b640836..12b3b5d0 100644 --- a/doc/joss/2016/paper.md +++ b/doc/joss/2016/paper.md @@ -28,7 +28,7 @@ authors: - name: Xiang Zhou orcid: 0000-0002-4331-7599 affiliation: University of Michigan - - name: Robert W. WIlliams + - name: Robert W. Williams orcid: 0000-0001-8924-4447 affiliation: University of Tennessee Health Science Center, USA - name: Pjotr Prins @@ -65,7 +65,7 @@ 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). +[here](https://github.com/genenetwork/genenetwork2/blob/master/doc/README.org). GNU Guix deployment makes it feasible to deploy and rebrand GN anywhere. -- cgit v1.2.3