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Re: [Gmod-tripal-devel] [Gmod-ajax] Nomination for new GMOD project
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From: Cook, M. <ME...@st...> - 2019-01-29 04:20:43
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Pro – I have used it and deployed it and integrated it with JBrowse and agree with all points Yannick raises – and it deserves more/better exposure and funding for further dev as needed. Malcolm Cook - Database Application Manager Computation Biology Group Stowers Institute for Medical Research 1000 E 50th Street Kansas City, Missouri 64110 From: Scott Cain <sc...@sc...> Sent: Monday, January 28, 2019 5:58 PM To: gmod-announce <gmo...@li...>; gmod-devel <gmo...@li...>; gmod-ajax <gmo...@li...>; gmod tripal devel <gmo...@li...>; Apollo Developers <apo...@li...>; Yannick Wurm <y....@qm...>; Anurag Priyam <anu...@gm...> Subject: [Gmod-ajax] Nomination for new GMOD project **CAUTION: Non-Stowers email** Hello GMOD, Last week, Yannick Wurm of SequenceServer fame approached me about adding SequenceServer as a GMOD project. It seems like a great fit to me as a general and widely used tool. Please take a moment to read a little about it if you aren't already familiar and if you have any thoughts (pro or con), please let me know. I included email groups of projects that I thought might be interested in SequenceServer. If you know of somebody else involved with GMOD who isn't covered by one of these lists, please feel free to forward it to them. In case you weren't aware, GMOD has guidelines for adding new projects: http://gmod.org/wiki/GMOD_Membership Here is what Yannick wrote in support of his nomination: ----------------------------------------------------------- Dear all, I would like to nominate SequenceServer as a GMOD tool. Background: A major hurdle I stumbled upon a few years ago as collaborators and I began to obtain transcriptome and genome assemblies from new species, was the lack of a simple manner of BLASTing unpublished data. Using a perl/cgi blast script was horrible - and it had a counterintuitive user interface. Same with the tool for custom databases that NCBI supplied at the time. To overcome this, Anurag Priyam (an undergraduate at the time) and I began developing SequenceServer. Its had 3 main aims: - provide an intuitive user interface and elegant user experience that increases researchers productivity - make it easy for individual users to run it autonomously on unpublished or custom data - make it easy to share a BLAST interface with others - in a lab or on a community database (including the - now deprecated antgenomes.org<http://antgenomes.org> which I ran) It was open source from the start, and has decent success: - 60,000 downloads - >50 citations. - >70 github forks and 130 stars - >190 members on mailing list It is used on dozens of GMOD-esque community sites - often in combination with jBrowse, including: reefgenomics.org<http://reefgenomics.org> http://www.daphnia-stressordb.uni-hamburg.de, hymenopterabase, http://spottedwingflybase.org , bovine genome database, Lepbase, http://www.wheat-tilling.com, PHIbase, GenomeHubs,http://pristionchus.org/about.html, http://planmine.mpi-cbg.de/planmine/begin.do, and many more. Allow me to provide specific comments regarding the GMOD membership criteria below. Please do not hesitate if you have any questions. Kind regards, Yannick ----- Meets a Common Need Growing citations & userbase demonstrate this. Useful Over Time Usage has steadily increased since 2012. The tool wraps BLAST (we are seeking funding to hopefully also wrap DIAMOND). We are implementing novel visualisations to increase analysis power/researchers productivity (including thanks to a recent GSoC). Configurable and Extensible All source code is open. Key configurable things are separated out. - e.g. can use built-tin "sinatra" web server - or go via apache or nginx (as we do on antgenomes.org<http://antgenomes.org>) - the most common customization is to add links from BLAST hits to specific databases (e.g. genome browser or other cross-ref) - this is done in a modular manner, using custom "links.rb" plugins that remain stable even when the rest of sequenceserver is upgraded. E.g. see http://gmod.org/wiki/JBrowse_FAQ#How_can_I_link_BLAST_results_to_JBrowse Open Source License for All Users GNU AGPL v3 Interoperable With Other GMOD Components All it needs is a directory of one or more FASTA files. There is no internal database (the directory is scanned on launch) - thus we don't connect to Chado. We do nothing with annotations and thus don't support GFF. (the jbrowse page actually has a decent section on linking things up - http://gmod.org/wiki/JBrowse_FAQ#How_can_I_link_BLAST_results_to_JBrowse ) Commitment of Support We've been supporting this without specfic funds since 2012 and hope to be able to continue doing so. Being part of GMOD will hopefully also help attract funding. Mailing list is here: https://groups.google.com/forum/?fromgroups#!forum/sequenceserver The code is well documented, the site and doc page are decent - http://www.sequenceserver.com and http://www.sequenceserver.com/doc/ Issue tracker is here: https://github.com/wurmlab/sequenceserver/issues We are happy to commit to continuing these efforts. We have encouraged (and attracted) code contributions in the past and will continue to do so. Users and Support Mailing List(s) https://groups.google.com/forum/?fromgroups#!forum/sequenceserver Issue tracker is here: https://github.com/wurmlab/sequenceserver/issues Public repository https://github.com/wurmlab/sequenceserver -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research |
