[Gmod-announce] Nomination for new GMOD project

[Scott C. <sc...@sc...>]

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the lack of a simple manner of BLASTing unpublished data.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 - make it easy for individual users to run it autonomously on unpublished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 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://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
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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)
 - 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