[MOBY-l] BioMoby and SeqHound

[Ian Donaldson]

Dear all:

SeqHound is a freely available bioinformatics database warehouse resource
that is available via a remote programming API in C, C++, Java and Perl.

A number of SeqHound API calls have been wrapped up as BioMoby services by
Mark Wilkinson.  We (the SeqHound development group) are considering setting
up our own BioMoby-SeqHound server that will make more SeqHound services
available to BioMoby users.  

In order to direct our development efforts, we are looking for feedback
(posted to this list) as to what API calls people would find most useful as
BioMoby services.

The capabilities of the SeqHound API include functions that return GenBank
sequence records, MMDB or PDB structure records, GO annotation assignments
and pre-computed BLAST and RPS-BLAST results.  There are many others.  A
complete list of the API is available at 
http://www.blueprint.org/seqhound/api_help/seqhound_help_guides.html. 

Any requests/feedback is most welcome.

Thanks

Ian

Ian Donaldson, Ph.D.
Manager of Bioinformatics Software Development
The Blueprint Initiative - North America
522 University Ave.
Toronto, Ontario, Canada
M5G 1W7
http://blueprint.org
ian.donaldson at blueprint.org


About SeqHound
SeqHound is a freely available bioinformatics database warehouse resource.
Over 300 Gigabytes of data are collected, integrated and updated from around
the world on a nightly basis.  Sources include the National Center for
Biotechnology Information and the Gene Ontology Consortium.  Programmers
have unrestricted access to up-to-date data via a remote Application
Programming Interface (API) written in Perl, Java, C and C++.  Over 150
function calls allow access to the complete collection of GenBank, RefSeq
and SwissProt sequences, 3-D structures, precomputed protein neighbours,
redundancies and conserved domain analyses.  Users may also access collected
sequence annotations including taxonomy, Gene Ontology assignments and
PubMed links.  All functions are fully documented and tested on a daily
basis.  The Blueprint SeqHound server is supported by a redundant
architecture (failover load-balancers, failover servers and, failover SANs)
for complete fault protection against component failure and to ensure rapid
response time. SeqHound encourages unrestricted 24x7 calls to its servers,
to allow programmers rapid, uninterrupted, access to biological data on a
global basis.  

SeqHound services over 700,000 hits per day.  All SeqHound code is freely
distributed under the GNU Public License. Find SeqHound at
www.blueprint.org.


SeqHound v3.0 is available for download now from
http://www.blueprint.org/seqhound/api_help/seqhound_help_guides.html.  

Major changes to this release include a port to a MySQL database backend
allowing users to install a virtually free bioinformatics-programming
platform in-house using instructions provided in the SeqHound Manual.  

The remote API (available in Java and Perl) is now supported by a FastCGI
server for even faster response times.

We are interested in identifying developers who are already using SeqHound.
If you are, please sign up for the seqhound.usergroup email list at
http://lists.blueprint.org/mailman/listinfo/seqhound.usergroup.  Feedback
and discussions on future development are welcome at this list.