[Biojava-l] Webservices clients in bio-java

[Scooter Willis]

Jim

I agree. I am planning on doing some testing of  a couple BLAST web services
interfaces(assuming more than one exists) and see what they truly have in
common and see how that would impact a BJ3 front end to multiple providers.
My assumption is that they will be the same. I noticed on the NCBI Blast
implementations the user was required to pass their email address as part of
the web service call. They are concerned with abuse from external processes
and they only allow one sequence per request.

>From wikipedia the following are listed as BLAST resources where more than
one may offer a web service interface. Should BioJava3 try and support more
than one?

Thanks

Scooter

Variations of BLAST

   - WU-BLAST <http://blast.wustl.edu/> — the original gapping BLAST with
   statistics, developed and maintained by Warren Gish at Washington
   University in St.
Louis<http://en.wikipedia.org/wiki/Washington_University_in_St._Louis>
   - EBI's BLAST Services <http://www.ebi.ac.uk/Tools/blast> —
EBI's<http://en.wikipedia.org/wiki/European_Bioinformatics_Institute>main
blast services page.
   - FSA-BLAST <http://www.fsa-blast.org/> — a new, faster but still
   accurate version of NCBI BLAST based on recently published algorithmic
   improvements
   - NBIC mpiBLAST <http://services.nbic.nl:4080/bb/cgi-bin/bb_login.cgi> —
   at the Netherlands Bioinformatics Centre
   - Parallel BLAST<http://www-users.cs.umn.edu/%7Erangwala/final_bglBLAST.pdf>—
a dual scheduling BLAST tested on the Blue Gene/L
   - mpiBLAST <http://www.mpiblast.org/> — open-source parallel BLAST
   - A/G BLAST <http://developer.apple.com/darwin/projects/blast/> —
   implementation for PowerPC G4/G5 processors and Mac OS X, from Apple
   Computer <http://en.wikipedia.org/wiki/Apple_Computer>'s Advanced
   Computation Group<http://en.wikipedia.org/wiki/Advanced_Computation_Group>and
   Genentech <http://en.wikipedia.org/wiki/Genentech>.
   - STRAP <http://3d-alignment.eu/> — the protein workbench
STRAP<http://www.charite.de/bioinf/strap/>contains a comfortable BLAST
front-end with a cache for BLAST results

 [edit<http://en.wikipedia.org/w/index.php?title=BLAST&action=edit&section=13>
] Commercial versions

   - ThermoBLAST by DNA Software
Inc.<http://dnasoftware.com/ThermoBLAST/tabid/110/Default.aspx>— scans
entire genomes quickly and accurately combing the power of BLAST
   with the most advanced thermodynamics parameters
   - PatternHunter<http://www.bioinformaticssolutions.com/products/ph/index.php>—
an alternative software which provides similar functionality to BLAST
   while claiming increased speed and sensitivity
   - KoriBlast <http://www.korilog.com/products> — a reliable graphical
   environment dedicated to sequence data mining. KoriBlast combines Blast
   searches with advanced data management capabilities and a state-of-the-art
   graphical user interface.
   - microbial identification BLAST <http://www.sepsitest-blast.de/> — a
   quality controlled database for in-vitro diagnostics. SepsiTest combines
   broad-range-PCR using ultra-pure reagents with Blast searches in a quality
   controlled environment.




On Thu, May 28, 2009 at 8:29 AM, James Procter <jimp at compbio.dundee.ac.uk>wrote:

> Hi All.
>
> Mark Schreiber wrote:
> > There was a recent discussion of generated code on the list. A good
> solution
> > for webservices may be to put the wsdl and high level api in the
> repository
> > and let jax-ws tools autogenerate the client biolerplate code.
>
> Just to clarify - by high-level API you mean the interface to the code
> that takes biojava objects as arguments and translates them into
> parameters for the service and vice versa for the results ?
>
> With regard to the recent(ish) discussion about modularisation in BJ3,
> I'd suggest that a module is created for each distinct WSDL containing
> the glue code for connecting BJ objects with the boilerplate code. The
> glue code implements factory methods to generate instances of
> appropriate BJ service APIs, which are defined in a core BJ module. This
> means that the WSDL + API implementation is decoupled from the BJ
> service API.
>
> Does that make sense (and/or am I simply stating the obvious here) ?
>
> Jim.
>
> --
> -------------------------------------------------------------------
> J. B. Procter  (ENFIN/VAMSAS)  Barton Bioinformatics Research Group
> Phone/Fax:+44(0)1382 388734/345764  http://www.compbio.dundee.ac.uk
> The University of Dundee is a Scottish Registered Charity, No. SC015096.
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>
>