[Biojava-l] BLAST/Java interface

[Brian Gilman]

On 8/23/02 9:18 AM, "Patrick McConnell" <MCCon012@mc.duke.edu> wrote:

> 
> ---------------------- Forwarded by Patrick McConnell/CanCtr/mc/Duke on
> 08/23/2002 09:19 AM ---------------------------
> 
> From:  Patrick McConnell on 08/23/2002 08:57 AM
> 
> To:    nathan whitehouse <nlwhitehouse@yahoo.com>
> cc:
> 
> Subject:    Re: [Biojava-l] BLAST/Java interface  (Document link: Patrick
>      McConnell)
> 

    Hello Patrick et al.

> I have developed a blast web service that takes all of the standard blast
> parameters and returns NCBI blast XML.  I have also generated classes that
> correspond to the blast XML complex types, so you don't even have to know
> anything about XML.

This is great! If you'd like to take a look at a complete analysis framework
you can sneak a peak in omnigene's CVS repository under analysis and
webservice/analysis. The jar can built by doing a jar-analysisjob and
jar-analysis.

If people would like to discuss how a generic analysis service can/has been
build I'd be happy to share my thoughts. It looks like we are all going to
be producing interesting services in the near future!!

Ours happens to use a database backend as a queue and EJB's to handle the
session and transaction layer.

                    -B

> 
> The web service is developed to be hosted by GLUE, but it should not be a
> problem to port it to another web service container.
> 
> I have release the source, as well as the compiled Java code.  I include
> the jar for the web services container, so you do not need to download
> anything else to get up and running.
> 
> See: http://mendel.mc.duke.edu:1755/services/blast/ for full source code
> and compiled classes.
> 
> I am currently developing servlets/jsps as a web front-end to this, which
> will format the XML into an NCBI-like html page.  Thus, it will be a full
> package for serving blast.
> 
> Good luck,
> 
> -Patrick
> 
> 
> 
> 
> nathan whitehouse <nlwhitehouse@yahoo.com>@biojava.org on 08/22/2002
> 04:39:05 PM
> 
> Sent by:    biojava-l-admin@biojava.org
> 
> 
> To:    biojava-l@biojava.org
> cc:
> 
> Subject:    [Biojava-l] BLAST/Java interface
> 
> 
> Hello people at BioJava,
> 
> I'm modifying an existing Java applet-servlet used
> by this lab.
> 
> People want us to add BLAST to this applet.
> 
> Anybody know of a good way to do this?
> 
>  Are there convenient BLAST libraries to call from
> the servlet?  We've talked about calling a C or C++
> library using the JNI.  I've looked around and it
> seems that there's no modularized BLAST lying around
> that would make this easy.
> The simple way to do it is just call BLASTAll from
> the shell with its arguments.  But this is a hack; I
> want to know if there is a better way to pass objects
> in and out of BLAST.
> 
> Thanks!
> Nathan
> 
> Nathan Whitehouse
> Shaulsky Lab
> Baylor College of Medicine
> Houston, Texas, USA
> 
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-- 
Brian Gilman <gilmanb@genome.wi.mit.edu>
Group Leader Medical & Population Genetics Dept.
MIT/Whitehead Inst. Center for Genome Research
One Kendall Square, Bldg. 300 / Cambridge, MA 02139-1561 USA
phone +1 617  252 1069 / fax +1 617 252 1902