[Biojava-l] BioJava discussion board

[Patrick McConnell]

I do not know of many other biology web services.  We are currently
developing some here for in-house use.  Of these, we have developed a web
service for blast that takes all of the blast parameters as structured XML,
and returns the blast output as structured XML.  The burden on the client
and server is great for parsing all of this.  Thus, we also give an option
to get the data back as a stream so that the client can parse it with SAX
or whatever.

I plan to donate all of this code to biojava (if they want it) in a new
webservices module.  I have developed the code with GLUE in mind, which I
see is the web services engine that you use.  Thus, if you'd like, you can
probably very easily plug the new biojava stuff into your infrastructure.

-Patrick





Yasumasa Shigemoto <yshigemo@genes.nig.ac.jp>@biojava.org on 08/28/2002
08:50:29 PM

Sent by:    biojava-l-admin@biojava.org


To:    Patrick McConnell <MCCon012@mc.duke.edu>
cc:    biojava-l@biojava.org

Subject:    Re: [Biojava-l] BioJava discussion board




> I am quite happy to see web services being applied.

Do you know the other web services for biology?
We receive Web services of other sites and open the WSDL.


> Do you plan to expand your services to return structured data instead of
> simple strings?  That is were some of the real power of WSDL and web
> services comes in.

I'm trying SOAP Attachment and InputStream.
As you know, SOAP applies XML technology at back end,
and SOAP client do parsing XML.
It is burden to do a large result for the client, then I think
SOAP Attachment is better for this problem.

And simple string is burden for the memory of the
server and client, I think InputStream is useful.

Further more I think BioJava object is more useful
for the SOAP result but I don't plan to do so.

Do you have any idea or suggestion?

Yasumasa Shigemoto

Patrick McConnell wrote:

> I am quite happy to see web services being applied.
>
> Do you plan to expand your services to return structured data instead of
> simple strings?  That is were some of the real power of WSDL and web
> services comes in.
>
> -Patrick
>
> Yasumasa Shigemoto <yshigemo@genes.nig.ac.jp>@biojava.org on 08/28/2002
> 01:47:53 AM
>
> Sent by:    biojava-l-admin@biojava.org
>
> To:    Brian Gilman <gilmanb@genome.wi.mit.edu>
> cc:    Thomas Down <td2@sanger.ac.uk>, biojava-l@biojava.org
>
> Subject:    Re: [Biojava-l] BioJava discussion board
>
> Hello all,
>
> >         I'd like to see more services built with biojava. Things like
> > performing SSAHA as an RPC/SOAP call would be nice. A deployable app
that
> > had an installer and set itself up as an "alignment service" would be
> > great....I think we could contribute some code to this endeavor. Other
> > things such as eponine service would be cool...
>
> Please let me introduce our SOAP project "XML Central of DDBJ".
>
> http://xml.nig.ac.jp/
>
> This project is the first public SOAP service for biology in Japan.
> There are some analysis programs like BLAST, FASTA and
> more than 20 public databases.
>
> You can access SOAP services freely.
>
> If you have any questions or idea, please let me know.
>
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l@biojava.org
> http://biojava.org/mailman/listinfo/biojava-l
>
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l@biojava.org
> http://biojava.org/mailman/listinfo/biojava-l

_______________________________________________
Biojava-l mailing list  -  Biojava-l@biojava.org
http://biojava.org/mailman/listinfo/biojava-l