[Biojava-l] To Do Question
David Block
dblock@gnf.org
Wed, 29 May 2002 07:58:33 -0700
> From: Dickson, Mike [mailto:mdickson@netgenics.com]
> Subject: RE: [Biojava-l] To Do Question
>
>
> I'm not aware of any direct support for UDDI access through
> JNDI. WSDL has
> its own endpoint management mechanism. You could bind URLs to WSDL
> documents in a registry and look them up. I'd imagine you
> could write an
> SPI for UDDI to integrate it with JNDI but UDDI is a bit more
> than a simple
> registry.
>
> I'm a bit dubious of home grown efforts to provide
> "standards" for name
> resolution when there already are clearly supportable efforts
> like UDDI and
> JDNI available. What's the value of the bio community
> rolling our own?
>
Exactly. We should definitely not re-invent this wheel. I am not a JNDI expert, but I guess I assumed Sun had thought about this already. JNDI seems to be for local look-up, and UDDI for remote service look-up. The I3C and BioMoby efforts are all about providing a better interface for remote look-up of databases and services. If the BioJava community were to throw some support to BioMoby, I believe that would provide web services support for BioJava. BioMoby is talking to XEMBL, etc., they are not out of any significant loops.
2 cents from me, anyway :)
Dave
> Mike
>
> > -----Original Message-----
> > From: David Block [mailto:dblock@gnf.org]
> > Sent: Tuesday, May 28, 2002 7:06 PM
> > To: Matthew Pocock; Dickson, Mike
> > Cc: Chaganthi, Madhusudan R.; smh1008@cus.cam.ac.uk; biojava-
> > l@biojava.org; Thomas Down
> > Subject: RE: [Biojava-l] To Do Question
> >
> > UDDI?
> >
> > Check out http://www.biomoby.org for a cross-platform
> service registry-in-
> > the-making - not just vaporware, Mark W. has funding for
> this, and there
> > are some heavyweights in on it.
> >
> > I would tend to stay in WSDL/UDDI space for this naming
> stuff, since it
> > integrates with JNDI (right?) and so you don't lose
> anything, and you get
> > all the SOAP services for free.
> >
> > --
> > David Block dblock@gnf.org
> > GNF - San Diego, CA http://www.gnf.org
> > Genome Informatics / Enterprise Programming
> >
> > > -----Original Message-----
> > > From: Matthew Pocock [mailto:matthew_pocock@yahoo.co.uk]
> > > Sent: Tuesday, May 28, 2002 3:24 PM
> > > To: Dickson, Mike
> > > Cc: 'Chaganthi, Madhusudan R.'; 'smh1008@cus.cam.ac.uk';
> > > biojava-l@biojava.org; Thomas Down
> > > Subject: Re: [Biojava-l] To Do Question
> > >
> > >
> > > Hi.
> > >
> > > This todo may be partly my fault. It was flagged before JNDI
> > > was mature,
> > > and it was discussed during an early boot camp. JNDI
> rocks. URNs/URIs
> > > are great too. There are several uses of resolvable names
> > > that would be
> > > usefull:
> > >
> > > well-known bioinformatics resources:
> > > e.g. sequence databases like embl
> > > e.g. sequences - perhaps compound id like
> db.version:seqid.version
> > >
> > > biojava objects
> > > e.g. alphabets by name
> > > e.g. a sequence you have named
> > > e.g. a named HMM
> > > e.g. a service like running blast
> > >
> > > Idealy, given a name, BioJava should be able to resolve that to an
> > > instance that behaves apropreately. So, the URI for
> adenosine should
> > > resolve to the apropreate symbol object, and the URI for
> > > genbank should
> > > resolve to an apropreate SequenceDB instance that can be used
> > > to fetch
> > > genbank records. If you create a novel alphabet (e.g. coin
> > > tosses) then
> > > another machine on the nework given a URI for this should
> be able to
> > > resolve or build (via RMI, CORBA, SOAP, serialization,
> whatever) an
> > > apropreate alphabet.
> > >
> > > If you have further use cases, please post them.
> > >
> > > The plumbing necisary would be some biojava register allowing
> > > names to
> > > be associated with objects or factories (and potentialy dropping
> > > unreachable objects), and some p2p or RMI or Naming-Directory
> > > solution
> > > for sharing this infrastructure between VMs that can communicate
> > > (presumably via network).
> > >
> > > Should the API or network protocols be open enough to let
> > > other Java or
> > > other non-Java apps plug in?
> > >
> > > Do we serve up stuff that gets resolved to remote
> objects, or is it
> > > replicated into the name-space of the discovering process?
> > >
> > > Does anyone have vast experience in doing this sort of thing?
> > > Has it all
> > > been done before?
> > >
> > > Should this be integrated with JavaSpaces or BeanContexts or
> > > any other
> > > well-known Java APIs?
> > >
> > > Matthew
> > >
> > > Dickson, Mike wrote:
> > > > I'd guess a few use cases would help.
> > > >
> > > > What sort of things are we looking up in a directory? How
> > > are names formed?
> > > > Is there a structure to them, like URN's? BioJava doesn't
> > > really (as far as
> > > > I'm aware) have a bias towards client or server code.
> > > Where in the codebase
> > > > would we expect directory and naming to get used?
> > > >
> > > > I don't have the answers, these are just questions I'd be
> > > inclined to ask.
> > > >
> > > > Mike
> > > >
> > > >
> > > >>-----Original Message-----
> > > >>From: Chaganthi, Madhusudan R. [mailto:mvc9@cdc.gov]
> > > >>Sent: Tuesday, May 28, 2002 4:55 PM
> > > >>To: 'Dickson, Mike'; Chaganthi, Madhusudan R.;
> > > 'smh1008@cus.cam.ac.uk'
> > > >>Cc: biojava-l@biojava.org; Thomas Down; Matthew Pocock
> > > >>Subject: RE: [Biojava-l] To Do Question
> > > >>
> > > >>I personally feel that JNDI is the way to go. I will be
> > > interested in
> > > >>hearing other suggestions too.
> > > >>
> > > >>My question is, has there been a vision about the hows and
> > > whats for this
> > > >>feature?
> > > >>
> > > >>Its too broad a feature for someone to envision. Maybe we
> > > need to break it
> > > >>up into chewable pieces.
> > > >>
> > > >>What do you say?
> > > >>
> > > >>
> > > >>-----Original Message-----
> > > >>From: Dickson, Mike [mailto:mdickson@netgenics.com]
> > > >>Sent: Tuesday, May 28, 2002 4:58 PM
> > > >>To: 'Chaganthi, Madhusudan R.'; 'smh1008@cus.cam.ac.uk'
> > > >>Cc: biojava-l@biojava.org; Thomas Down; Matthew Pocock
> > > >>Subject: RE: [Biojava-l] To Do Question
> > > >>
> > > >>
> > > >>Is there a reason we wouldn't just use JNDI for this?
> > > >>
> > > >>
> > > >>>-----Original Message-----
> > > >>>From: Chaganthi, Madhusudan R. [mailto:mvc9@cdc.gov]
> > > >>>Sent: Tuesday, May 28, 2002 4:10 PM
> > > >>>To: 'smh1008@cus.cam.ac.uk'; Chaganthi, Madhusudan R.
> > > >>>Cc: biojava-l@biojava.org; Thomas Down; Matthew Pocock
> > > >>>Subject: RE: [Biojava-l] To Do Question
> > > >>>
> > > >>>Ok.
> > > >>>
> > > >>>If I can get any formal requirements documentation on
> > > this, that will be
> > > >>>helpful for me.
> > > >>>
> > > >>>
> > > >>>
> > > >>>-----Original Message-----
> > > >>>From: David Huen [mailto:david.huen@ntlworld.com]
> > > >>>Sent: Tuesday, May 28, 2002 3:28 PM
> > > >>>To: Chaganthi, Madhusudan R.
> > > >>>Cc: biojava-l@biojava.org; Thomas Down; Matthew Pocock
> > > >>>Subject: Re: [Biojava-l] To Do Question
> > > >>>
> > > >>>
> > > >>>On Tuesday 28 May 2002 7:37 pm, Chaganthi, Madhusudan R. wrote:
> > > >>>
> > > >>>>Longer term features
> > > >>>>* Naming and directory services throughout
> > > >>>>
> > > >>>>What exactly are the features that are to be supported
> > > here in this
> > > >>>>context? If I find the time at home, I will be more than
> > > happy to help
> > > >>>>you out in this area.
> > > >>>>
> > > >>>>Thanks
> > > >>>>Madhu
> > > >>>>
> > > >>>
> > > >>>I don't think we have any yet although both Matt and
> Thomas have
> > > >>
> > > >>discussed
> > > >>
> > > >>>it. Is there even an agreed standard amongst the Bio*
> projects for
> > > >>
> > > >>these
> > > >>
> > > >>>services yet?
> > > >>>
> > > >>>Regards,
> > > >>>David
> > > >>>_______________________________________________
> > > >>>Biojava-l mailing list - Biojava-l@biojava.org
> > > >>>http://biojava.org/mailman/listinfo/biojava-l
> > > >>
> > > >
> > >
> > >
> > >
> > > _______________________________________________
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> > > http://biojava.org/mailman/listinfo/biojava-l
> > >
>