[Biojava-l] To Do Question

Tue, 28 May 2002 20:27:22 -0400

One other point.  To do the web services thingy from Java the Sun way you'd
use JAXR, which has bindings to ebXML and UDDI.  I'm not aware as I said of
a direct integration with JNDI of JAXR but I suppose it could be done.

> -----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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> >