> From: Dickson, Mike [mailto:[EMAIL PROTECTED]] > 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:[EMAIL PROTECTED]] > > Sent: Tuesday, May 28, 2002 7:06 PM > > To: Matthew Pocock; Dickson, Mike > > Cc: Chaganthi, Madhusudan R.; [EMAIL PROTECTED]; biojava- > > [EMAIL PROTECTED]; 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 [EMAIL PROTECTED] > > GNF - San Diego, CA http://www.gnf.org > > Genome Informatics / Enterprise Programming > > > > > -----Original Message----- > > > From: Matthew Pocock [mailto:[EMAIL PROTECTED]] > > > Sent: Tuesday, May 28, 2002 3:24 PM > > > To: Dickson, Mike > > > Cc: 'Chaganthi, Madhusudan R.'; '[EMAIL PROTECTED]'; > > > [EMAIL PROTECTED]; 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:[EMAIL PROTECTED]] > > > >>Sent: Tuesday, May 28, 2002 4:55 PM > > > >>To: 'Dickson, Mike'; Chaganthi, Madhusudan R.; > > > '[EMAIL PROTECTED]' > > > >>Cc: [EMAIL PROTECTED]; 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:[EMAIL PROTECTED]] > > > >>Sent: Tuesday, May 28, 2002 4:58 PM > > > >>To: 'Chaganthi, Madhusudan R.'; '[EMAIL PROTECTED]' > > > >>Cc: [EMAIL PROTECTED]; 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:[EMAIL PROTECTED]] > > > >>>Sent: Tuesday, May 28, 2002 4:10 PM > > > >>>To: '[EMAIL PROTECTED]'; Chaganthi, Madhusudan R. > > > >>>Cc: [EMAIL PROTECTED]; 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:[EMAIL PROTECTED]] > > > >>>Sent: Tuesday, May 28, 2002 3:28 PM > > > >>>To: Chaganthi, Madhusudan R. > > > >>>Cc: [EMAIL PROTECTED]; 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 - [EMAIL PROTECTED] > > > >>>http://biojava.org/mailman/listinfo/biojava-l > > > >> > > > > > > > > > > > > > > > > _______________________________________________ > > > Biojava-l mailing list - [EMAIL PROTECTED] > > > http://biojava.org/mailman/listinfo/biojava-l > > > > _______________________________________________ Biojava-l mailing list - [EMAIL PROTECTED] http://biojava.org/mailman/listinfo/biojava-l
