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
