[MOBY-l] RE: [Biojava-l] To Do Question

David Block dblock at gnf.org
Fri May 31 17:09:07 UTC 2002 

BioMoby is in its infancy.  A Java client is certainly in the works; rolling your own will be trivial initially, since it is a standard SOAP service.  Hopefully the java client will be a library that you can plug in to your existing application, so that a right click in any application that has the plugin will get you access to the Moby central list of web services - and then let you launch the appropriate ones based on the data you have in your application (ie, I have a sequence, who can do something with it, and what can they do? - just from a right click).

I'll cross-post this to the biomoby list so the experts on both sides can get fertilized...

--
David Block                    dblock at gnf.org
GNF - San Diego, CA        http://www.gnf.org     
Genome Informatics  /  Enterprise Programming

> -----Original Message-----
> From: Chaganthi, Madhusudan R. [mailto:mvc9 at cdc.gov]
> Sent: Friday, May 31, 2002 9:44 AM
> To: 'David Block'; Dickson, Mike; Matthew Pocock
> Cc: Chaganthi, Madhusudan R.; smh1008 at cus.cam.ac.uk;
> biojava-l at biojava.org; Thomas Down
> Subject: RE: [Biojava-l] To Do Question
> 
> 
> I agree with your observations regarding UDDI and JNDI.
> 
> From what little I read from their site, BioMoby seems to have a Perl
> interface for the clients. Do they have a java interface too? 
> If they have ONL Perl interface, how are we (BioJava) 
> thinking of accessing
> it?:
> 
> 
> I am not sure if my earlier mail made it to the list but I 
> thought this link
> was an interesting read.
> Talks about accessing XEMBL via SOAP as well as RPC.
> http://www.oreillynet.com/pub/a/webservices/2002/05/14/biows.html
> 
> 
> Thanks
> Madhu
> 
> -----Original Message-----
> From: David Block [mailto:dblock at gnf.org]
> Sent: Wednesday, May 29, 2002 10:59 AM
> To: Dickson, Mike; Matthew Pocock
> Cc: Chaganthi, Madhusudan R.; smh1008 at cus.cam.ac.uk;
> biojava-l at biojava.org; Thomas Down
> Subject: RE: [Biojava-l] To Do Question
> 
> 
> > From: Dickson, Mike [mailto:mdickson at 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 at gnf.org]
> > > Sent: Tuesday, May 28, 2002 7:06 PM
> > > To: Matthew Pocock; Dickson, Mike
> > > Cc: Chaganthi, Madhusudan R.; smh1008 at cus.cam.ac.uk; biojava-
> > > l at 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 at gnf.org
> > > GNF - San Diego, CA        http://www.gnf.org
> > > Genome Informatics  /  Enterprise Programming
> > > 
> > > > -----Original Message-----
> > > > From: Matthew Pocock [mailto:matthew_pocock at yahoo.co.uk]
> > > > Sent: Tuesday, May 28, 2002 3:24 PM
> > > > To: Dickson, Mike
> > > > Cc: 'Chaganthi, Madhusudan R.'; 'smh1008 at cus.cam.ac.uk';
> > > > biojava-l at 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 at cdc.gov]
> > > > >>Sent: Tuesday, May 28, 2002 4:55 PM
> > > > >>To: 'Dickson, Mike'; Chaganthi, Madhusudan R.;
> > > > 'smh1008 at cus.cam.ac.uk'
> > > > >>Cc: biojava-l at 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 at netgenics.com]
> > > > >>Sent: Tuesday, May 28, 2002 4:58 PM
> > > > >>To: 'Chaganthi, Madhusudan R.'; 'smh1008 at cus.cam.ac.uk'
> > > > >>Cc: biojava-l at 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 at cdc.gov]
> > > > >>>Sent: Tuesday, May 28, 2002 4:10 PM
> > > > >>>To: 'smh1008 at cus.cam.ac.uk'; Chaganthi, Madhusudan R.
> > > > >>>Cc: biojava-l at 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 at ntlworld.com]
> > > > >>>Sent: Tuesday, May 28, 2002 3:28 PM
> > > > >>>To: Chaganthi, Madhusudan R.
> > > > >>>Cc: biojava-l at 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 at biojava.org
> > > > >>>http://biojava.org/mailman/listinfo/biojava-l
> > > > >>
> > > > >
> > > >
> > > >
> > > >
> > > > _______________________________________________
> > > > Biojava-l mailing list  -  Biojava-l at biojava.org
> > > > http://biojava.org/mailman/listinfo/biojava-l
> > > >
> > 
>

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