[Biojava-l] To Do Question
Dickson, Mike
mdickson@netgenics.com
Fri, 31 May 2002 13:28:47 -0400
I avoided responding earlier because I just wasn't sure how to respond
constructively. I'm still a bit mystified that new software specific to the
life sciences is being developed to connect to a web services directory.
Why re-solve in possibly incompatible ways problems that platform and
infrastructure vendors are already addressing?
JAXR already exists to provide a simple access mechanism in Java to talk to
web services registries. The calls are easy to use. I don't know what soap
layer is being targeted for Perl projects but I do know at least SOAP:Lite
includes a simple mechanism for access to UDDI. There are a couple of
open-source implementations of UDDI directories available now to support
private directory services. Why create new mechanisms and semantics for
this?
This is clearly me on a soapbox so take it for what its worth. One of the
things I think has slowed progress and adoption of standards in life
sciences is the constant tendency to reinvent platform technology. There's
been some really cool stuff done (like DAS for instance) that solves
important scientific problems. It seems to me that's a much better place
for us to focus and simply use the platform stuff as is (even if it seems
"yucky" or we think we can do it slightly better).
Mike
> -----Original Message-----
> From: David Block [mailto:dblock@gnf.org]
> Sent: Friday, May 31, 2002 1:09 PM
> To: Chaganthi, Madhusudan R.; David Block; Dickson, Mike; Matthew Pocock
> Cc: smh1008@cus.cam.ac.uk; biojava-l@biojava.org; Thomas Down; Biomoby (E-
> mail)
> Subject: RE: [Biojava-l] To Do Question
>
> 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@gnf.org
> GNF - San Diego, CA http://www.gnf.org
> Genome Informatics / Enterprise Programming
>
> > -----Original Message-----
> > From: Chaganthi, Madhusudan R. [mailto:mvc9@cdc.gov]
> > Sent: Friday, May 31, 2002 9:44 AM
> > To: 'David Block'; Dickson, Mike; Matthew Pocock
> > Cc: Chaganthi, Madhusudan R.; smh1008@cus.cam.ac.uk;
> > biojava-l@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@gnf.org]
> > Sent: Wednesday, May 29, 2002 10:59 AM
> > To: Dickson, Mike; Matthew Pocock
> > Cc: Chaganthi, Madhusudan R.; smh1008@cus.cam.ac.uk;
> > biojava-l@biojava.org; Thomas Down
> > Subject: RE: [Biojava-l] To Do Question
> >
> >
> > > 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
> > > > > >>
> > > > > >
> > > > >
> > > > >
> > > > >
> > > > > _______________________________________________
> > > > > Biojava-l mailing list - Biojava-l@biojava.org
> > > > > http://biojava.org/mailman/listinfo/biojava-l
> > > > >
> > >
> >