[Biojava-l] To Do Question
Schreiber, Mark
mark.schreiber@agresearch.co.nz
Wed, 29 May 2002 10:50:29 +1200
Hi -
Is it possible that feature types could be resolved using JNDI. For
example could a GenBank parser be aware of a register of feature tags
and their appropriate Feature subclass mapping?
Would this be a useful use case or better handled by other means?
- Mark
> -----Original Message-----
> From: Matthew Pocock [mailto:matthew_pocock@yahoo.co.uk]
> Sent: Wednesday, 29 May 2002 10:24 a.m.
> 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
>
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