[Biojava-l] To Do Question

[Matthew Pocock]

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
>>
>