[Biojava-dev] RE: [Biojava-l] BioJava discussion board

[Schreiber, Mark]

> 	BioJava does not work well in a distributed environment 
> in terms of RMI calls or in the "weservices" stack. Custom 
> serializers/deserializers need to be made for each and every 
> object that exists in the feature heirarchy. This is painful 
> to say the least. T
>

Agreed, I think most of the serialization issues have been fixed but I
havn't looked at the feature serialization/deserialization yet.

 
> 	Where's the contructor!! There are a lot of factories 
> that make, while making client side programming very easy to 
> do, kill a middleware guy like myself. 
>

There needs to be some valid bean implementations of simple cases of
Sequence/ SymbolList etc otherwise the binding of said objects to XML is
a lot more difficult than it should be.
 

> 	I'd like to see more services built with biojava. 
> Things like performing SSAHA as an RPC/SOAP call would be 
> nice. A deployable app that had an installer and set itself 
> up as an "alignment service" would be great....I think we 
> could contribute some code to this endeavor. Other things 
> such as eponine service would be cool...
>

One of the questions that has come up is where should these services
reside, should they be part of biojava or part of omnigene, any
thoughts?

 
> 	Annotations are too loosely scoped for my taste. I'd 
> like to confine a user to a specific set of ontologies and 
> throw an exception if I didn't understand their terminology. 
> 

I think they have become more restrictive in recent versions of the CVS
distribution. Take a look at one of the new snapshots.


Mark


> 	Saving sequence in BioSQL is fun but most of us have a 
> schema to do this already. And why are we trying to make 
> things interoperate at the database level?? Can't we come up 
> with a defined set of objects to pass around?? Isn't BioJava 
> a great place to start on that? Shouldn't we look towards the 
> webservices (w3c/industry groups that are innovating) 
> paradigm when designing this object model?? 
> 
> 	Of course these are my opinions and I may be way off 
> base...What do other's think?? Enterprise BioJava?? I think 
> it's doable...
> 
> 				Best, 
> 
> 					-B
> 
> -----------------------
> Brian Gilman <gilmanb@genome.wi.mit.edu>
> Group Leader Medical & Population Genetics Dept.
> MIT/Whitehead Inst. Center for Genome Research
> One Kendall Square, Bldg. 300 / Cambridge, MA 02139-1561 USA 
> phone +1 617  252 1069 / fax +1 617 252 1902
> 
> 
> On Mon, 26 Aug 2002, Thomas Down wrote:
> 
> > Hi...
> > 
> > This is something of a new departure for BioJava, but a 
> couple of us 
> > on the BioJava IRC channel (#biojava on irc.openprojects.
> > net) were wondering if there would be interest in some kind of 
> > discussion board for biojava developers.
> > 
> > Web boards have been fairly successful discussion media in
> > a lot of areas.  Their particular strength, as far as I can 
> see it, is 
> > for cases where there's a fairly extended discussion on one 
> particular 
> > topic, and where people might want to refer back to this in the 
> > future.  Mailing lists don't always handle this particularly well, 
> > especially for people who don't have threaded mail readers. 
>  A typical 
> > example might be a request for enhancement to a program, where 
> > developers might reply with several different solutions, 
> then discuss 
> > their relative merits.
> > 
> > To see how this works, I've set up and experimental BioJava 
> board at:
> > 
> >       http://firechild.dyndns.org/
> > 
> > (This is running on my home machine -- it should be 
> available most of 
> > the time, but I can't promise 100% uptime).  It's nothing formal at 
> > the moment, but if you're interested, please drop by and 
> have a play.
> > 
> > It's running on mod_virgule, the system behind 
> > http://www.advocato.org/ and http://www.ghostscript.com/.  This is 
> > fairly clean and simple, and was pleasingly easy to 
> install.  It works 
> > on a `certification' system -- anyone can create an 
> account, but you 
> > must be certified by someone before you're allowed to post aricles 
> > (you can post diary entries without certification, though). 
>  I'll be 
> > certifying anyone I see who I recognize from this mailing list.
> > 
> > 
> > Hope people find this useful,
> > 
> >        Thomas.
> > 
> > 
> > _______________________________________________
> > 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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