[Biojava-l] BioJava discussion board

Brian Gilman gilmanb@genome.wi.mit.edu
Wed, 28 Aug 2002 00:09:05 -0400 (EDT)

Hello Thomas,

	I'd be interested in this. You've asked me for a gripes list about
BioJava in general. I'm still thinking about this but, some things that
come to mind are:

	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

	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. 

	JSP tag libraries that do simple things for me such as converting
a fasta file/genbank file etc. from DNA <--> protein would be nice. Server
side image maps would be a nice thing to have in there as well...Applets
are good, applications are better, XML with XSLT would be wonderful! 

	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...

	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. 

	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...



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.
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