[Biojava-l] Re: [BioXML-dev] Hello!! (fwd)

Brian gilmanb@dipswitch.penguinpowered.com
Sat, 3 Jun 2000 00:14:40 -0400 (EDT)


	I have been working on an API to take sequence, quality, etc data
nd produce an XML format that is easily distributable. This API has grown
substantially and will soon be released as open source! Below you will
find the structure of this API. I hope I can contribute to your project
and perhaps flesh out some of the things that you may need (ie. XML API
for easy genome annotation).


Brian Gilman		
Scientific Programmer
WhiteHead Institute 

---------- Forwarded message ----------
Date: Mon, 22 May 2000 17:47:48 -0400 (EDT)
From: Brian <gilmanb@dipswitch.penguinpowered.com>
To: chris.dag <dag@fedayi.sonsorol.org>
Cc: Bradley Marshall <bradmars@yahoo.com>, bioxml-dev@bioxml.org,
Subject: Re: [BioXML-dev] Hello!!

Hello once again, 

	I feel as if I put my foot in my mouth because now it looks like I
need to get permission from Whitehead to release the source code! So, once
I get this little snag untangled I'll post what I have. 

	What I can say for now is that I am leveraging the apache
ECS/Xerces/Sun's JAXP API's heavily. Will this pose other problems?? I
can't answer that question. 

	The API is structured into modules which perform different tasks:
	1) DataReader/DataWriter:
		Take FASTA(others later) files and, based upon file
attributed  ie. ">" emit XML declarations.

	2) Consumer/Producer 
		Consumer and Produce XML documents via the SAX/DOM API
set's. This allows users to easily manipulate documents to suit their

	3) Util

		Has the ability to extract or split FASTA database into
separate documents or return stream with FASTA information.

	4) Jar 

		xml doucments are generated and jarred together to make
one large XML "database" (we use this to associate sequence with quality
score information). Jar has the ability to list all documents or extract
one document from the jar archive. 

		This module allows other language bindings through the use
of JINI and TCP/IP protocols. Modelled after ftp. 
	5) XMLFactory 
		This class coordinates the above mentioned modules to
produce/manipulate XML. (right now we have the ability to take a FASTA
database of sequence and quality scores and produce XML. 

	6) WICGRFactory

		Gives instances of XMLFactory as well as a convienient way
to access JAR database. 

	So there you have it. Hopefully we will be able to coordinate ou
efforts (release my source!! :-) )  and start really playing.



Brian Gilman		
Scientific Programmer
WhiteHead Institute 

On Mon, 22 May 100, chris.dag wrote:

> If any of the core bioXML people give me the goahead
> I will be happy to set up a user account and CVS
> repository. 
> As for license issues I can speak for the bioperl.org
> project in that all of our code is released under the
> (a) GPL or the (b) Perl Artistic License.
> Our license status should eventually be formally
> clarified as one or the other but the overall message
> is that everything we release is free and open.
> --Chris
> -- 
> Chris Dagdigian         (Home:Work) Genetics Insitute, Dept. of Genomics
> dag@sonsorol.org             :      cdagdigian@genetics.com
> http://www.sonsorol.org      :      (617) 665-8345 / FAX (978) 684-9345
> http://bio.perl.org          :      email to pager skydag@sonsorol.org
> _______________________________________________
> BioXML-dev mailing list  -  BioXML-dev@bioxml.org
> http://bioxml.org/mailman/listinfo/bioxml-dev