There is a Perl-XML FAQ at http://www.perlxml.com/faq/perl-xml-faq.html Also, Activestate.com has a bunch of perl mail-lists running, one of which is the PERL-XML list (http://www.activestate.com/lyris/lyris.pl). You can browse the archives as a guest. CPAN has several XML related modules. http://www.perl.com/CPAN/modules/by-category/15_World_Wide_Web_HTML_HTTP_CGI /XML/ David > -----Original Message----- > From: Harry Mangalam [mailto:hjm at cx408397-a.irvn1.occa.home.com] > Sent: Sunday, January 24, 1999 12:38 AM > To: tulip-list at busboy.sped.ukans.edu > Subject: Re: [Pipet Devel] BioML vs BSML > > > Hi Jeff et al, > > As you probably have found out now, BioML is being used by > the bio.perl > group and the perl masters at perl.org already have a pretty > large archive of > useful scripts for manipulating XML. > > And it looks like, in a VERY fast spin thru the docs, that > using their XML > parser tools, it may be possible to use both of these XMLs, > using these perl > modules to handle parsing and interconversion. > > ie: > http://www.perl.com/pace/pub/perldocs/1998/11/xml.html > http://www.perl.com/pace/pub/perldocs/1998/12/cooper-01.html > > perl also has gtk bindings and in general, I've heard about > and done more > things using perl in the bio world than with python. Not to > say python > doesn't make some or even most things easier - just that perl > has a proven > track record in the bio area. > > It seems not to be at cross purposes to the objectives of > LOCI to implement > chunks of it in perl, no? As long as it remains easliy > implementable, and > usable, and freely re-distributable, perl is as much of an option as > python, isn't it? > > Also, how is the LOCI project planning on handling the display of the > results of this effort? Both the BioML and the BSML browsers that are > available are MS-centric and certainly do not use gtk. The > only browser > that I'm aware of that does is gzilla (www.gzilla.com) and mnemonic ( > http://www.mnemonic.org/). Are you planning on using either > of these for > your display dev platform? Or are you not implementing any display > technology? > > VisualGenomics is planning a Java-based BSML browser, but I'm > sure that it > won't use gtk, unless heavily funded. It'll probably be > written with the > swing classes - what's the redist controls on swing - I'm not a Java > follower - sorry. > > OK - enough mind rot from me for the present... > > Cheers > harry > > On Sat, 23 Jan 1999, J.W. Bizzaro wrote: > > > Harry, > > > > We had some rather lengthy exchanges about the use of BSML > and CML in Loci. We > > were looking for an XML that would work well for both > sequence and structure > > information. But it seemed that neither was good at both. > > > > In sort, we stepped back from the issue, and decided we > would try to support > > BOTH, until something better came along. We even > considered making our own XML > > (we would call it BMML, "BioMolecule Markup Language"). > What we really wanted > > was just one language that would give us an excellent > description of large bio > > macromolecules. Well, of course that would have been too > much to take on right > > now. > > > > Konrad actually has a lot to say about descriptive > languages for macromolecule > > structure. He had corresponded with Peter Murray Rust, the > author of CML and > > someone rather influential in the development of XML. > Konrad, as he can tell > > you, is not satisfied with any current format. > > > > BioML comes as a bit of a surprise to me. It seems to be > brand new. Looking it > > over a bit, it does seem to do a better job at handling > structure than BSML, and > > I like the inclusion of all sorts of biological information > (it can describe > > organisms as well, it seems)...although some may argue this > is "bloat". > > > > I would like Konrad to give us his impression of BioML. It > would be nice to use > > one XML rather than two. My big question, however, is the > licensing. The Web > > page says to contact David Fenyo about the "commercial" use > of BioML. I wonder > > if this is one of those "well, as long as you don't make > money on it" licenses. > > If so, we have problems: It won't fit with GNU GPL. > > > > I wrote a message to David Fenyo about this, and to see if > he can give us a > > contrast between BioML and BSML. A cc will be sent to the > Tulip list. > > > > > > Cheers! > > Jeff > > bizzaro at bc.edu > > > > > > Harry Mangalam wrote: > > > > > > Hi All, > > > > > > Having only recently come to this arena, what's the > group's evaluation of > > > the relative merits of BSML: > > > http://www.visualgenomics.com/sbir/rfc.htm > > > > > > vs BioML: > > > http://www.proteometrics.com/BIOML/ > > > > > > I'm still going thru the text of the specs but if any of > you have strong > > > arguments regarding either approaches, I'd very much > appreciate it. The > > > bioperl people seem to like the BioML approach. > > > > > > Also, if you have come to an approach that can > rationalize the competing > > > stds, please let me know. > > > > > > Cheers > > > Harry > > > > -- > > J.W. Bizzaro Phone: 617-552-3905 > > Boston College mailto:bizzaro at bc.edu > > Department of Chemistry http://www.uml.edu/Dept/Chem/Bizzaro/ > > -- > > > > Cheers, > Harry > > Harry J Mangalam, Developmental + Cell Biology > Rm 4201, Biological Sciences II, UC Irvine, Irvine, CA, 92697 > (949) 824 4824[vox], (949) 824 8551[fax], mangalam at uci.edu > http://hornet.bio.uci.edu/~hjm/ >