[Pipet Devel] BioML vs BSML

J.W. Bizzaro bizzaro at bc.edu
Sun Jan 24 02:05:04 EST 1999

Harry Mangalam wrote:
> 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?

Errrr mmmmmmmmmm argggggghh!  I'm having convulsions here ;-)  It seems at every
turn, there's something supposedly better to use, and I'm left having to defend
what I have chosen.  If I don't give in, I'm too stubborn.  But if I do, Loci
more closely resembles a smorgasbord of technologies.

I am trying to keep Loci homogenous in terms of technology.  I think Python is a
knock-out language, beating even Perl in most respects.  I know Perl is very
prominent in sequence analyses...It's prominent in just about everything.  But I
think Python is not far behind in acceptance, and is gaining momentum.

What can we do?  If there is absolutely no other choice, we can go with
something in Perl, ***providing we consider it a temporary option.  If we can
find something later in Python or can convert it to Python, then we will.  But
don't give in too easily.

> 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?

You're talking about gtk-based XML browsers?  The Gnome libraries have a canvas
that is rather powerful.  I think we can make our own XML-to-display modules
using Python-Gnome bindings.  Of course what we are doing is unique.  The only
other bioinformatics XML browsers out there are the two you mentioned for BioML
and BSML.  So there are no standard libraries for handling this sort of thing.

Thomas is working on a sequence editor, I think with the Gnome canvas.  How have
things been developing, Thomas?

Harry, each Loci GUI tool will be a rather small XML browser, designed to
specifically handle *one* type of display.  For example, we will have separate
tools for the display of short DNA sequences, circular genomes, chromosomes,
protein sequences with secondary structure, 3D DNA structures, 3D protein
structures, phylogenic trees, DNA sequence editing, protein sequence editing,
data plots, and others we haven't thought of yet.  The idea is to keep things
small and modular.  There really won't be any very large apps in Loci.

> 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.

Yeah, if it uses Java, it will almost certainly use Swing.  I think Swing is now
a part of the standard distribution of Java, which is supposed to be fairly easy
to obtain.  The license is not nearly GNU GPL.

J.W. Bizzaro                  Phone: 617-552-3905
Boston College                mailto:bizzaro at bc.edu
Department of Chemistry       http://www.uml.edu/Dept/Chem/Bizzaro/

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