[Pipet Devel] Another XML proposal - Part 3.

J.W. Bizzaro bizzaro at bc.edu
Thu Apr 8 09:49:41 EDT 1999

Humberto Ortiz Zuazaga wrote:
> Gnome has another html browser called Express, designed to be expanded with
> plugins, it looks a little like what we're talking about.
> http://www.cse.unsw.edu.au/~conradp/express/

I actually wrote to this guy about helping with Loci.  I put his last e-mail to
me at the bottom of this message.

Since no one from Grail replied to my message (surprisingly), we may want to
take a look at Express.

Humberto, I like the proposal you gave.  It's good to see the discussion of some
of the low-level mechanics.

But I still have one question for you, and I'm not sure you have answered it

    Do you think there should be a layer of Python that sits between the
    skeleton locus (or locus browser) and the low-level code that will
    complete the viewer.

    What in fact are you calling a "viewer"?  Is it the browser + script +
    megawidgets, as I've been saying, or do you think the user will be
    downloading self-contained executable programs, as Netscape does?

Well, that's more than one question.

> When I was writing the proposal, I thought it wold be neat to have a file type
> like "multifile python module" that contained the source to a viewer, we could
> also have a type like "i386/libc6/rpm" for a viewer.  The app broker can
> return a list like
> python - ftp://bar.baz/pub/viewer.py
> compressed-multifile-python-tarfile - ftp://bar.baz/pub/fancy-viewer.tar.gz
> i386/libc6/rpm - ftp://rpmfind.net/libc6/i386/viewer1.0-2.rpm
> and the user can select which one he wants to retreive.

Good idea.  But these aren't executables, are they?

bizzaro at bc.edu

------------message from Conrad Parker-------------------------

On Thu, Nov 12, 1998 at 09:39:16PM -0400, J.W. Bizzaro wrote:
> Conrad,
> Are you still developing Express?  I noticed that the Web site
> hasn't changed in some 6 months.

yes, I'd still like to though I haven't worked on it in a while.

> Do you have any plans on joining the Mnemonic Project?

no, I have different (just leaner) design goals. But their work looks

> I am the coordinator for the TULIP Project, a GNU application
> for DNA and protein analyses.
>   http://www.uml.edu/Dept/Chem/UMLBIC/Apps/TULIP/
> TULIP will be highly modular, very much plug and play for
> the analysis algorithms.  Part of this plan for modularity,
> is the use of an XML called, "Bioinformatic Sequence Markup
> Language," or BSML.  We hope to use BSML as the language
> of communication between modules and the user.  Check out
> these links for more info on BSML:
>   http://www.oasis-open.org/cover/xml.html#xml-bsml
>   http://visualgenomics.com/sbir/rfc.htm
> Since BSML works in a "browser" environment, we would like
> to have a specialized BSML-browser as a central part of

ok, I've had a quick read of the BSML spec and the TULIP homepage ...

> A question I have for you is, would you like to help transform
> Express into a BSML browser for TULIP and be a part of the
> TULIP development team?  If not, could we use the Express code
> to make one ourselves? (I would prefer the former ;-) )

I'm planning on making Express handle XML applications nicely, though I haven't
looked into it much yet. Insofar as my contribution involves writing a
browser which can support various XML applications, yes I'd like to be involved
with TULIP :) Beyond that I don't think I can help much - my knowledge of
biochemistry doesn't extend too much beyond high school and brief encounters in
studying information theory and genetic algorithms :)

However, I am planning on XML support for mathematics (MathML) as I am working
on a symbolic computation program which is currently console based (and as yet
unreleased). It would be a good test of XML support to be able to test with
both MathML and BSML applications.

As for using the Express code ... of course you're free to (it's GPL'd after
all!) but it wouldn't be much use to you - at the moment it's not much more
than a container for the gtk-xmhtml widget, with a history list.

> The insentive for you is that a BSML browser for biological
> analyses would be very unique, and maybe even more of a
> challenge than an HTML browser :-)
> What do you think?

cool :) looking at your developer's page, if Jay Painter is working on the
BSML implementation then it should probably be ok for me to just do the web
browser support (which will of course give networking etc).

Now for some ideas :) ...

My main project this year (and the reason express hasn't moved much) is AUBE, a
sound synthesis/sequencing/processing system. You can find out more about it


AUBE processes sound streams in real time, and gets its power from being able
to connect up many different modules in arbitrary ways.

The reason I mention it is because its architecture is similar to your ideas
for TULIP. In particular, looking at your ideas for GCL (do you have an
implementation yet?) it looks like the way you want to be able to connect up
components (tools) is similar to the way aube works - however aube's system is
currently entirely graphical (ie. you can connect up various components, but
not load/save the state of connections). I am looking at using XML to handle
this information, as it can save parameters of each component more cleanly than
a scripting language could.

So, if you'd like to save yourself some coding you can use the system I've got
going with aube, including some widgets for selecting inputs and connecting up
components. I'll soon be adding an overview widget for editing the whole graph
of connections

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