[Pipet Devel] Stuff

J.W. Bizzaro bizzaro at bc.edu
Sat Nov 7 17:30:07 EST 1998

Hello Konrad.

Thank you for your willingness to add to the TULIP project!

I have made some modifications to the TULIP home page.  I hope
you won't mind if I add your name to the developer's list.

By the way, Jay Painter will be joining the developer team.
He tells me he developed a substantial part of the GTK
graphics library plus the GNOME e-mail client called "Balsa."
He has a degree in biochemistry plus one in computer science
and one in physics.  This is his home page:


He seems to be willing to work at a fast pace on this.  He
wrote to me about some ideas he has about implementing the
concept, and he says he will write something this weekend.
His original messages are attached.

> > behave in a similar fashion.  It can be an application,
> > but it can provide standard "widgets" that can be called
> Let's better say "modules", because that's what it is!
> At least for computational code. The user interface is
> indeed best structured as a set of widgets; plugging them
> together is then a trivial exercise.

Sure, that's correct.  I was calling them widgets from a
GUI builder's point of view.

> Hopefully. I don't really know the traditions in that field; many
> people in computational chemistry are very secretive, to the extent
> that even the publications don't contain a complete description of the
> methods.

It may be around 50/50.  I have come across some algorithms that
are liberally shared.  The important thing is that they can become
GNU GPL licensed, if they are to be distributed with TULIP.

> Another problem is licensing; if the resulting collection has a
> different set of conditions for each submodule, people won't be
> willing to use it for fear of legal problems.

Again, we need to be sure the core is GNU.  I think we can package
pluggable algorithms under separate licenses, as long as it is clear
what the licenses are. 

> The first step should be an evaluation of what people use most
> in the existing commercial packages.

Yes.  I know someone (Tom Graf of BU and Harvard) who gives seminars
on GCG use at least once a week.  I will contact him to see if he
will be an advisor/evaluator.

J.W. Bizzaro                  Phone: 617-552-3905
Boston College                mailto:bizzaro at bc.edu
Department of Chemistry       http://www.uml.edu/Dept/Chem/Bizzaro/
-------------- next part --------------
Date: Fri, 6 Nov 1998 12:26:34 -0800 (PST)
Subject: TULIP

Hi there,
  It just so happens that I actually have a biochem degree and have some
interest in this.  I'm also a huge Python fan, and have written XML
parsers with the libxml Python module.  Anyways, I'm sure I can help out
with this.

Jay Painter -- jpaint at serv.net -- jpaint at gimp.org -- jpaint at real.com

-------------- next part --------------
Date: Sat, 7 Nov 1998 02:05:50 -0800 (PST)
Subject: Re: TULIP

> I checked out your home page, and I see that you are
> involved in Balsa and some other GNOME/GTK projects.
> To what extent are you involved in these?

I was the origional Balsa author, but I don't work on it much anymore.  I
also wrote about 7-8% of GTK, wich doesn't seem like much now but at the
time it was a much higher %

> I started with Linux at RedHat 4.0, which is not
> as far back as some guys go.  I've been making a
> transition to Linux programming from Windows, and
> I'm sticking with Linux because of its versatility
> with scientific programming.

I started using it in '93 when I was working a the Hanford Nuclear
Reservation doing computational thermo.  

> Where did you get your degree in biochemistry?  Have
> you written any biochem apps?

I got my degree at Western Wash. University.  I was working on NMR/protein
structure.  Well, actually it was just an excuse for learning how to spell
'protein' correctly, and hit on the students in the Biology department ;)
I had to think of another degree to get because I already had two in
Physics and CS.

> By the way, the other developer for this project
> is Konrad Hinsen.  He is a Ph.D. in physics working
> in computational biophysics in France.  You may have
> come across his "Scientific Python" Web site, where
> he posted some science modules of his own.

I'll have to look at it.

> Since neither Konrad nor I have quite yet mastered
> GTK+ and GNOME, I think your help will be quite
> valuable.  Thanks!

I've got that covered.  I want to impliment a threaded messaging system
where we don't use Python bindings for GTK, but we instead impliment the
interface as a Python-C module running in a Python thread.  I'll start
working on how to pass messages to and from the UI running in C in one
thread to the other threads.  The other threads could launch parsers,
modules that do fast computation, etc; and best of all this would be
highly scriptable.  I'll try to come up with a prototype application
working like this this weekend.

More information about the Pipet-Devel mailing list