Subject: Re: CCL:DCD and software reuse (was Qmol: Molecular viewer for Windows)

From: Konrad Hinsen <[email-masked]>
Date: Mon, 19 Mar 2001 18:55:06 +0100

> I don't know what can be done to limit this (in my mind)
> needless duplication of effort.

Open Source code would be an important first step. In fact, I do not
understand why this concept isn't standard for academic applications.
Much academic code is already free, so why not take the next step and
make it freely redistributable, also in modified form? And for those
academic packages that are not free, I seriously doubt that they are
in any sense profitable.

If Open Source were common in computational chemistry, then probably
there would also be corresponding Web sites that organize and
catalogue development efforts (perhaps even the same that take care of
OpenSource development in other application domains).
-- 
-------------------------------------------------------------------------------
Konrad Hinsen                            | E-Mail: [email-masked]
Centre de Biophysique Moleculaire (CNRS) | Tel.: +33-2.38.25.56.24
Rue Charles Sadron                       | Fax:  +33-2.38.63.15.17
45071 Orleans Cedex 2                    | Deutsch/Esperanto/English/
France                                   | Nederlands/Francais
-------------------------------------------------------------------------------

---

From: Geoff Hutchison <[email-masked]>
Date: Mon, 19 Mar 2001 19:45:33 -0600

>OpenSource development in other application domains).

Indeed, isn't this partly the aim of the OpenScience project at 
openscience.org? (I will note that I am not affiliated with the 
group, but have encountered it using the JMol and JChemPaint 
programs.) And, of course, there are several chemistry-related 
projects hosted at places like SourceForge.

I'll also echo your call for more use of open source and free 
licenses in academic computational chemistry. I can think of more 
than a few cases where code has fallen by the wayside as groups move 
to other projects, etc. Proper citation is still required in 
publications, so am I wrong in saying that an academic group loses 
little by releasing the source to the community?

Do others have a different viewpoint? I would be glad to summarize 
responses to the list one way or the other.

Best regards,
-- 
--
-Geoff Hutchison	<[email-masked]>
Ratner/Marks Groups	(847) 491-3295
Northwestern Chemistry	http://www.chem.nwu.edu/

---

From: "Warren DeLano" <[email-masked]>
Date: Mon, 19 Mar 2001 19:36:02 -0800

> academic packages that are not free, I seriously doubt that they are

Some academic code is very profitable.  MSI and others make a living (or should I
say a killing?) off of academic packages that have been commercialized.  I think
the critical question is whether we as computational Scientists are happy with this
arrangement or whether we and our Science would benefit from more free source code
written by other scientists.  My guess is that the impact of significant amounts of
*reusable* source-code building blocks would be profound and world changing.  At
the very least, competition from open-source would force commercial software
developers to greatly improve the quality of their packages.

I applaud the work Konrad has done in this direction with the MMTK package.  My
efforts to create a free professional-strength, interoperable, and open-source
molecular graphics/editing system (PyMOL) reflect this shared vision.  If only more
scientists/developers would do likewise with their projects!

After all, if you are not going to commercialize your code, then why not make it
available to other scientists unconditionally?  Instead of allowing your great work
to languish on some back-up tape, please release it to the world and allow it to be
*modified* and *redistributed*.  By doing so, you will change the field irrevocably
and enable the next generation of computational research tools to be built on
*your* foundation.  As it stands, each of us is so busy pouring foundations that we
never get around to building cathedrals.  Let's change that.

Thanks to the internet's exceedingly low distribution costs, and the advent of
modular, extensible scripting languages such as Perl and Python, you now have no
excuse other than vanity for allowing your good code to remain restricted and
unutilized.

I propose initiating an effort to accumulate unrestricted computational chemistry
source-code into a single curated distribution, probably on a SourceForge
instance.  This "Free Molecule Project" would require a significant number of
volunteers -- so I am going to float this trail balloon:    If you have interest in
such a project and would consider contributing, please email me directly.  Assuming
there are enough interested parties, I'll set up a mailing list, and we will start
a discussion about how such a project might come together.

- Warren

--
mailto:[email-masked]
Warren L. DeLano, Ph.D.
Informatics Scientist
Sunesis Pharmaceuticals, Inc.
3696 Haven Ave., Suite C
Redwood City, CA 94063
(650)-562-3106 fax: (650)-556-8824