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

From: Konrad Hinsen <[email-masked]>
Date: Wed, 21 Mar 2001 19:08:13 +0100

> >After all, if you are not going to commercialize your code, then why not
> make it
> >available to other scientists unconditionally?
> 
> Commercialization means different things to different people.  When someone
> develops code that gives them a 'competitive advantage' in getting grant
> money, they aren't inclined to distribute the code to others.  Isn't that
> another form of 'commercialization'?

That would mean not releasing the code at all. Personally I think that
this is against the principles of science (because others can't check
a computational study if an essential ingredient remains
inaccessible), but that's not the problem we are discussion at the
moment.

The question was why some code is available for a small fee, or for
free but only after signing a license contract, which typically
forbids redistribution. One reason I have heard is that people want to
keep track of all users, in order to mention the popularity of their
product to their sponsors. But I am sure that other counting schemes
can be found (e.g. references to some publication).
-- 
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Konrad Hinsen                            | E-Mail: [email-masked]
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From: Rick Venable <[email-masked]>
Date: Thu, 22 Mar 2001 11:17:46 -0500

>> Commercialization means different things to different people.  When
>> someone develops code that gives them a 'competitive advantage' in
>> getting grant money, they aren't inclined to distribute the code to
>> others.  Isn't that another form of 'commercialization'?

On Wed, 21 Mar 2001, Konrad Hinsen wrote:
> forbids redistribution. One reason I have heard is that people want
> to keep track of all users, in order to mention the popularity of
> their product to their sponsors. But I am sure that other counting
> schemes can be found (e.g. references to some publication).

In the case of CHARMM, it is commercialization in the more classic
sense; the existence of CHARMm as a product from MSI has placed
contractual limits on the redistribution of the academic source code.  
This can hamper independent development projects which might wish to be
able to read and write CHARMM-DCD files (which we call CHARMM binary
trajectories).  Note that code divergence may mean that XPLOR-DCD,
CHARMm-DCD, and CHARMM-DCD formats may not be completely identical.

In particular, CHARMM simulations run with features such as 4D dynamics,
free energy perturbation, or fragment replicas may produce trajectory
files which only CHARMM could read.

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Rick Venable
FDA/CBER/OVRR Biophysics Lab
1401 Rockville Pike    HFM-419
Rockville, MD  20852-1448  U.S.A.
(301) 496-1905   [email-masked]
ALT email:  [email-masked]
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