Subject: software evaluation / validation

From: Andras.Borosy-.at.-givaudan.com
Date: Thu, 4 Mar 2004 09:02:41 +0100

Dear Colleagues,

On February 27, 2004 07:40 am, Csaba wrote:
...
> In my view, using commercial modelling (e.g. docking, MD,
> etc.) softwares is quite questionable from a scientific point of view.
> The main criterion of scientific work is reproducibility. My question: 
how
> is it possible to reproduce scientific results obtained by commercial
> softwares which are not available for the whole scientific community???
> (That is, if you do not have several thousands of dollars just for 
yearly
> licences you cannot check the reliability of data published with
> commercial softwares by others. Not to speak about the
> availability of source codes...)
> There are good initiatives, like the AutoDock, GROMACS, etc. projects
> (free programs for academic users) which should be considered by
> software developers in the future.

I think that ALL of the software providers (commercial, non-profit, 
academic 
etc.) would freely give a copy for a limited time period (e.g. 1-2 months) 

for evaluation / validation purposes. This time period should be enough to 

run the software through the validation set of your choice.

Source code is not necessary for testing or validation. It is only 
necessary 
if you want to modify, enhance, integrate, build onto an existing code 
base. 

I agree with the first part, which is indeed a _VERY_ important point:
"The main criterion of scientific work is reproducibility."
However, my question about this would be:
How is it possible  to reproduce scientific results obtained by commercial
_OR_ academic software which relies on _RANDOM_ methods ?
(e.g. GOLD, AutoDock, ICM-dock etc. employ random methods).

Best regards,

Andras Borosy
PhD Computational Chemist
Givaudan Schweiz AG
Fragrance Research
Ueberlandstr. 138
8600 D|bendorf
Switzerland
tel: + 41-1-8242164
fax: +41-1-8242926
e-mail: andras.borosy-.at.-givaudan.com