Subject: RE: Anybody agrees with me?

From: "Leif Laaksonen" <[email-masked]>
Date: Fri, 11 Feb 2000 07:55:21 +0200

Hi,

I myself find this discussion quite interesting. However, I do not
agree about all presented and then I'm a bit confused about some
things but all in all I think it's good to talk about these matters
>from time to time.

After all we have to remember that we have come a long way along the
standardization lines. Most graphics applications use OpenGL and
Motif is specially used in the Unix field. Thinking about the situation
some 15 years ago was a bit chaotic. So the libraries and tools
"under the hood" have converged. This also makes the GUIs look very
much alike, how they are setup and how they work is an other matter.

Not so far in the past (a few monts) we had a discussion about XML/RDF
on the CCL list. These tools will standardize again the data (knowledge)
exchange between applications.
 
Looking at the work the Computer-Human interface Usability group is
doing at the close by Helsinki University of Technology I understand
that my program(s) will always have an unusable GUI. This really takes time
and money.

Looking at things on a short time scale things might look chaotic but
on a longer time scale I'm not so worried.

This was my two Finn marks wort opinion as long as they are valid before
the Euro comes...

Regards,

-leif laaksonen

-----Original Message-----
From: Computational Chemistry List [mailto:[email-masked]]On
Behalf Of Ray Crawford
Sent: 10. helmikuuta 2000 19:58
To: Angelo R. Rossi
Cc: Renxiao Wang; Computational Chemistry List
Subject: CCL:Anybody agrees with me? 

Howdy:

Actually, I'm going to go against the grain here and post a message in
support of the gentleman who challenged the various software companies to
develop "standards".  I find his view quite refreshing and it actually is
in line with something I've been thinking about for quite a while.

While I don't know if I agree with standardizing the various algorithms as
he proposed, I do believe standardization would ease the frustration felt
by general modelers like myself.  For example, I don't think that a
"standard" should be developed for, say, molecular mechanics in that every
package has the same mechanics force fields.  I do, however, think there
should be (outside of the sometimes-obscure literature references) a
documented way that all companies using the Sybyl or MMFF94 force fields
should parameterize and code those particular algorithms (for example).  I
think standardization would also help on the file-format issue.  RFC-like
documents should be drafted on the standard formats such as mol2, pdb,
maccs, etc. and all companies should be coerced to make various import and
export formats available within their products.

I think this general effort would be faciliated by the design of a testing
set -- somewhat like what has been done in the PC realm with SPEC tests.
With the design of such a set, all software companies would have a
benchmark to which they could measure their software's quality.  Does it
load and save the data in this way?  Can the statistical methods find this
known relationship in the data?  Are the descriptors computed correctly?
Does this ab initio method, when coded up in our interface, give the
correct answer?  These are all questions that such a data set could
answer.

That's just my two cents worth...  However, I must say that since I have
apparently suffered frustrations similar to those of Renxiao, my bank has
a whole lot more than those two cents in it...  

I also find it humorous that when some one posts a far out message like
the one about the rockets destroying our ecosystem, nobody makes a peep
(outside of the one by the list admin)...  However, when some one raises
a relevant issue in an intellectual context that affects the daily
opperations of us all, people move to defame his ideas and his character.
This is quite interesting.  

Thank you, Jan, for "letting such a message through".

	Ray Crawford.

On Thu, 10 Feb 2000, Angelo R. Rossi wrote:

> 
> Hello:
> 
> I am somewhat disappointed with the CCL coordinator for allowing a
> posting whose content contains intensely disparaging comments about 
> particular software applications.
> 
> Surely, there is a better and more constructive way to discuss the
> topic of underlying principles of application software unification
> without engaging innuendo. 
> 
> Regards,
> 
> A. R. Rossi
> 
> 
> 
> 
> 
> 

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