Subject: Re: CCL:Anybody agrees with me?

From: "Angelo R. Rossi" <[email-masked]>
Date: Thu, 10 Feb 2000 08:46:04 -0500

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

---

From: Ray Crawford <[email-masked]>
Date: Thu, 10 Feb 2000 12:57:58 -0500

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:

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