From owner-chemistry@ccl.net Thu Sep 15 18:56:07 2005
From: "CCL" <owner-chemistry---server.ccl.net>
To: CCL
Subject: CCL: W:Disclose your data, or not publish !
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X-Original-From: jle <jle---theworld.com>
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Date: Thu, 15 Sep 2005 18:43:46 -0400
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Sent to CCL by: jle [jle---theworld.com]

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On Sep 15, 2005, at 4:15 PM, CCL wrote:

>
> Sent to CCL by: "Ivanciuc, Ovidiu I." [oiivanci+*+utmb.edu]
>
> Re: Disclose your data, or not publish !
>
> While computational models of proteins can be deposited in PDB,
> there is no public database for computational models of
> organic compounds (including MD simulations and docking
> results).
> A simple solution for publishers would be to ask for
> mandatory deposition of such data as supplementary materials.

Perhaps interesting in the abstract, but a number of problems
come to mind:

1. If publishers hold the data, would we not have to check with
each publisher in turn to get the information?  And if so, how much
would it cost?

2. We are, err, blessed with a wide range of file formats, many of
which aren't described, or even readable.  Whose formats would
be supported, and would the vendors and other authors provide
the necessary conversion routines?

3. I would think the modeling community produces WAY more
data than the Xtal community.  I am unaware of modeling packages
which sit atop databases so as to organize a single user's or site's
data.  How can those holding the data organize the sheer mass
of data provided by the manuscript's authors.

If we're going to even start proposing "modeling databases",
lets first settle the data/file format and other mundane yet
necessary things first.

Joe Leonard
jle---theworld.com
>
> Regards,
> Ovidiu
> *********************************
> Ovidiu Ivanciuc
> Sealy Center for Structural Biology,
> Department of Human Biological Chemistry & Genetics,
> University of Texas Medical Branch,
> 301 University Boulevard,
> Galveston, Texas 77555-0857
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