From owner-chemistry@ccl.net Mon Oct 17 16:05:00 2011
From: "Andrew Dalke dalke . dalkescientific.com" <owner-chemistry{:}server.ccl.net>
To: CCL
Subject: CCL:G: Science code manifesto
Message-Id: <-45667-111017124001-8650-GgQGGE73fv3xAgOALoDHjA{:}server.ccl.net>
X-Original-From: Andrew Dalke <dalke()dalkescientific.com>
Content-Transfer-Encoding: 8bit
Content-Type: text/plain; charset=windows-1252
Date: Mon, 17 Oct 2011 18:42:14 +0200
Mime-Version: 1.0 (Apple Message framework v1084)


Sent to CCL by: Andrew Dalke [dalke%dalkescientific.com]
On Oct 14, 2011, at 11:18 PM, Brian.James.Duke{:}gmail.com wrote:
> I just encountered the Science Code Manifesto, which essentially states
> that all computer code used for scientific analysis and modeling should
> be available for review.

To be precise:

  All source code written specifically to process data
  for a published paper must be available to the reviewers
  and readers of the paper.

I interpret that to mean that you don't need to ship source
code for the entire operating system, analysis tools, compiler,
and so on. For that matter, you can publish your Gaussian
script, and not need to include the source for Gaussian itself.

It does seems like it leaves a hole for people who write
a general purpose program for one project, then use it
(unchanged) for something which is published. Of course, the
editors may object to that practice.


There's also a problem with:

    Researchers who use or adapt science source code in
    their research must credit the code’s creators in
    resulting publications

Consider the 70 authors and 15 libraries which make up
the CDK chemistry toolkit. There might be 100+ creators.
It's beyond reason to include everyone in the publications,
and the general expectation is to reference the project,
not all of the code's creators.

Finally, if you are a follower of the Free Software Foundation's
ideas on software freedom, then you agree that there's a freedom
to sell software (http://www.gnu.org/philosophy/selling.html )
for as much money as you want. This manifesto is almost at odds
with the FSF viewpoint; I see it omits any discussion of how
much it should cost to access the curated software.

These aren't big problems, but they do point out that this
is a complex issue.

				Andrew Dalke
				dalke]~[dalkescientific.com