Sorry, but I disagree.
"but if there are real concerns about the work, it is
necessary that the scientific
community can look seriously at the code to see exactly what the program is
doing."
In my opinion:
If anyone has real concerns about any work, the best way
for science development is to write (or use) a different code and compare the
results.
JoÃo BrandÃo
Em 16-10-2011 22:33, Brian Salter-Duke brian.james.duke.:.gmail.com
escreveu:
Sent to CCL by: Brian Salter-Duke [brian.james.duke(~)gmail.com]
The review of manuscripts by referees prior to publication is just a
small part of what this is all about. The main point is about proper
review by the scientific community after publication. There, while not
everyone has access to a 600MHz NMR or has paid to get Gaussian, some
people in the community will have. The guys who paid for Gaussian
however, may not have bought the code and in some cases, it is
impossible to buy the code, as they are commercial secrets. This
manifesto is saying that commercial secrets are not compatible with
good science.
Of course the need to this kind of review is not common, but if there
are real concerns about the work, it is necessary that the scientific
community can look seriously at the code to see exactly what the
program is doing.
Brian.
On Sun, Oct 16, 2011 at 8:05 PM, Sebastian Kozuch kozuchs^_^yahoo.com
<owner-chemistry:+:ccl.net> wrote:
I like the idea of open software, and in principle I support
the proposal of
having access to the software code for the possibility of full review of a
theoretical work. However, I feel that this is more wishful thinking than
real scientific life.
Letâs say that I receive a manuscript for review that uses program X, which
I may have access to its code now (since Iâm the reviewer). Do I have to
spend a week trying to understand its algorithms to check if the frequencies
are correctly calculated? For me, most (if not all) the programs are in
practice black boxes, as Iâm hardly a programmer. Therefore, open or closed
software (usually) doesnât make me any difference, except from a
philosophical perspective.
Now, let me consider an analogy from experimental chemistry. I have to
review a manuscript where the authors tested some compound with a 600 MHz
NMR. My lab is much more humble, and I only have access to a 400 MHz NMR. Id
est, I cannot reproduce the results of the paper that Iâm reviewing. Is
here
any difference compared to the theoretical case?
I had in a couple of cases problems to reproduce the results of papers,
mostly because the authors didnât provide enough information. However, for
100% reproducibility I need 100% the same conditions (and a lot of resources
and time). This makes the selection of the software just a small issue.
I would like to hear the thoughts of other people about this issue, as I
consider the peer reviewing process a very complex and far from perfect
system.
Sebastian
________________________________
> From: Brian.James.Duke{:}gmail.com <owner-chemistry()ccl.net>
To: "Kozuch, Sebastian " <kozuchs()yahoo.com>
Sent: Friday, October 14, 2011 11:18 PM
Subject: CCL: Science code manifesto
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. It appears to have started with the Climate
Code Foundation. I encourage you to visit the web site and consider
endorsing the Manifesto.
http://sciencecodemanifesto.org/
Note that this is not specifying open source code, so GAMESS(US),
GAMESS(UK), DALTON etc., as well as open source codes such as PSI3 amd
MPQC satisfies the points of the manifesto. Of course some other quantum
chemistry codes do not. I think we should be putting pressure on the
authors of such codes to meet the criteria in this manifesto.
Brian.
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