-----Original Message-----
From: owner-chemistry+ccl_nospam==kressworks.com ~~ ccl.net
[mailto:owner-chemistry+ccl_nospam==kressworks.com ~~
ccl.net] On Behalf
Of Brian Salter-Duke brian.james.duke.:.gmail.com
Sent: Sunday, October 16, 2011 5:33 PM
To: Kress, Jim
Subject: CCL:G: Science code manifesto
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.
--
Brian Salter-Duke (aka Brian Duke)
Brian.James.Duke:+:gmail.com>