>
>
> 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.
> >
> > Let’s say that I receive a manuscript for review that uses
program X,
> > which I may have access to its code now (since I’m 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 I’m hardly a
programmer.
> > Therefore, open or closed software (usually) doesn’t 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
I’m
> > 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 didn’t 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.
> >
> >
>
>
>