CCL:G: Science code manifesto

 Sent to CCL by: "Jim Kress" [ccl_nospam .. kressworks.com]
 Although it may be the kiss of death, I agree with Brian.
 The fundamental requisite of scientific work is that it must be reproducible by
 ANY OTHER SCIENTIST skilled in the art.  The lack of access to the tools
 necessary to establish reproducibility should obviate the publication of any
 scientific paper until such access and detailed examination is made available.
 Jim Kress
 > -----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>