CCL:G: Science code manifesto

 Sent to CCL by: Brian Salter-Duke [brian.james.duke^_^gmail.com]
 Just using a different code leads to confusion. Code A gives X. Code B
 gives Y, But why? A known example of this confusion is the differing
 meanings of B3LYP in different programs, but what if the reason is not
 clear.
 Also, what if it is an entirely new development that is not in any
 other program. Of course I assume the paper explains the method and
 someone else could code it up, but that is time consuming. It would be
 much preferable to check the code that gave the results.
 However, I am a total open source supporter and nothing is going to
 convince me that keeping scientific code closed to the users of the
 program is anything other than bad science and really rather
 offensive. Science does not progress by secrecy.
 Brian.
 2011/10/17 JoÃo BrandÃo jbrandao+/-ualg.pt
 <owner-chemistry^^^ccl.net>:
 > 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.
 >
 >
 >
 >
 >
 >
 --
 Brian Salter-Duke (aka Brian Duke)
 Brian.James.Duke^^^gmail.com