From owner-chemistry@ccl.net Mon Oct 17 15:29:00 2011 From: "Dr W.R. Pitt wrp24*_*cam.ac.uk" To: CCL Subject: CCL: Science code manifesto Message-Id: <-45666-111017143732-8473-GHRDN5EK5qrRKAanIBUWng!^!server.ccl.net> X-Original-From: "Dr W.R. Pitt" Content-Transfer-Encoding: 8bit Content-Type: text/plain; format=flowed; charset=ISO-8859-1 Date: 17 Oct 2011 19:37:24 +0100 Mime-Version: 1.0 Sent to CCL by: "Dr W.R. Pitt" [wrp24!=!cam.ac.uk] I have two points to add to the discussion: 1/ As far as I can tell the the Science Code Manifesto does not insist on the use of open source software. In the discussion page it states "Use of languages, libraries, systems, and tools which are widely available is strongly recommended." The data analysis script should be made available but the manifesto seems to leave room for that script to be written using a commercial toolkit. I use commercial software as well as free software. Sometimes the former is only way (within the time I have available) of doing the job I have in mind. From my point of view, it is better to do science using commercial software and publish it than not doing it all. 2/ I do agree that the analysis scripts should be made public. However, I'm not sure it is necessary for a referee to be able to re-run the analysis script and check every last detail. The wider peer community would have the opportunity to do this. A natural consequence of this would be multiple versions of results in papers, derived from bug-fixes, following reader input. Much more rigorous testing of work prior to publication should result, which can only be a good thing. Relivant articles : Peer reviewers swamped, so extras get the heave-ho http://www.timeshighereducation.co.uk/story.asp?storyCode=413390§ioncode=26 Report from the Publishing Open Data Working Group meeting http://blogs.openaccesscentral.com/blogs/bmcblog/entry/report_from_the_publishing_open On Oct 17 2011, Jordi Villà i Freixa jordi.villafreixa/agmail.com wrote: >Allow me to be drastic here. > > In my opinion this is a quite absurd discussion. Having the ability to > make code transparent for others to reuse and build on top of is > obviously way better for science than having black boxes. It is not > needed to provide the ability to the referee (who by definition is a busy > guy) to rerun the calculations, but to the scientific community as a > whole. It may be the time already to reduce the often over-critic referee > system and move to a more open science schema. Repositories for code have > been extremely useful in the past and I think being concerned about the > ability of the scientific community to improve our results is way more > positive that believing that we and only we can run a code and understand > its results. > > Having myself a foot in enterpreneourship in addition to academia, I > think that closing/selling code is futurless in a world with tens of > thousands of developers ready for better implementations for each new > idea. What makes sense is understanding the possible use of each > technology, not closing them in a useless effort of overprotection. > >So, the need for the manifesto is clear. Start opening our eyes to a wider >conception of science, far from egoistic and closed minded uses of it. The >system should follow this, one day or another. > > > >2011/10/17 Pedro Silva pedros^ufp.edu.pt > >> >> Sent to CCL by: Pedro Silva [pedros(_)ufp.edu.pt] >> 2011/10/17 João Brandão jbrandao+/-ualg.pt : >> > 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. >> > >> >> The problem is: if the results do not agree with each other, how can >> you adjudicate between the competing claims without access to the >> code?> >> >> > > >