Re: [OT - or may be not] The case for open computer programs
On Tue, May 29, 2012 at 08:29:21PM +0200, Michael Hanke wrote: On Tue, May 29, 2012 at 08:00:57AM +0200, Andreas Tille wrote: http://www.nature.com/nature/journal/v482/n7386/full/nature10836.html In case you don't want to pay Nature to read about this, you can alternatively pay Science... http://www.sciencemag.org/content/336/6078/159 Another editorial on this, this time in an OA journal: http://www.scfbm.org/content/7/1/2/abstract Michael -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20120531104834.gm10...@nighthawk.chemicalconnection.dyndns.org
Re: [OT - or may be not] The case for open computer programs
On Tue, May 29, 2012 at 11:14 PM, Yaroslav Halchenko deb...@onerussian.comwrote: Exactly! And there is more to it. Someone bold could event exaggerate that requiring open code on its own is **useless** besides for being an ideal description of the method implementation. Why useless? Because in majority of the cases open code will hardly be usable by a considerable part of scientific community for one reason (e.g. as you pointed out commercial base) or another. Quite often simply because that code was not created to be used by others. +1 Very good point. Open Code is just a Beginning. I have indeed seen a lot of research code that I'll be afraid to use...:-) and a lot of code, that just plain doesn't work... We need to promote a culture of scientific programming in which researchers adopt sound software development practices, and learn about software development practices that are rooted in quality assurance. Researchers tend to make the mistake of: Not taking the time to go fast As it is nicely put in the Clean Code book by Robert Martin. http://www.informit.com/articles/article.aspx?p=1235624seqNum=3 When it comes to chose our daily practices of software development it is too common to write code: just for the next paper. A more modern culture of sound software development practices needs to be grown in the field of research. In particular, Unit testing (which is indeed basic reproducibility), revision control, tutorials and documentation. Great work in this front is done by the Software Carpentry: http://software-carpentry.org/ We need to figure out how to further scale this type of initiatives. Luis
[OT - or may be not] The case for open computer programs
Hi, you might like to read: The case for open computer programs Darrel C. Ince, Leslie Hatton John Graham-Cumming Scientific communication relies on evidence that cannot be entirely included in publications, but the rise of computational science has added a new layer of inaccessibility. Although it is now accepted that data should be made available on request, the current regulations regarding the availability of software are inconsistent. We argue that, with some exceptions, anything less than the release of source programs is intolerable for results that depend on computation. The vagaries of hardware, software and natural language will always ensure that exact reproducibility remains uncertain, but withholding code increases the chances that efforts to reproduce results will fail. http://www.nature.com/nature/journal/v482/n7386/full/nature10836.html Kind regards Andreas. -- http://fam-tille.de -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20120529060057.gc18...@an3as.eu
Re: [OT - or may be not] The case for open computer programs
On Tue, May 29, 2012 at 2:00 PM, Andreas Tille andr...@an3as.eu wrote: Hi, you might like to read: The case for open computer programs Darrel C. Ince, Leslie Hatton John Graham-Cumming Seems it's been recommended before in the list. Scientific communication relies on evidence that cannot be entirely included in publications, but the rise of computational science has added a new layer of inaccessibility. Although it is now accepted that data should be made available on request, the current regulations regarding the availability of software are inconsistent. We argue that, with some exceptions, anything less than the release of source programs is intolerable for results that depend on computation. The vagaries of hardware, software and natural language will always ensure that exact reproducibility remains uncertain, but withholding code increases the chances that efforts to reproduce results will fail. http://www.nature.com/nature/journal/v482/n7386/full/nature10836.html Thanks, Kind regards Andreas. -- http://fam-tille.de -- To UNSUBSCRIBE, email to debian-science-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20120529060057.gc18...@an3as.eu -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/CAG9cJmkxiAQQQi1utS5Z=en56n0obpmY6i=br1cf_7h-ofg...@mail.gmail.com
Re: [OT - or may be not] The case for open computer programs
Hi All, Indeed strong words, published in Nature where you need to pay $32 to read what we all know already. Regards, Oz On Tue, May 29, 2012 at 8:00 AM, Andreas Tille andr...@an3as.eu wrote: Hi, you might like to read: The case for open computer programs Darrel C. Ince, Leslie Hatton John Graham-Cumming Scientific communication relies on evidence that cannot be entirely included in publications, but the rise of computational science has added a new layer of inaccessibility. Although it is now accepted that data should be made available on request, the current regulations regarding the availability of software are inconsistent. We argue that, with some exceptions, anything less than the release of source programs is intolerable for results that depend on computation. The vagaries of hardware, software and natural language will always ensure that exact reproducibility remains uncertain, but withholding code increases the chances that efforts to reproduce results will fail. http://www.nature.com/nature/journal/v482/n7386/full/nature10836.html Kind regards Andreas. -- http://fam-tille.de -- To UNSUBSCRIBE, email to debian-science-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20120529060057.gc18...@an3as.eu -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/cadkmuwm_ijlk15dlak142u8si2fpqe4ptrx6oumutzthkr7...@mail.gmail.com
Re: [OT - or may be not] The case for open computer programs
What is more interesting is the reaction that followed in serious scientific journals: 1) PLoS ONE (the Open Access Mega Journal that currently publishes 3% of all the STM literature) now requires software papers to include the source code under an Open Source license: http://www.plosone.org/static/guidelines.action#software http://www.plosone.org/static/policies.action quote *Software.* PLoS supports the development of open source software and believes that, for submissions in which software is the central part of the paper, adherence to appropriate open source standards will ensure that the submission conforms to (1) our requirements that methods be described in sufficient detail that another researcher can reproduce the experiments described, (2) our aim to promote openness in research, and (3) our intention that all work published in PLoS journals can be built upon by future researchers. Therefore, if new software or a new algorithm is central to a PLoS paper, the authors must confirm that the software conforms to the Open Source Definition http://www.opensource.org/docs/osd, have deposited the following three items in an open software archive, and included in the submission as Supporting Information: - *The associated source code of the software described by the paper.*This should, as far as possible, follow accepted community standards and be licensed under a suitable license such as BSD, LGPL, or MIT (see http://www.opensource.org/licenses/alphabetical for a full list). Dependency on commercial software such as Mathematica and MATLAB does not preclude a paper from consideration, although complete open source solutions are preferred. - *Documentation for running and installing the software.* For end-user applications, instructions for installing and using the software are prerequisite; for software libraries, instructions for using the application program interface are prerequisite. - *A test dataset with associated control parameter settings.* Where feasible, results from standard test sets should be included. Where possible, test data should not have any dependencies — for example, a database dump. /quote One of the new Journals in BiomedCentral, http://www.openresearchcomputation.com/about which is also Open Access, developed a similar policy: quote - Reproducibility Verificationhttp://www.openresearchcomputation.com/about - *Software: Open Research Computation* differs from other journals with a software focus in i*ts requirement for the software source code to be made available* under an *Open Source* Initiative compliant license, and in its assessment of the quality of documentation and * testing* of the software. - *Data*: *Open Research Computation* has very high standards for *data availability* and *reproducibility*. It is expected that all the *data *, *code*, and *software required to reproduce *any examples in the paper* will be made freely available for download* from an appropriate recognized repository or the journal website. - Review criteria for Source Code - Code and Licensehttp://www.openresearchcomputation.com/about/reviewers - Is the source code as well as executables and/or an instance of the service (of a clearly defined version) available on appropriate * public repository*? - Is the source code made available under an *Open Source *Initiative (http://www.opensource.org/licenses/category) compliant license? Specifically users must have the right to examine, compile, run and modify the code for any purpose. - Are project authors and contributors clearly defined, ideally through a Description of a Project [ http://en.wikipedia.org/wiki/DOAP, http://trac.usefulinc.com/doap] document? We recommend the use of the automatic DOAP generator such as those linked here: http://trac.usefulinc.com/doap/wiki/Generatorhttp://trac.usefulinc.com/doap/wiki/Generators /quote It has been said that Open Source was the application of the Scientific Method to the process of Software development. These recent developments show that Open Source has a lot to give back to the scientific community where the practice of Reproducibility Verification has been lost and substituted by the inferior and quite defective practice of peer-reviews based on simple opinions instead of reproducible experiments. For one thing, the simple practice of doing revision control, and implementing unit testing frameworks that can be executed over and over again, will already revolutionize the way software is managed in many research institutions. It is sadly too common that nobody in a lab can replicate a computational experiment even days after it has been performed. More on this by Victoria Stodden: http://www.stanford.edu/~vcs/talks/CaltechMay122011-STODDEN.pdf
Re: [OT - or may be not] The case for open computer programs
If you have 15$ left have you read the Nature paper, then you could also read less particular about details version of the same thing from Science: http://www.sciencemag.org/content/336/6078/159.full Research Priorities Shining Light into Black Boxes A. Morin, J. Urban, P. D. Adams, I. Foster, A. Sali, D. Baker, P. Sliz,* The publication and open exchange of knowledge and material form the backbone of scientific progress and reproducibility and are obligatory for publicly funded research. Despite increasing reliance on computing in every domain of scientific endeavor, the computer source code critical to understanding and evaluating computer programs is commonly withheld, effectively rendering these programs “black boxes” in the research work flow. Exempting from basic publication and disclosure standards such a ubiquitous category of research tool carries substantial negative consequences. Eliminating this disparity will require concerted policy action by funding agencies and journal publishers, as well as changes in the way research institutions receiving public funds manage their intellectual property (IP). and publicly available press-release for it from Scientific American: Secret Computer Code Threatens Science http://www.scientificamerican.com/article.cfm?id=secret-computer-code-threatens-science Meanwhile we can just keep going forward making it all possible ;) Cheers, On Tue, 29 May 2012, Oz Nahum Tiram wrote: Hi All, Indeed strong words, published in Nature where you need to pay $32 to read what we all know already. Regards, Oz On Tue, May 29, 2012 at 8:00 AM, Andreas Tille andr...@an3as.eu wrote: Hi, you might like to read: The case for open computer programs Darrel C. Ince, Leslie Hatton John Graham-Cumming Scientific communication relies on evidence that cannot be entirely included in publications, but the rise of computational science has added a new layer of inaccessibility. Although it is now accepted that data should be made available on request, the current regulations regarding the availability of software are inconsistent. We argue that, with some exceptions, anything less than the release of source programs is intolerable for results that depend on computation. The vagaries of hardware, software and natural language will always ensure that exact reproducibility remains uncertain, but withholding code increases the chances that efforts to reproduce results will fail. http://www.nature.com/nature/journal/v482/n7386/full/nature10836.html Kind regards Andreas. -- http://fam-tille.de -- To UNSUBSCRIBE, email to debian-science-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20120529060057.gc18...@an3as.eu -- Yaroslav O. Halchenko Postdoctoral Fellow, Department of Psychological and Brain Sciences Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755 Phone: +1 (603) 646-9834 Fax: +1 (603) 646-1419 WWW: http://www.linkedin.com/in/yarik -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20120529180732.go11...@onerussian.com
Re: [OT - or may be not] The case for open computer programs
On Tue, May 29, 2012 at 08:00:57AM +0200, Andreas Tille wrote: http://www.nature.com/nature/journal/v482/n7386/full/nature10836.html In case you don't want to pay Nature to read about this, you can alternatively pay Science... http://www.sciencemag.org/content/336/6078/159 -- Michael Hanke http://mih.voxindeserto.de -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20120529182921.GA15178@meiner
Re: [OT - or may be not] The case for open computer programs
Hi, Yaroslav Halchenko wrote (May 29, 2012): If you have 15$ left have you read the Nature paper, then you could also read less particular about details version of the same thing from Science: http://www.sciencemag.org/content/336/6078/159.full [snip] Meanwhile we can just keep going forward making it all possible ;) Actually, this brings to mind an interesting point. The articles mentioned in this thread, from what I can see, do not address open operating systems, but rather they specifically focus on open access to the specialized code that is used to back scientific conclusions. So it seems there is a distinction between what we are making possible with Debian, and what is being called for here. In this context, open _code_ and open _platforms_ are two different (albeit related) beasts. The articles really don't go far enough. Given the prevalence of closed proprietary platforms (e.g. Windows, Matlab, Mathematica, LabVIEW), the fact that the foundations of science that relies on computation in various forms (which, I assert, is probably most of science these days) are not necessarily open seems to me to be a rather significant elephant in the room. How can one be certain their results are valid and true if the platform on which those results are acquired cannot similarly be scrutinized? Ideally the whole system should be open, not just the chunk of code unique to each experiment. Peace, Brendon -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/201205291455.18362.blhigg...@gmail.com
Re: [OT - or may be not] The case for open computer programs
On Tue, May 29, 2012 at 2:55 PM, Brendon Higgins blhigg...@gmail.comwrote: Ideally the whole system should be open, not just the chunk of code unique to each experiment. +1 Luis
Re: [OT - or may be not] The case for open computer programs
On Tue, 29 May 2012, Brendon Higgins wrote: http://www.sciencemag.org/content/336/6078/159.full [snip] Meanwhile we can just keep going forward making it all possible ;) ... In this context, open _code_ and open _platforms_ are two different (albeit related) beasts. ... Ideally the whole system should be open, not just the chunk of code unique to each experiment. Exactly! And there is more to it. Someone bold could event exaggerate that requiring open code on its own is **useless** besides for being an ideal description of the method implementation. Why useless? Because in majority of the cases open code will hardly be usable by a considerable part of scientific community for one reason (e.g. as you pointed out commercial base) or another. Quite often simply because that code was not created to be used by others. Moreover, we all know, that even providing usable binaries accompanied by FOSS code, without formalized build procedures and clearly specified dependencies would complicate any extension of the code, thus often significantly reducing the benefit of having that code under FOSS license to begin with. As the result, mandating open code to accompany research papers would be of limited practical importance to the science due to difficulty of its adoption and extension. And that is where a platform which addresses those demands would be indispensable; but neither of those papers indeed goes that far. Overall all these recent trends are only of benefit for us to promote Debian because of its unique organization and wealth ;) -- Yaroslav O. Halchenko Postdoctoral Fellow, Department of Psychological and Brain Sciences Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755 Phone: +1 (603) 646-9834 Fax: +1 (603) 646-1419 WWW: http://www.linkedin.com/in/yarik -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20120530031432.gw11...@onerussian.com
