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 Verification<http://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 License<http://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/Generator<http://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
Technology and the Scientific Method: Tools and Policies for Addressing the
Credibility Crisis in Computational
Science<http://www.stanford.edu/%7Evcs/talks/CaltechMay122011-STODDEN.pdf>
."
For more in the story behind that Nature paper:
http://videolectures.net/cancerbioinformatics2010_baggerly_irrh/
and since the topic of Open Access came up,
there is still time to sign this petition to the White House:
http://wh.gov/6TH
to make all US Federally Funded research
available as Open Access to the public.
More details in:
http://blog.wikimedia.org/2012/05/25/wikimedia-foundation-endorses-mandates-for-free-access-to-publicly-funded-research/
http://lj.libraryjournal.com/2012/05/legislation/acrl-urges-librarians-to-sign-research-access-petition/
Luis
---------------------------------------------------------
On Tue, May 29, 2012 at 3:20 AM, lina <[email protected]> wrote:
> On Tue, May 29, 2012 at 2:49 PM, Oz Nahum Tiram <[email protected]> wrote:
> > Hi All,
> > Indeed strong words, published in Nature where you need to pay $32 to
> > read what we all know already.
>
> There is a link, probably you may access (temporarily) to read if you
> are interested.
>
> https://docs.google.com/open?id=0B93SVRfpVVg3aW0tX3RLanRKdUE
>
>
> Best regards,
> >
> > Regards,
> > Oz
> >
> > On Tue, May 29, 2012 at 8:00 AM, Andreas Tille <[email protected]> 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
> >>
> >>
> >> --
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