Reproducible Research academic reference

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Reproducible Research academic reference

Daniele Nicolodi
Hello,

sorry for the slightly off-topic question, but I do not know of a better
place where to ask. I'm looking for academic references to the topic of
"Reproducible Research", in the form of papers of peer review magazines,
but also less "formal" resources.

Thank for your help. Cheers,
--
Daniele, in the stressful process of PhD thesis writing... :-)
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Re: Reproducible Research academic reference

Gael Varoquaux
On Fri, Feb 25, 2011 at 10:36:37AM +0100, Daniele Nicolodi wrote:
> sorry for the slightly off-topic question, but I do not know of a better
> place where to ask. I'm looking for academic references to the topic of
> "Reproducible Research", in the form of papers of peer review magazines,
> but also less "formal" resources.

A central reference is:
http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.53.6201

CiSE had a special issue on the topic recently:
http://www.computer.org/portal/web/csdl/doi/10.1109/MCSE.2009.14

G
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Re: Reproducible Research academic reference

Fernando Perez
In reply to this post by Daniele Nicolodi
Hi,

On Fri, Feb 25, 2011 at 1:36 AM, Daniele Nicolodi <[hidden email]> wrote:
> sorry for the slightly off-topic question, but I do not know of a better
> place where to ask. I'm looking for academic references to the topic of
> "Reproducible Research", in the form of papers of peer review magazines,
> but also less "formal" resources.

I just came back from presenting at a symposium at the annual AAAS
meeting (publishers of Science) in Washington precisely on this very
topic; details here:

http://blog.fperez.org/2011/02/reproducible-research-at-aaas-2011.html

There's an ongoing discussion on some of these ideas with several of
the participants from the symposium at the google group:

http://groups.google.com/group/reproducible-research

Cheers,

f
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Re: Reproducible Research academic reference

Fernando Perez
On Fri, Feb 25, 2011 at 8:42 AM, Fernando Perez <[hidden email]> wrote:
>
> I just came back from presenting at a symposium at the annual AAAS
> meeting (publishers of Science) in Washington precisely on this very
> topic; details here:
>
> http://blog.fperez.org/2011/02/reproducible-research-at-aaas-2011.html

I should add that the organizer of the symposium, Victoria Stodden,
did her PhD under David Donoho, the author of the reference Gael
provided for you (Donoho also was there); this event was pretty much a
direct descendant of that original and key reference.  Donoho is now
working on a URI system for computations with his graduate student,
some of that discussion has been going on at the google group I
linked.

Cheers,

f
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Re: Reproducible Research academic reference

Gökhan SEVER-2
In reply to this post by Daniele Nicolodi


On Fri, Feb 25, 2011 at 2:36 AM, Daniele Nicolodi <[hidden email]> wrote:
Hello,

sorry for the slightly off-topic question, but I do not know of a better
place where to ask. I'm looking for academic references to the topic of
"Reproducible Research", in the form of papers of peer review magazines,
but also less "formal" resources.

Thank for your help. Cheers,
--
Daniele, in the stressful process of PhD thesis writing... :-)
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Two semi-related links from me:



These are on the fun side of the subject...




--
Gökhan

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Re: Reproducible Research academic reference

Fernando Perez
On Fri, Feb 25, 2011 at 9:24 AM, Gökhan Sever <[hidden email]> wrote:
>
> Two semi-related links from me:

This reminded my that I had a little link dump of stuff I read while
preparing my talk, might be useful here...

Killed by Code: Software Transparency in Implantable Medical Devices
====================================================================

    * Karen Sandler
    * Lysandra Ohrstrom
    * Laura Moy
    * Robert McVay

http://www.softwarefreedom.org/resources/2010/transparent-medical-devices.html

The Climate Code Foundation
===========================

http://clearclimatecode.org/the-climate-code-foundation/

Welcome to EuSpRIG, the World’s premier site for information, action,
conferences and dialogue on Spreadsheet Risk Management.

http://www.eusprig.org/index.htm

Wikipedia Entry on Iraq War Turned Into Actual Encyclopedia
http://newsfeed.time.com/2010/09/07/wikipedia-entry-on-iraq-war-turned-into-actual-encyclopedia/


GSOC summit session on open science
===================================

Summary notes:
http://etherpad.osuosl.org/open-source-science

Other links
=========

>From a Kitware developer:
http://www.kitware.com/blog/home/post/67

What is "Reproducibility," Anyway?
http://www.scimatic.com/node/361

>From Titus Brown: mock reply to NSF data management request
http://ivory.idyll.org/blog/may-10/data-management.html

UTOSC: Applying open source ideals to more than software
http://lwn.net/Articles/410555/#Comments

How science funding is putting scientific data at risk
http://arstechnica.com/science/news/2010/10/how-science-funding-is-putting-scientific-data-at-risk.ars


Preserving science: what data do we keep? What do we discard?
By John Timmer
http://arstechnica.com/science/news/2010/11/preserving-science-choosing-what-data-to-discard.ars

Science's burden: storing terabytes of research data for decades
http://arstechnica.com/science/news/2011/02/how-to-handle-data-in-science.ars


http://www.sciencemag.org/content/331/6018/649.full
“To address the growing complexity of data and analyses, Science is
extending our data access requirement listed above to include computer
codes involved in the creation or analysis of data.”
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Re: Reproducible Research academic reference

Daniele Nicolodi
In reply to this post by Gael Varoquaux
On 25/02/11 10:39, Gael Varoquaux wrote:
> A central reference is:
> http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.53.6201
>
> CiSE had a special issue on the topic recently:
> http://www.computer.org/portal/web/csdl/doi/10.1109/MCSE.2009.14

Thank you Gael, and thank to all the others that gave me pointers on the
mailing list and via private mail.

Cheers,
--
Daniele
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Re: Reproducible Research academic reference

Fernando Perez
On Sun, Feb 27, 2011 at 5:42 AM, Daniele Nicolodi <[hidden email]> wrote:
>
> Thank you Gael, and thank to all the others that gave me pointers on the
> mailing list and via private mail.

Another detailed discussion on the topic that was just posted to a
climate modeling blog, which you might find useful:

http://wattsupwiththat.com/2011/02/26/the-code-of-nature-making-authors-part-with-their-programs/

Cheers,

f
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