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Re: [O] A manuscript on "reproducible research" introducing org-mode

From: Thomas S. Dye
Subject: Re: [O] A manuscript on "reproducible research" introducing org-mode
Date: Wed, 15 Feb 2012 09:36:50 -1000

Aloha Christophe,

Has this article appeared in print?  If so, can you forward publication

All the best,

Christophe Pouzat <address@hidden> writes:

> "Thomas S. Dye" <address@hidden> a écrit&nbsp;:
>> Christophe Pouzat <address@hidden> writes:
>>> Dear all,
>>> M. Delescluse, R. Franconville, S. Joucla, T. Lieury and myself (C.
>>> Pouzat) have just put a manuscript entitled: "Making
>>> neurophysiological data analysis reproducible. Why and how?" on a
>>> pre-print server: http://hal.archives-ouvertes.fr/hal-00591455/fr/
>>> Although the paper has been written for a neurobiological journal, the
>>> reader does not have to be a neuroscientist to read and understand it.
>>> A toy example illustrating the use of org-mode + Babel (with Python
>>> and Octave) takes a fair part of the manuscript. Other tools like R +
>>> Sweave are presented and many more are mentioned.
>>> I thank Eric Schulte for comments on the manuscript and Eric (again)
>>> together with the whole org-mode / Babel community for developing such
>>> a great tool.
>>> Any comment, remark, suggestion on the manuscript is of course welcome.
>>> Christophe
>> Aloha Christophe,
>> Thank you for an interesting and useful paper.  I was happy with the
>> distinction you draw between reproducible analysis and reproducible
>> research, which certainly applies to my field of archaeology where
>> unique sites are typically destroyed by the data collection effort.  I
>> also think the emphasis you place on data preprocessing is just the
>> right approach; inclusion of the raw data in a reproducible analysis
>> opens up many possibilities, which must be a benefit to a scientific
>> community's pursuit of knowledge.
>> May I offer a suggestion?  Carsten Dominik published the Org Mode 7
>> Manual last year and it would be nice to see it cited in your paper.
>> @book{dominik10:_org_mode_refer_manual,
>>   author =       {Carsten Dominik},
>>   title =        {The Org Mode 7 Reference Manual: Organize Your Life
>>   with GNU Emacs},
>>   publisher =    {Network Theory Ltd.},
>>   year =         2010
>> }
>> All the best,
>> Tom
>> --
>> Thomas S. Dye
>> http://www.tsdye.com
> Dear Tom,
> Thanks for these interesting and positive comments. I apologize for
> forgetting the obvious reference to Carsten's reference manual. I will
> definitely include it in the next version.
> I hope that people in my field will come to think the way you do about
> sharing their raw data. I'm just afraid that the way is still long…
> but the goal is reachable. Raw data aside, org-mode is surely a tool
> which should help people experimenting with the "reproducible research
> paradigm". As I wrote to Eric (Schulte), M. Delescluse and I wrote a
> first RR manuscript 6 years ago based on R/Sweave. The manuscript
> never got submitted for different reasons, among them, the amount of
> work required to learn R and LaTeX. Learning about org-mode convinced
> me that it would be worth re-activating the project.
> Christophe
> Most people are not natural-born statisticians. Left to our own
> devices we are not very good at picking out patterns from a sea of
> noisy data. To put it another way, we are all too good at picking out
> non-existent patterns that happen to suit our purposes.
> Bradley Efron & Robert Tibshirani (1993) An Introduction to the Bootstrap
> --
> Christophe Pouzat
> Laboratoire de Physiologie Cerebrale
> CNRS UMR 8118
> UFR biomedicale de l'Universite Paris-Descartes
> 45, rue des Saints Peres
> 75006 PARIS
> France
> tel: +33 (0)1 42 86 38 28
> fax: +33 (0)1 42 86 38 30
> mobile: +33 (0)6 62 94 10 34
> web: http://www.biomedicale.univ-paris5.fr/physcerv/C_Pouzat.html

Thomas S. Dye

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