From: tsd@tsdye.com (Thomas S. Dye)
To: Christophe Pouzat <christophe.pouzat@parisdescartes.fr>
Cc: emacs-orgmode@gnu.org
Subject: Re: A manuscript on "reproducible research" introducing org-mode
Date: Wed, 15 Feb 2012 09:36:50 -1000 [thread overview]
Message-ID: <m1lio3rir1.fsf@tsdye.com> (raw)
In-Reply-To: <20110908120651.18821k1s7dd2ob0g@www.biomedicale.univ-paris5.fr> (Christophe Pouzat's message of "Thu, 08 Sep 2011 12:06:51 +0200")
Aloha Christophe,
Has this article appeared in print? If so, can you forward publication
details?
All the best,
Tom
Christophe Pouzat <christophe.pouzat@parisdescartes.fr> writes:
> "Thomas S. Dye" <tsd@tsdye.com> a écrit :
>
>> Christophe Pouzat <christophe.pouzat@parisdescartes.fr> 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
http://www.tsdye.com
next prev parent reply other threads:[~2012-02-15 19:37 UTC|newest]
Thread overview: 12+ messages / expand[flat|nested] mbox.gz Atom feed top
2011-09-05 13:55 A manuscript on "reproducible research" introducing org-mode Christophe Pouzat
2011-09-05 17:41 ` Thomas S. Dye
2011-09-08 10:06 ` Christophe Pouzat
2012-02-15 19:36 ` Thomas S. Dye [this message]
2012-02-15 20:40 ` Christophe Pouzat
2012-02-16 8:58 ` Jambunathan K
2012-02-16 9:21 ` Christophe Pouzat
2012-02-15 19:52 ` Samuel Wales
2012-02-16 20:24 ` Stephen Eglen
2012-02-16 20:59 ` Samuel Wales
2012-02-18 18:13 ` Thomas S. Dye
2012-02-19 1:59 ` Rasmus
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