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

[Thomas S. Dye]

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
>
> 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
>
>
>
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