From mboxrd@z Thu Jan 1 00:00:00 1970 From: Christophe Pouzat Subject: Re: A manuscript on "reproducible research" introducing org-mode Date: Thu, 08 Sep 2011 12:06:51 +0200 Message-ID: <20110908120651.18821k1s7dd2ob0g@www.biomedicale.univ-paris5.fr> References: <20110905155520.18046s4zu5o3tbwg@www.biomedicale.univ-paris5.fr> Mime-Version: 1.0 Content-Type: text/plain; charset=UTF-8; DelSp="Yes"; format="flowed" Content-Transfer-Encoding: quoted-printable Return-path: Received: from eggs.gnu.org ([140.186.70.92]:55506) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1R1bVb-000474-Cf for emacs-orgmode@gnu.org; Thu, 08 Sep 2011 06:07:04 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1R1bVW-0002uA-4v for emacs-orgmode@gnu.org; Thu, 08 Sep 2011 06:06:59 -0400 Received: from www.biomedicale.univ-paris5.fr ([193.51.86.27]:38277 helo=gargas.biomedicale.univ-paris5.fr) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1R1bVV-0002tn-Lv for emacs-orgmode@gnu.org; Thu, 08 Sep 2011 06:06:54 -0400 In-Reply-To: Content-Disposition: inline List-Id: "General discussions about Org-mode." List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: emacs-orgmode-bounces+geo-emacs-orgmode=m.gmane.org@gnu.org Sender: emacs-orgmode-bounces+geo-emacs-orgmode=m.gmane.org@gnu.org To: "Thomas S. Dye" Cc: emacs-orgmode@gnu.org "Thomas S. Dye" a =C3=A9crit : > Christophe Pouzat 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 =3D {Carsten Dominik}, > title =3D {The Org Mode 7 Reference Manual: Organize Your Life > with GNU Emacs}, > publisher =3D {Network Theory Ltd.}, > year =3D 2010 > } > > All the best, > Tom > -- > Thomas S. Dye > http://www.tsdye.com > Dear Tom, Thanks for these interesting and positive comments. I apologize for =20 forgetting the obvious reference to Carsten's reference manual. I will =20 definitely include it in the next version. I hope that people in my field will come to think the way you do about =20 sharing their raw data. I'm just afraid that the way is still long=E2=80=A6 = =20 but the goal is reachable. Raw data aside, org-mode is surely a tool =20 which should help people experimenting with the "reproducible research =20 paradigm". As I wrote to Eric (Schulte), M. Delescluse and I wrote a =20 first RR manuscript 6 years ago based on R/Sweave. The manuscript =20 never got submitted for different reasons, among them, the amount of =20 work required to learn R and LaTeX. Learning about org-mode convinced =20 me that it would be worth re-activating the project. Christophe Most people are not natural-born statisticians. Left to our own =20 devices we are not very good at picking out patterns from a sea of =20 noisy data. To put it another way, we are all too good at picking out =20 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