From mboxrd@z Thu Jan 1 00:00:00 1970 From: tsd@tsdye.com (Thomas S. Dye) Subject: Re: A manuscript on "reproducible research" introducing org-mode Date: Wed, 15 Feb 2012 09:36:50 -1000 Message-ID: References: <20110905155520.18046s4zu5o3tbwg@www.biomedicale.univ-paris5.fr> <20110908120651.18821k1s7dd2ob0g@www.biomedicale.univ-paris5.fr> Mime-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable Return-path: Received: from eggs.gnu.org ([140.186.70.92]:37764) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1Rxkf2-00061k-Vf for emacs-orgmode@gnu.org; Wed, 15 Feb 2012 14:37:09 -0500 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1Rxkeu-000697-Bj for emacs-orgmode@gnu.org; Wed, 15 Feb 2012 14:37:04 -0500 Received: from oproxy8-pub.bluehost.com ([69.89.22.20]:46863) by eggs.gnu.org with smtp (Exim 4.71) (envelope-from ) id 1Rxket-00068d-V5 for emacs-orgmode@gnu.org; Wed, 15 Feb 2012 14:36:56 -0500 In-Reply-To: <20110908120651.18821k1s7dd2ob0g@www.biomedicale.univ-paris5.fr> (Christophe Pouzat's message of "Thu, 08 Sep 2011 12:06:51 +0200") 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: Christophe Pouzat Cc: emacs-orgmode@gnu.org Aloha Christophe, Has this article appeared in print? If so, can you forward publication details?=20 All the best, Tom Christophe Pouzat writes: > "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 > 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=E2=80= =A6 > 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 > --=20 Thomas S. Dye http://www.tsdye.com