From mboxrd@z Thu Jan 1 00:00:00 1970 From: Christophe Pouzat Subject: Re: A manuscript on "reproducible research" introducing org-mode Date: Wed, 15 Feb 2012 21:40:00 +0100 Message-ID: <87zkcjn84f.fsf@xtof-netbook.home> References: <20110905155520.18046s4zu5o3tbwg@www.biomedicale.univ-paris5.fr> <20110908120651.18821k1s7dd2ob0g@www.biomedicale.univ-paris5.fr> Mime-Version: 1.0 Content-Type: multipart/mixed; boundary="=-=-=" Return-path: Received: from eggs.gnu.org ([140.186.70.92]:41991) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1Rxle7-0001A9-VI for emacs-orgmode@gnu.org; Wed, 15 Feb 2012 15:40:18 -0500 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1Rxle2-0003pE-OU for emacs-orgmode@gnu.org; Wed, 15 Feb 2012 15:40:11 -0500 Received: from mail-wi0-f169.google.com ([209.85.212.169]:50075) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1Rxle2-0003no-DC for emacs-orgmode@gnu.org; Wed, 15 Feb 2012 15:40:06 -0500 Received: by wibhj13 with SMTP id hj13so1059787wib.0 for ; Wed, 15 Feb 2012 12:40:04 -0800 (PST) In-Reply-To: (Thomas S. Dye's message of "Wed, 15 Feb 2012 09:36:50 -1000") 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: Christophe Pouzat , emacs-orgmode@gnu.org --=-=-= Aloha Tom, Not yet in print, still on the accepted papers list (http://www.sciencedirect.com/science/journal/aip/09284257), sorry. It seems that I chose the "slowest" neuroscience journal! Your JSS paper of last month (with Eric, Dan and Carsten) is great by the way. It seems that I missed the announcements on the list when the pre-print was posted, otherwise I would have managed to cite it in mine. The bibtex entry for my paper (just downloaded from Elsevier site) is: --=-=-= Content-Type: text/x-bibtex; charset=utf-8 Content-Disposition: inline; filename*=us-ascii''Delescluse+%3a2012.bib Content-Transfer-Encoding: quoted-printable @article{Delescluse2011, title =3D "Making neurophysiological data analysis reproducible: Why and ho= w?", journal =3D "Journal of Physiology-Paris", volume =3D "", number =3D "0", pages =3D " - ", year =3D "2011", note =3D "", issn =3D "0928-4257", doi =3D "10.1016/j.jphysparis.2011.09.011", url =3D "http://www.sciencedirect.com/science/article/pii/S0928425711000374= ", author =3D "Matthieu Delescluse and Romain Franconville and S=C3=A9bastien = Joucla and Tiffany Lieury and Christophe Pouzat", keywords =3D "Software", keywords =3D "R", keywords =3D "Emacs", keywords =3D "Matlab", keywords =3D "Octave", keywords =3D "LATEX", keywords =3D "Org-mode", keywords =3D "Python", abstract =3D "Reproducible data analysis is an approach aiming at complemen= ting classical printed scientific articles with everything required to inde= pendently reproduce the results they present. =E2=80=9CEverything=E2=80=9D = covers here: the data, the computer codes and a precise description of how = the code was applied to the data. A brief history of this approach is prese= nted first, starting with what economists have been calling replication sin= ce the early eighties to end with what is now called reproducible research = in computational data analysis oriented fields like statistics and signal p= rocessing. Since efficient tools are instrumental for a routine implementat= ion of these approaches, a description of some of the available ones is pre= sented next. A toy example demonstrates then the use of two open source sof= tware programs for reproducible data analysis: the =E2=80=9CSweave family= =E2=80=9D and the org-mode of emacs. The former is bound to R while the lat= ter can be used with R, Matlab, Python and many more =E2=80=9Cgeneralist=E2= =80=9D data processing software. Both solutions can be used with Unix-like,= Windows and Mac families of operating systems. It is argued that neuroscie= ntists could communicate much more efficiently their results by adopting th= e reproducible research paradigm from their lab books all the way to their = articles, thesis and books." } --=-=-= Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable I will post on the list the "official" bibliographic reference as soon as the paper is in print. Take care, Christophe=20=20 tsd@tsdye.com (Thomas S. Dye) writes: > 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 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 MAP5 - Math=C3=A9matiques Appliqu=C3=A9es =C3=A0 Paris 5 CNRS UMR 8145 45, rue des Saints-P=C3=A8res 75006 PARIS France tel: +33142863828 mobile: +33662941034 web: http://www.biomedicale.univ-paris5.fr/physcerv/C_Pouzat.html --=-=-=--