I will post on the list the "official" bibliographic reference as soon as the paper is in print. Take care, Christophe tsd@tsdye.com (Thomas S. Dye) writes: > Aloha Christophe, > > Has this article appeared in print? If so, can you forward publication > details? > > All the best, > Tom > > Christophe Pouzat writes: > >> "Thomas S. Dye" a écrit : >> >>> 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 = {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 >> -- 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 - Mathématiques Appliquées à Paris 5 CNRS UMR 8145 45, rue des Saints-Pères 75006 PARIS France tel: +33142863828 mobile: +33662941034 web: http://www.biomedicale.univ-paris5.fr/physcerv/C_Pouzat.html