From mboxrd@z Thu Jan 1 00:00:00 1970 From: William Denton Subject: Re: org-mode in the wild Date: Sat, 2 Nov 2013 20:55:24 -0400 (EDT) Message-ID: References: Mime-Version: 1.0 Content-Type: MULTIPART/MIXED; BOUNDARY="658601964-1826569960-1383440124=:13500" Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:33771) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1VclyT-0000Dl-Jl for emacs-orgmode@gnu.org; Sat, 02 Nov 2013 20:55:33 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1VclyP-0007Dy-90 for emacs-orgmode@gnu.org; Sat, 02 Nov 2013 20:55:29 -0400 Received: from shell.miskatonic.org ([65.39.236.119]:36923) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1VclyP-0007Di-4j for emacs-orgmode@gnu.org; Sat, 02 Nov 2013 20:55:25 -0400 Received: from wtd (helo=localhost) by shell.miskatonic.org with local-esmtp (Exim 4.72) (envelope-from ) id 1VclyO-0003WC-1a for emacs-orgmode@gnu.org; Sat, 02 Nov 2013 20:55:24 -0400 In-Reply-To: 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: "emacs-orgmode@gnu.org" This message is in MIME format. The first part should be readable text, while the remaining parts are likely unreadable without MIME-aware tools. --658601964-1826569960-1383440124=:13500 Content-Type: TEXT/PLAIN; charset=UTF-8; format=flowed Content-Transfer-Encoding: QUOTED-PRINTABLE On 2 November 2013, John Kitchin wrote: > We had another manuscript written in org-mode accepted in Topics in > Catalysis (http://link.springer.com/article/10.1007%2Fs11244-013-0166-3)! > Check out references 14, 39 and 40 ;) Lovely! Here's the start of section 4, "Manuscript Preparation Method:" "This manuscript was prepared in a manner sufficiently different than=20 standard methods that we feel it warrants discussion. In this work, we=20 have prepared a single document containing all of the raw data, the=20 analysis of the raw data that has led to the figures and conclusions in=20 the manuscript, and the manuscript itself. The document is in plain text=20 format, marked up using org-mode syntax [14]. Org-mode is a lightweight=20 text markup language that enables intermingling of narrative text, data=20 and analysis code in an active document [39] when viewed in the editor=20 Emacs (http://www.gnu.org/software/emacs/). This approach is known as=20 literate programming and reproducible research [40]. Notably, files in=20 org-mode syntax can be exported to a variety of other formats including=20 LaTEX, PDF and html. The export can be done selectively to include only=20 portions of the complete document. The published manuscript was exported=20 from this document to create LaTEX source which was submitted to this=20 journal. The Supplementary information file is the document itself, which= =20 includes all of the data used in the analysis. All analysis was done using= =20 Python (http://python.org), and figures were generated with Matplotlib=20 [24]. All of these software packages are open-source and freely=20 available." The citations: 14. Dominik C (2010) The Org Mode 7 Reference Manual: Organize your life wi= th GNU Emacs. Network Theory, UK. 39. Schulte E, Davison D (2011) Active documents with org-mode. Comput Sci = Eng 13(3):66=E2=80=9373 40. Schulte E, Davison D, Dye T, Dominik C (2012) A multi-language computin= g environment for literate programming and reproducible research. J Stat So= ftw 46(3):1=E2=80=9324 Bill --=20 William Denton Toronto, Canada http://www.miskatonic.org/ --658601964-1826569960-1383440124=:13500--