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Re: [O] org-mode in the wild

From: William Denton
Subject: Re: [O] org-mode in the wild
Date: Sat, 2 Nov 2013 20:55:24 -0400 (EDT)
User-agent: Alpine 2.00 (DEB 1167 2008-08-23)

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 standard methods that we feel it warrants discussion. In this work, we have prepared a single document containing all of the raw data, the analysis of the raw data that has led to the figures and conclusions in the manuscript, and the manuscript itself. The document is in plain text format, marked up using org-mode syntax [14]. Org-mode is a lightweight text markup language that enables intermingling of narrative text, data and analysis code in an active document [39] when viewed in the editor Emacs (http://www.gnu.org/software/emacs/). This approach is known as literate programming and reproducible research [40]. Notably, files in org-mode syntax can be exported to a variety of other formats including LaTEX, PDF and html. The export can be done selectively to include only portions of the complete document. The published manuscript was exported from this document to create LaTEX source which was submitted to this journal. The Supplementary information file is the document itself, which includes all of the data used in the analysis. All analysis was done using Python (http://python.org), and figures were generated with Matplotlib [24]. All of these software packages are open-source and freely available."

The citations:

14. Dominik C (2010) The Org Mode 7 Reference Manual: Organize your life with 
GNU Emacs. Network Theory, UK.
39. Schulte E, Davison D (2011) Active documents with org-mode. Comput Sci Eng 
40. Schulte E, Davison D, Dye T, Dominik C (2012) A multi-language computing 
environment for literate programming and reproducible research. J Stat Softw 

William Denton
Toronto, Canada

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