Re: [O] org-mode in the wild

[William Denton]

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 
13(3):66–73
40. Schulte E, Davison D, Dye T, Dominik C (2012) A multi-language computing 
environment for literate programming and reproducible research. J Stat Softw 
46(3):1–24


Bill
--
William Denton
Toronto, Canada
http://www.miskatonic.org/