From: William Denton <wtd@pobox.com>
To: "emacs-orgmode@gnu.org" <emacs-orgmode@gnu.org>
Subject: Re: org-mode in the wild
Date: Sat, 2 Nov 2013 20:55:24 -0400 (EDT) [thread overview]
Message-ID: <alpine.DEB.2.00.1311022048510.13500@shell.miskatonic.org> (raw)
In-Reply-To: <CAJ51ETr1nJj5y+weMf=if6nh9MYz9FMz_pwdtwwA8UOu5qv7KA@mail.gmail.com>
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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/
next prev parent reply other threads:[~2013-11-03 0:55 UTC|newest]
Thread overview: 8+ messages / expand[flat|nested] mbox.gz Atom feed top
2013-11-03 0:25 org-mode in the wild John Kitchin
2013-11-03 0:55 ` William Denton [this message]
2013-11-03 5:48 ` Thomas S. Dye
2013-11-03 13:37 ` Rasmus
2013-11-04 23:35 ` John Kitchin
2013-11-04 9:23 ` Rainer M Krug
2013-11-05 10:43 ` Julian M. Burgos
2013-11-06 15:19 ` Karl Voit
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