org-mode in the wild

org-mode in the wild

[John Kitchin]

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Hi everyone,

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 ;)

The supporting information seems to be freely available (
http://link.springer.com/content/esm/art:10.1007/s11244-013-0166-3/file/MediaObjects/11244_2013_166_MOESM1_ESM.pdf)
was also prepared in org-mode. It is probably best read with the Adobe PDF
reader. This file is an interesting hybrid of data sharing methods. Some of
the data is in the pdf, some of it is embedded in the pdf, including the
org-mode files for the manuscript and the supporting information file
itself. Anyone interested in seeing how we did it can check it out.

John

-----------------------------------
John Kitchin
Associate Professor
Doherty Hall A207F
Department of Chemical Engineering
Carnegie Mellon University
Pittsburgh, PA 15213
412-268-7803
http://kitchingroup.cheme.cmu.edu

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Re: org-mode in the wild

[William Denton]

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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/

Re: org-mode in the wild

[Thomas S. Dye]

Aloha John,

This is wonderful! The pdf file is a user-friendly entry into the Org
mode compendium *and* an effective way to distribute it. Thanks for your
pioneering efforts.

All the best,
Tom

John Kitchin <jkitchin@andrew.cmu.edu> writes:

> Hi everyone,
>
> 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 ;)
>
> The supporting information seems to be freely available (
> http://link.springer.com/content/esm/art:10.1007/s11244-013-0166-3/file/MediaObjects/11244_2013_166_MOESM1_ESM.pdf)
> was also prepared in org-mode. It is probably best read with the Adobe PDF
> reader. This file is an interesting hybrid of data sharing methods. Some of
> the data is in the pdf, some of it is embedded in the pdf, including the
> org-mode files for the manuscript and the supporting information file
> itself. Anyone interested in seeing how we did it can check it out.
>
> John
>
> -----------------------------------
> John Kitchin
> Associate Professor
> Doherty Hall A207F
> Department of Chemical Engineering
> Carnegie Mellon University
> Pittsburgh, PA 15213
> 412-268-7803
> http://kitchingroup.cheme.cmu.edu
> Hi everyone,
>
> 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 ;)
>
> The supporting information seems to be freely available
> (http://link.springer.com/content/esm/art:10.1007/s11244-013-0166-3/file/MediaObjects/11244_
> 2013_166_MOESM1_ESM.pdf) was also prepared in org-mode. It is probably
> best read with the Adobe PDF reader. This file is an interesting
> hybrid of data sharing methods. Some of the data is in the pdf, some
> of it is embedded in the pdf, including the org-mode files for the
> manuscript and the supporting information file itself. Anyone
> interested in seeing how we did it can check it out. 
>
> John
>
> -----------------------------------
> John Kitchin
> Associate Professor
> Doherty Hall A207F
> Department of Chemical Engineering
> Carnegie Mellon University
> Pittsburgh, PA 15213
> 412-268-7803
> http://kitchingroup.cheme.cmu.edu
>
>

-- 
Thomas S. Dye
http://www.tsdye.com

Re: org-mode in the wild

[Rasmus]

John Kitchin <jkitchin@andrew.cmu.edu> writes:

> 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 ;)

Congrats!  And thanks for sharing.

> The supporting information seems to be freely available (
> http://link.springer.com/content/esm/art:10.1007/s11244-013-0166-3/file/MediaObjects/11244_2013_166_MOESM1_ESM.pdf)
> was also prepared in org-mode. It is probably best read with the Adobe PDF
> reader. This file is an interesting hybrid of data sharing methods. Some of
> the data is in the pdf, some of it is embedded in the pdf, including the
> org-mode files for the manuscript and the supporting information file
> itself. Anyone interested in seeing how we did it can check it out.

With Evince 3.10, the GNOME document viewer, I'm able to save
attachments.  Do you use other features?.  It's catching up.
Supposedly, Okular is also quite feature-rich.

On matplotlib: looks great!
Are you aware that matplotlib now supports pgf out-of-the-box?  You
just specify it as an extension (pgf).  .pgf is also recognized as an
image in Org for a while.  The main benefit is that fonts magically
get the right size.

–Rasmus

-- 
Dung makes an excellent fertilizer

Re: org-mode in the wild

[John Kitchin]

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I wasn't familiar with pgf at all. we are usually limited by what
publishers will accept in terms of formats, which is usually pdf, eps, png
or tiff where we publish.

for other features in pdf, we did not use any for these manuscripts, but
sometimes I use some adobe specific javascript for making interactive
features in course notes(using acrotex). some of those do not work well in
any other browser.

John

-----------------------------------
John Kitchin
Associate Professor
Doherty Hall A207F
Department of Chemical Engineering
Carnegie Mellon University
Pittsburgh, PA 15213
412-268-7803
http://kitchingroup.cheme.cmu.edu



On Sun, Nov 3, 2013 at 8:37 AM, Rasmus <rasmus@gmx.us> wrote:

> John Kitchin <jkitchin@andrew.cmu.edu> writes:
>
> > 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 ;)
>
> Congrats!  And thanks for sharing.
>
> > The supporting information seems to be freely available (
> >
> http://link.springer.com/content/esm/art:10.1007/s11244-013-0166-3/file/MediaObjects/11244_2013_166_MOESM1_ESM.pdf
> )
> > was also prepared in org-mode. It is probably best read with the Adobe
> PDF
> > reader. This file is an interesting hybrid of data sharing methods. Some
> of
> > the data is in the pdf, some of it is embedded in the pdf, including the
> > org-mode files for the manuscript and the supporting information file
> > itself. Anyone interested in seeing how we did it can check it out.
>
> With Evince 3.10, the GNOME document viewer, I'm able to save
> attachments.  Do you use other features?.  It's catching up.
> Supposedly, Okular is also quite feature-rich.
>
> On matplotlib: looks great!
> Are you aware that matplotlib now supports pgf out-of-the-box?  You
> just specify it as an extension (pgf).  .pgf is also recognized as an
> image in Org for a while.  The main benefit is that fonts magically
> get the right size.
>
> –Rasmus
>
> --
> Dung makes an excellent fertilizer
>
>
>

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Re: org-mode in the wild

[Rainer M Krug]

John Kitchin <jkitchin@andrew.cmu.edu> writes:

> Hi everyone,
>
> 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 ;)
>
> The supporting information seems to be freely available (
> http://link.springer.com/content/esm/art:10.1007/s11244-013-0166-3/file/MediaObjects/11244_2013_166_MOESM1_ESM.pdf)
> was also prepared in org-mode. It is probably best read with the Adobe PDF
> reader. This file is an interesting hybrid of data sharing methods. Some of
> the data is in the pdf, some of it is embedded in the pdf, including the
> org-mode files for the manuscript and the supporting information file
> itself. Anyone interested in seeing how we did it can check it out.

Thanks - this is brilliant and gives quite a few ideas how to write
paper, but especially how to do an analysis and graphs for a paper, in
org.

Incidently, we have just submitted a paper which was written by the main
author in MS Office, but the graphs were generated and the analysis was
doine using org. In a similar manner, I included the complete analysis
in the supporting information. But I relly like the \attachfile{} - I'll
add this to the supporting informateion as werll as a paragraph aboiut
org.

Cheers,

Rainer

>
> John
>
> -----------------------------------
> John Kitchin
> Associate Professor
> Doherty Hall A207F
> Department of Chemical Engineering
> Carnegie Mellon University
> Pittsburgh, PA 15213
> 412-268-7803
> http://kitchingroup.cheme.cmu.edu
<#secure method=pgpmime mode=sign>

-- 
Rainer M. Krug

email: RMKrug<at>gmail<dot>com

Re: org-mode in the wild

[Julian M. Burgos]

Thank you very much John!!! Your document contains a wealth of information on how to
use org-mode for reproducible research!  I really like the idea of
embedding the supporting documents (bibliography, additional analysis) into the
document. Very nice.

Perhaps it would be good to have a repository of practices and examples
for reproducible research, maybe a section in Worg?

All the best,

Julian

John Kitchin writes:

> Hi everyone,
>
> 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 ;)
>
> The supporting information seems to be freely available (
> http://link.springer.com/content/esm/art:10.1007/s11244-013-0166-3/file/MediaObjects/11244_2013_166_MOESM1_ESM.pdf)
> was also prepared in org-mode. It is probably best read with the Adobe PDF
> reader. This file is an interesting hybrid of data sharing methods. Some of
> the data is in the pdf, some of it is embedded in the pdf, including the
> org-mode files for the manuscript and the supporting information file
> itself. Anyone interested in seeing how we did it can check it out.
>
> John
>
> -----------------------------------
> John Kitchin
> Associate Professor
> Doherty Hall A207F
> Department of Chemical Engineering
> Carnegie Mellon University
> Pittsburgh, PA 15213
> 412-268-7803
> http://kitchingroup.cheme.cmu.edu


-- 
Julian Mariano Burgos, PhD
Hafrannsóknastofnun/Marine Research Institute
Skúlagata 4, 121 Reykjavík, Iceland
Sími/Telephone : +354-5752037
Bréfsími/Telefax:  +354-5752001
Netfang/Email: julian@hafro.is

Re: org-mode in the wild

[Karl Voit]

* Julian M. Burgos <julian@hafro.is> wrote:
> Thank you very much John!!! Your document contains a wealth of information on how to
> use org-mode for reproducible research!  I really like the idea of
> embedding the supporting documents (bibliography, additional analysis) into the
> document. Very nice.

A agree!

> Perhaps it would be good to have a repository of practices and examples
> for reproducible research, maybe a section in Worg?

If would be very cool if John could link the repos and the PDF on:
http://orgmode.org/worg/org-contrib/babel/uses.html#sec-6

-- 
mail|git|SVN|photos|postings|SMS|phonecalls|RSS|CSV|XML to Org-mode:
       > get Memacs from https://github.com/novoid/Memacs <

https://github.com/novoid/extract_pdf_annotations_to_orgmode + more on github