Scientific papers related to Org-mode

Scientific papers related to Org-mode

[Karl Voit]

Hi!

Since I am writing a paper about Memacs[1] I want to link any
existing relevant white paper.

I already know «A Multi-Language Computing Environment for Literate
Programming and Reproducible Research»[2] which will be cited fore
sure.

The short report on [3] is nothing worth quoting, I'm afraid. There
is also a paper about a GNOWSIS Emacs client using Org-mode [4]
which sounds great but I could not find any screencast demo
mentioned.

In [5] Org-mode is mentioned only in one section. (See the source of
it also on github[6]).

The paper on [7] is focused on reproducible research just like [2].


Is there any other important paper I missed?


  1. https://github.com/novoid/Memacs
  2. http://www.jstatsoft.org/v46/i03
  3. http://www.warwick.ac.uk/statsdept/useR-2011/abstracts/010411-lehaandreas.pdf
  4. http://gnowledge.org/~nagarjun/gnowsys-mode-4-sw-demo.pdf
  5. http://www.kieranhealy.org/files/misc/workflow-apps.pdf
  6. https://github.com/kjhealy/workflow-paper
  7. http://www.sciencedirect.com/science/article/pii/S0928425711000374
-- 
Karl Voit

Re: Scientific papers related to Org-mode

[Bastien]

Hi Karl,

Karl Voit <devnull@Karl-Voit.at> writes:

> Is there any other important paper I missed?

Check: http://orgmode.org/fr/org-mode-documentation.html

There are these two other publications:

  Schulte, E.; Davison, D.; Active Documents with Org-Mode, Computing in
  Science & Engineering, Vol. 13, Issue 3, May-June 2011.

  Delescluse M., Franconville R., Joucla S., Lieury T. and Pouzat C.,
  Making neurophysiological data analysis reproducible: Why and how?,
  Journal of Physiology-Paris, N°0, 2011.

HTH,

-- 
 Bastien

Re: Scientific papers related to Org-mode

[Eric Schulte]

Hi Karl,

I think the Org-mode manual is also citable.

@book{dominik10:_org_mode_refer_manual,
  author =       {Carsten Dominik},
  title =        {The \pkg{Org-Mode} 7 Reference Manual: Organize
                  Your Life with GNU Emacs},
  publisher =    {Network Theory},
  year =         2010,
  address =      {UK},
  note =         {with contributions by David O`Toole, Bastien Guerry,
                  Philip Rooke, Dan Davison, Eric Schulte, and Thomas
                  Dye}
}

Best,

Bastien <bzg@gnu.org> writes:

> Hi Karl,
>
> Karl Voit <devnull@Karl-Voit.at> writes:
>
>> Is there any other important paper I missed?
>
> Check: http://orgmode.org/fr/org-mode-documentation.html
>
> There are these two other publications:
>
>   Schulte, E.; Davison, D.; Active Documents with Org-Mode, Computing in
>   Science & Engineering, Vol. 13, Issue 3, May-June 2011.
>
>   Delescluse M., Franconville R., Joucla S., Lieury T. and Pouzat C.,
>   Making neurophysiological data analysis reproducible: Why and how?,
>   Journal of Physiology-Paris, N°0, 2011.
>
> HTH,

-- 
Eric Schulte
http://cs.unm.edu/~eschulte/

Re: Scientific papers related to Org-mode

[Rainer M Krug]

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On 09/04/12 19:30, Eric Schulte wrote:
> Hi Karl,
> 
> I think the Org-mode manual is also citable.

Never thought about that - good to know.

Why not put that into org? e.g. R has a function citation(), which returns the bibtex for citing R
or packages.

I think it would be very useful to have a similar functionality in org - similar to "show version"
in the Documentation, a "Show citation" entry which always prints the most recent citation which
can be used in publications?
I think it could give org even more publicity.

Cheers,

Rainer

> 
> @book{dominik10:_org_mode_refer_manual, author =       {Carsten Dominik}, title =        {The
> \pkg{Org-Mode} 7 Reference Manual: Organize Your Life with GNU Emacs}, publisher =    {Network
> Theory}, year =         2010, address =      {UK}, note =         {with contributions by David
> O`Toole, Bastien Guerry, Philip Rooke, Dan Davison, Eric Schulte, and Thomas Dye} }
> 
> Best,
> 
> Bastien <bzg@gnu.org> writes:
> 
>> Hi Karl,
>> 
>> Karl Voit <devnull@Karl-Voit.at> writes:
>> 
>>> Is there any other important paper I missed?
>> 
>> Check: http://orgmode.org/fr/org-mode-documentation.html
>> 
>> There are these two other publications:
>> 
>> Schulte, E.; Davison, D.; Active Documents with Org-Mode, Computing in Science & Engineering,
>> Vol. 13, Issue 3, May-June 2011.
>> 
>> Delescluse M., Franconville R., Joucla S., Lieury T. and Pouzat C., Making neurophysiological
>> data analysis reproducible: Why and how?, Journal of Physiology-Paris, N°0, 2011.
>> 
>> HTH,
> 


- -- 
Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation Biology, UCT), Dipl. Phys.
(Germany)

Centre of Excellence for Invasion Biology
Stellenbosch University
South Africa

Tel :       +33 - (0)9 53 10 27 44
Cell:       +33 - (0)6 85 62 59 98
Fax :       +33 - (0)9 58 10 27 44

Fax (D):    +49 - (0)3 21 21 25 22 44

email:      Rainer@krugs.de

Skype:      RMkrug
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Re: Scientific papers related to Org-mode

[suvayu ali]

On Tue, Apr 10, 2012 at 09:55, Rainer M Krug <r.m.krug@gmail.com> wrote:
> Why not put that into org? e.g. R has a function citation(), which returns the bibtex for citing R
> or packages.

Nice idea, why not submit a patch? ;)

-- 
Suvayu

Open source is the future. It sets us free.

Re: Scientific papers related to Org-mode

[Rainer M Krug]

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On 10/04/12 10:57, suvayu ali wrote:
> On Tue, Apr 10, 2012 at 09:55, Rainer M Krug <r.m.krug@gmail.com> wrote:
>> Why not put that into org? e.g. R has a function citation(), which returns the bibtex for
>> citing R or packages.
> 
> Nice idea, why not submit a patch? ;)
> 

Because I unfortunately have effectively no idea about elisp, only that it uses *many* brackets...

and I have at the moment =no time to learn it.

Cheers,

Rainer

- -- 
Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation Biology, UCT), Dipl. Phys.
(Germany)

Centre of Excellence for Invasion Biology
Stellenbosch University
South Africa

Tel :       +33 - (0)9 53 10 27 44
Cell:       +33 - (0)6 85 62 59 98
Fax :       +33 - (0)9 58 10 27 44

Fax (D):    +49 - (0)3 21 21 25 22 44

email:      Rainer@krugs.de

Skype:      RMkrug
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Re: Scientific papers related to Org-mode

[Bastien]

Hi Rainer,

Rainer M Krug <r.m.krug@gmail.com> writes:

> On 10/04/12 10:57, suvayu ali wrote:
>> On Tue, Apr 10, 2012 at 09:55, Rainer M Krug <r.m.krug@gmail.com> wrote:
>>> Why not put that into org? e.g. R has a function citation(), which returns the bibtex for
>>> citing R or packages.
>> 
>> Nice idea, why not submit a patch? ;)
>
> Because I unfortunately have effectively no idea about elisp, only
> that it uses *many* brackets...
>
> and I have at the moment =no time to learn it.

it's okay.  Still, could you describe a bit more precisely the function:
how does it work?  In what contexts?  What does it insert?

Thanks,

-- 
 Bastien

Re: Scientific papers related to Org-mode

[Rainer M Krug]

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On 10/04/12 11:13, Bastien wrote:
> Hi Rainer,
> 
> Rainer M Krug <r.m.krug@gmail.com> writes:
> 
>> On 10/04/12 10:57, suvayu ali wrote:
>>> On Tue, Apr 10, 2012 at 09:55, Rainer M Krug <r.m.krug@gmail.com> wrote:
>>>> Why not put that into org? e.g. R has a function citation(), which returns the bibtex
>>>> for citing R or packages.
>>> 
>>> Nice idea, why not submit a patch? ;)
>> 
>> Because I unfortunately have effectively no idea about elisp, only that it uses *many*
>> brackets...
>> 
>> and I have at the moment =no time to learn it.
> 
> it's okay.  Still, could you describe a bit more precisely the function: how does it work?  In
> what contexts?  What does it insert?

It just returns the citation.

- From the help:

     Execute function ‘citation()’ for information on how to cite the
     base R system in publications.  If the name of a non-base package
     is given, the function either returns the information contained in
     the ‘CITATION’ file of the package or auto-generates citation
     information.  In the latter case the package ‘DESCRIPTION’ file is
     parsed, the resulting citation object may be arbitrarily bad, but
     is quite useful (at least as a starting point) in most cases.

Some examples:

This prints the citation for R:

#+begin_src R :results output
  citation()
#+end_src

#+RESULTS:
#+begin_example

To cite R in publications use:

  R Development Core Team (2012). R: A language and environment for
  statistical computing. R Foundation for Statistical Computing,
  Vienna, Austria. ISBN 3-900051-07-0, URL http://www.R-project.org/.

A BibTeX entry for LaTeX users is

  @Manual{,
    title = {R: A Language and Environment for Statistical Computing},
    author = {{R Development Core Team}},
    organization = {R Foundation for Statistical Computing},
    address = {Vienna, Austria},
    year = {2012},
    note = {{ISBN} 3-900051-07-0},
    url = {http://www.R-project.org/},
  }

We have invested a lot of time and effort in creating R, please cite it
when using it for data analysis. See also ‘citation("pkgname")’ for
citing R packages.

#+end_example

And if a package name is given, it prints the citation info of this package:

#+begin_src R :results output
  citation("graphics")
#+end_src

#+RESULTS:
#+begin_example

The ‘graphics’ package is part of R.  To cite R in publications use:

  R Development Core Team (2012). R: A language and environment for
  statistical computing. R Foundation for Statistical Computing,
  Vienna, Austria. ISBN 3-900051-07-0, URL http://www.R-project.org/.

A BibTeX entry for LaTeX users is

  @Manual{,
    title = {R: A Language and Environment for Statistical Computing},
    author = {{R Development Core Team}},
    organization = {R Foundation for Statistical Computing},
    address = {Vienna, Austria},
    year = {2012},
    note = {{ISBN} 3-900051-07-0},
    url = {http://www.R-project.org/},
  }

We have invested a lot of time and effort in creating R, please cite it
when using it for data analysis. See also ‘citation("pkgname")’ for
citing R packages.

#+end_example

Hope this helps,

Rainer



> 
> Thanks,
> 



- -- 
Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation Biology, UCT), Dipl. Phys.
(Germany)

Centre of Excellence for Invasion Biology
Stellenbosch University
South Africa

Tel :       +33 - (0)9 53 10 27 44
Cell:       +33 - (0)6 85 62 59 98
Fax :       +33 - (0)9 58 10 27 44

Fax (D):    +49 - (0)3 21 21 25 22 44

email:      Rainer@krugs.de

Skype:      RMkrug
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Re: Scientific papers related to Org-mode

[Bastien]

Hi Rainer,

Rainer M Krug <r.m.krug@gmail.com> writes:

> It just returns the citation.

Okay.  I've added this to the Worg FAQ:

* Is there a bibtex entry for the Org manual?

Yes.  Please evaluate this function and run =M-x
org-insert-manual-bitex-citation-at-point RET=.

#+begin_src emacs-lisp
(defun org-insert-manual-bitex-citation-at-point ()
  "Insert a Bibtex citation of the Org manual at point."
  (interactive)
  (insert
  "@book{dominik10:_org_mode_refer_manual,
  author =       {Carsten Dominik},
  title =        {The \pkg{Org-Mode} 7 Reference Manual: Organize
                  Your Life with GNU Emacs},
  publisher =    {Network Theory},
  year =         2010,
  address =      {UK},
  note =         {with contributions by David O`Toole, Bastien Guerry,
                  Philip Rooke, Dan Davison, Eric Schulte, and Thomas
                  Dye}
}"
  (message "Thanks for quoting the Org manual!")))
#+end_src

I don't think we need this in Org's core, but it's good to have it
somewhere.

Thanks!

-- 
 Bastien

Re: Scientific papers related to Org-mode

[Rainer M Krug]

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On 10/04/12 22:34, Bastien wrote:
> Hi Rainer,
> 
> Rainer M Krug <r.m.krug@gmail.com> writes:
> 
>> It just returns the citation.
> 
> Okay.  I've added this to the Worg FAQ:
> 
> * Is there a bibtex entry for the Org manual?

I would actually suggest:
* How can I cite org when I am using it for a publication?

Yes.  Please cite the manual. Evaluate this function and run =M-x
org-insert-manual-bitex-citation-at-point RET=.

> 
> Yes.  Please evaluate this function and run =M-x org-insert-manual-bitex-citation-at-point
> RET=.


> 
> #+begin_src emacs-lisp (defun org-insert-manual-bitex-citation-at-point () "Insert a Bibtex
> citation of the Org manual at point." (interactive) (insert 
> "@book{dominik10:_org_mode_refer_manual, author =       {Carsten Dominik}, title =        {The
> \pkg{Org-Mode} 7 Reference Manual: Organize Your Life with GNU Emacs}, publisher =    {Network
> Theory}, year =         2010, address =      {UK}, note =         {with contributions by David
> O`Toole, Bastien Guerry, Philip Rooke, Dan Davison, Eric Schulte, and Thomas Dye} }" (message
> "Thanks for quoting the Org manual!"))) #+end_src

Looks good.

> 
> I don't think we need this in Org's core, but it's good to have it somewhere.

I would actually put it into Org's core and also add it to the org - documentation menu, so that
it is easy to find and can easily be updated. In addition, a function in the FAQ needs to be added
manually, and I think a way to cite the manual should be in the product itself.

Cheers,

Rainer


> 
> Thanks!
> 


- -- 
Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation Biology, UCT), Dipl. Phys.
(Germany)

Centre of Excellence for Invasion Biology
Stellenbosch University
South Africa

Tel :       +33 - (0)9 53 10 27 44
Cell:       +33 - (0)6 85 62 59 98
Fax :       +33 - (0)9 58 10 27 44

Fax (D):    +49 - (0)3 21 21 25 22 44

email:      Rainer@krugs.de

Skype:      RMkrug
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Re: Scientific papers related to Org-mode

[Bastien]

Rainer M Krug <r.m.krug@gmail.com> writes:

> I would actually suggest:
> * How can I cite org when I am using it for a publication?
>
> Yes.  Please cite the manual. Evaluate this function and run =M-x
> org-insert-manual-bitex-citation-at-point RET=.

Please submit a patch for this.

(Clone Worg, edit it, then `C-x v =' to see the diff.)

>> I don't think we need this in Org's core, but it's good to have it somewhere.
>
> I would actually put it into Org's core and also add it to the org - documentation menu, so that
> it is easy to find and can easily be updated. In addition, a function in the FAQ needs to be added
> manually, and I think a way to cite the manual should be in the
> product itself.

Adding it to org.texi would be okay, please submit a patch.

Thanks,

-- 
 Bastien

Re: Scientific papers related to Org-mode

[Sebastien Vauban]

Hi Bastien,

Bastien wrote:
> #+begin_src emacs-lisp
> (defun org-insert-manual-bitex-citation-at-point ()
>   "Insert a Bibtex citation of the Org manual at point."
>   (interactive)
>   (insert
>   "@book{dominik10:_org_mode_refer_manual,
>   author =       {Carsten Dominik},
>   title =        {The \pkg{Org-Mode} 7 Reference Manual: Organize
>                   Your Life with GNU Emacs},
>   publisher =    {Network Theory},
>   year =         2010,
>   address =      {UK},
>   note =         {with contributions by David O`Toole, Bastien Guerry,
>                   Philip Rooke, Dan Davison, Eric Schulte, and Thomas
>                   Dye}
> }"
>   (message "Thanks for quoting the Org manual!")))
> #+end_src

Wouldn't it be David O'Toole instead?  I mean: with a normal (or forward, at
least) quote?

Best regards,
  Seb

-- 
Sebastien Vauban

Re: Scientific papers related to Org-mode

[Thomas S. Dye]

"Sebastien Vauban"
<wxhgmqzgwmuf-geNee64TY+gS+FvcfC7Uqw@public.gmane.org> writes:

> Hi Bastien,
>
> Bastien wrote:
>> #+begin_src emacs-lisp
>> (defun org-insert-manual-bitex-citation-at-point ()
>>   "Insert a Bibtex citation of the Org manual at point."
>>   (interactive)
>>   (insert
>>   "@book{dominik10:_org_mode_refer_manual,
>>   author =       {Carsten Dominik},
>>   title =        {The \pkg{Org-Mode} 7 Reference Manual: Organize
>>                   Your Life with GNU Emacs},
>>   publisher =    {Network Theory},
>>   year =         2010,
>>   address =      {UK},
>>   note =         {with contributions by David O`Toole, Bastien Guerry,
>>                   Philip Rooke, Dan Davison, Eric Schulte, and Thomas
>>                   Dye}
>> }"
>>   (message "Thanks for quoting the Org manual!")))
>> #+end_src
>
> Wouldn't it be David O'Toole instead?  I mean: with a normal (or forward, at
> least) quote?
>
> Best regards,
>   Seb
Aloha Seb,

Sharp eye!  I found this error in two places on Worg, both fixed now.
Thanks.

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

Re: Scientific papers related to Org-mode

[Karl Voit]

* Bastien <bzg@gnu.org> wrote:
> Hi Karl,
>
> Karl Voit <devnull@Karl-Voit.at> writes:
>
>> Is there any other important paper I missed?
>
> Check: http://orgmode.org/fr/org-mode-documentation.html

Bien sur, c'est formidable! :-)

Since the page is in french (only), I'd vote for creating a page on
Worg containing all papers relevant to Org-mode.

I'll start with the papers mentioned above and my short research
from the email before.

-- 
Karl Voit

Worg-page about Org-mode papers (was: Scientific papers related to Org-mode)

[Karl Voit]

* Karl Voit <devnull@Karl-Voit.at> wrote:
>
> I'd vote for creating a page on Worg containing all papers
> relevant to Org-mode.

http://orgmode.org/worg/org-papers.html

I'd love to link bib-files with every entry. Where should I put them
on Worg?

Some paths I can think of:

        code/bibtex/*
        org-contrib/bibtex/*

To allow navigational accessability for users interested in
Org-mode, I would link «org-papers» on [1] in the section «Dive
Deeper into Org-Mode». What do you think?

PS: If I violated any Worg convention, please feel free to refactor
my commit accordingly :-) 

  1. http://orgmode.org/worg/
-- 
Karl Voit

Linking bibtex on Worg (was: Worg-page about Org-mode papers)

[Karl Voit]

* Karl Voit <devnull@Karl-Voit.at> wrote:
>
> http://orgmode.org/worg/org-papers.html
>
> I'd love to link bib-files with every entry. Where should I put them
> on Worg?
>
> Some paths I can think of:
>
>         code/bibtex/*
>         org-contrib/bibtex/*

I placed it in «org-contrib/bibtex/».

Unfortunately I can not publish it. Can someone give me a hint,
where I am failing at?

In the Org-mode file, I've liked it with
    [[file:org-contrib/bibtex/Dominik2010.bib][bibtex]]
but http://orgmode.org/worg/org-contrib/bibtex/Dominik2010.bib does
not appear accessible on the server.

-- 
Karl Voit

Re: Linking bibtex on Worg

[Bastien]

Hi Karl,

Karl Voit <devnull@Karl-Voit.at> writes:

> * Karl Voit <devnull@Karl-Voit.at> wrote:
>>
>> http://orgmode.org/worg/org-papers.html
>>
>> I'd love to link bib-files with every entry. Where should I put them
>> on Worg?
>>
>> Some paths I can think of:
>>
>>         code/bibtex/*
>>         org-contrib/bibtex/*
>
> I placed it in «org-contrib/bibtex/».
>
> Unfortunately I can not publish it. Can someone give me a hint,
> where I am failing at?

You are not failing at anything, just the website publishing config
should be updated when there is a new area with specific attachments.

> In the Org-mode file, I've liked it with
>     [[file:org-contrib/bibtex/Dominik2010.bib][bibtex]]
> but http://orgmode.org/worg/org-contrib/bibtex/Dominik2010.bib does
> not appear accessible on the server.

Fixed, thanks.

-- 
 Bastien

Re: Scientific papers related to Org-mode

[Bastien]

Bastien <bzg@gnu.org> writes:

>> Is there any other important paper I missed?
>
> Check: http://orgmode.org/fr/org-mode-documentation.html

English: http://orgmode.org/org-mode-documentation.html
Spanish: http://orgmode.org/es/org-mode-documentation.html
Japanese: http://orgmode.org/ja/org-mode-documentation.html

-- 
 Bastien

Re: Scientific papers related to Org-mode

[Karl Voit]

* Bastien <bzg@gnu.org> wrote:
> Bastien <bzg@gnu.org> writes:
>
>>> Is there any other important paper I missed?
>>
>> Check: http://orgmode.org/fr/org-mode-documentation.html
>
> English: http://orgmode.org/org-mode-documentation.html
> Spanish: http://orgmode.org/es/org-mode-documentation.html
> Japanese: http://orgmode.org/ja/org-mode-documentation.html

Oh, cool.

Since the pages above are specific to Org-mode documentation, I do
think that the extra-Worg-page is still useful.

Maybe the documentation-pages can link the Worg-page so that there
is one central place to collect Org-mode related papers ...

-- 
Karl Voit

Re: Scientific papers related to Org-mode

[Bastien]

Karl Voit <devnull@Karl-Voit.at> writes:

> * Bastien <bzg@gnu.org> wrote:
>> Bastien <bzg@gnu.org> writes:
>>
>>>> Is there any other important paper I missed?
>>>
>>> Check: http://orgmode.org/fr/org-mode-documentation.html
>>
>> English: http://orgmode.org/org-mode-documentation.html
>> Spanish: http://orgmode.org/es/org-mode-documentation.html
>> Japanese: http://orgmode.org/ja/org-mode-documentation.html
>
> Oh, cool.
>
> Since the pages above are specific to Org-mode documentation, I do
> think that the extra-Worg-page is still useful.
>
> Maybe the documentation-pages can link the Worg-page so that there
> is one central place to collect Org-mode related papers ...

Sure.  Let's mention the most important references on orgmode.org (the
manual and the article about Babel), then list all references on Worg.

Thanks for taking care of this!

-- 
 Bastien