Re: how do scientists use org mode?

[tsd@tsdye.com (Thomas S. Dye)]

Aloha Chris,

There is a tutorial of sorts on LaTeX export.  It includes information
on how to use bibtex with Org mode.

http://orgmode.org/worg/org-tutorials/org-latex-export.html#sec-17

Eric Schulte has written some elisp helpers for managing bibliographies
in Org mode.  I believe this is in the contrib directory of the Org mode
distribution. 

All the best,
Tom

Christopher W Ryan <cryan@binghamton.edu> writes:

> Ah, now I'm beginning to understand: I can export a *part* of an
> org-mode file; I'm not limited to exporting the whole thing. Cool!
>
> I also use bibtex/biblatex a lot. I've started to read that these
> tools work with Org-mode also. Can anyone speak to that from
> experience?
>
> Thanks.
>
> --Chris
>
> On Mon, Jan 30, 2012 at 2:51 PM,  <cberry@tajo.ucsd.edu> wrote:
>> "Christopher W. Ryan" <cryan@binghamton.edu> writes:
>>
>>> I'm fairly experienced with emacs, ESS, Sweave, and R, but I've only
>>> started to dabble in Org mode in the past couple of weeks. Just as
>>> Christoph is, I'm trying to decide whether/how Org-mode might be useful
>>> in organizing and carrying out research projects, presentations, etc. So
>>> this thread has been very useful and timely.
>>>
>>> I'm trying to envision what a small research project, managed via a
>>> single Org file, might look like. There would be notes from meetings,
>>> thoughts from brainstorming sessions, scheduled appointments, data, R
>>> code, R output, and manuscript/presentation prose. Some of this might be
>>> destined for a manuscript, some for a beamer presentation, and some only
>>> for "internal consumption." How are all these pieces differentiated in
>>> the Org file, so that Org knows what to put in the
>>> presentation/manuscript, and what not to? Could anyone share or point to
>>> a short, perhaps fictional, example?
>>
>> Have you looked at
>>
>>     http://orgmode.org/worg/org-contrib/babel/uses.html
>> ??
>>
>> There are almost too many possibilities --- it is a bit overwhelming.
>>
>> Here are three things I find useful:
>>
>> 1) The ability to export a subtree allows you to have many documents
>> within the *.org file. Setting EXPORT_* properties for the subtree gives
>> you a lot of flexibility. And it is easy to do with TAB completion to
>> prompt you to fill in the needed pieces.
>>
>> 2) Internal hyperlinks are really useful in staying on course in a big,
>> complicated document.
>>
>> 3) Noweb syntax allows you to mix and match different parts of the
>> document. Below is a minimal example. The latex chunks can be used
>> anywhere I need them. Navigating to '* mini report' and typing
>>
>>         'C-c @ C-c C-e l'
>>
>> produces mini.tex.
>>
>>
>> ,----
>> | * COMMENT latex chunks
>> |
>> | #+name: chunk1
>> | #+begin_src latex
>> |   \begin{displaymath}
>> |     y = r\sin\theta
>> |   \end{displaymath}
>> | #+end_src
>> |
>> | #+name: chunk2
>> | #+begin_src latex
>> |   \begin{displaymath}
>> |     x = s\cos\theta
>> |   \end{displaymath}
>> | #+end_src
>> |
>> |
>> | * mini report
>> |   :PROPERTIES:
>> |   :EXPORT_FILE_NAME: mini.tex
>> |   :EXPORT_TITLE: Minimal Report
>> |   :EXPORT_AUTHOR: Mister CCB
>> |   :END:
>> |
>> | #+begin_src latex :noweb yes
>> | <<chunk1>>
>> | <<chunk2>>
>> | #+end_src
>> `----
>>
>> HTH,
>>
>> Chuck
>>
>>>
>>> Thanks very much.
>>>
>>> --Chris
>>
>> [snip]
>>
>> --
>> Charles C. Berry                            Dept of Family/Preventive Medicine
>> cberry at ucsd edu                          UC San Diego
>> http://famprevmed.ucsd.edu/faculty/cberry/  La Jolla, San Diego 92093-0901
>>
>>
>
>

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