Re: how do scientists use org mode?

[Christopher W Ryan <cryan@binghamton.edu>]

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
>
>