From mboxrd@z Thu Jan  1 00:00:00 1970
From: regcl <regcl@channing.harvard.edu>
Subject: How to write medical journal articles with org-mode
Date: Mon, 20 Jan 2014 02:54:08 -0500
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I am looking for advice regarding how to write medical journal
articles using org-mode.

My primary motivations are the desire to ... automate the flow of data
from computation to publication, avoid clerical errors, speed up the
conversion of computational results to manuscript, and do 99.9% of my
typing in emacs ;)

My primary computation platform is linux clusters with OS X desktops.
I have used org-mode for project management and HTML export of
provisional computational results in working papers for ~1 year.

I recently started using org-mode/babel/ESS/R to export computation
results to HTML.

It looks like the medical journals require MS word submissions.  I
have used the scheme shown below to get MSword to/from my
collaborators for comments & corrections ...

doc.org----------------------------------+
|                                        |
v                                        |
M-x org-odt-export-to-odt                |
|                                        |
v                                        | 
Open office                              |
|                                        |
v                                        |
MS Word                                  |
|                                        |
v                                        |
doc.docx                                 |
|                                        |
v                                        |
colaborator                              |
|                                        |
v                                        |
doc.docx                                 |
|                                        |
v                                        |
/http://docx2txt.sourceforge.net/        |
|                                        |
v                                        |
doc.docx.txt                             |
|                                        |
v                                        |
ediff<-----------------------------------+  
|
v
doc.org

I am hopeful of using a similar approach for journal submission, but I
need references. I have endnote, and have used it a bit, but I feel
like I would be happier using ...

https://github.com/wash/pubmode 

... for bibtex pubmed search results + reftex + org-mode as reference
manager. I have experimented with this approach to feed references
into HTML via ox-bibtex.el and it looks encouraging.

So here are my questions...

1) Has anyone out there used org-mode to produce medical journal
articles (other than demonstration of reproducible research)?

2) I am mystified by all of these org-reftex-... functions.  Can
someone please point me to an overview of how to use
bibtex/reftex/orgmode/emacs/etc as reference manager?

3) How do I get references into MS word?

Any other comments or suggestions would be most welcome.

Many thanks,
george