How to write medical journal articles with org-mode

How to write medical journal articles with org-mode

[regcl]

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

Re: How to write medical journal articles with org-mode

[Jambunathan K]

regcl <regcl@channing.harvard.edu> writes:

> 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                                        |

You can do it in a single step with
`org-odt-preferred-output-format'. See

    (info "(org) Extending ODT export").

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

> 3) How do I get references into MS word?

You can use ODT Export with JabRef using ox-jabref.el.  You may want to
check whether the JabRef project has layout files that can create
citations in a format acceptable to Medical Journals.  (Search the list
reverse chronologically.)

Re: How to write medical journal articles with org-mode

[Erik Hetzner]

At Mon, 20 Jan 2014 02:54:08 -0500,
regcl wrote:
> 
> 
> 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 ;)
>
> […]
>
> 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.

Hi George,

For question 3, you might have a look at pandoc
(http://johnmacfarlane.net/pandoc/), which can convert from markdown
to docx (MS Word) with citation support. You might find it simpler to
export from org-mode to markdown and use pandoc to produce your docx
files, thus saving some steps above.

best, Erik

-- 
Sent from my free software system <http://fsf.org/>.

Re: How to write medical journal articles with org-mode

[regcl]

Erik Hetzner <egh@e6h.org> writes:

> At Mon, 20 Jan 2014 02:54:08 -0500,
> regcl wrote:
>> 
>> 3) How do I get references into MS word?
>> 
> Hi George,
>
> For question 3, you might have a look at pandoc
> (http://johnmacfarlane.net/pandoc/), which can convert from markdown
> to docx (MS Word) with citation support. You might find it simpler to
> export from org-mode to markdown and use pandoc to produce your docx
> files, thus saving some steps above.
>
> best, Erik

Hi Erik, Thank you for the suggestion.  

WRT this approach, I see that Rick Frankel has said ...

> From:	 Rick Frankel
> Subject:	 Re: [O] Org Table Export to Markdown Table Question
> Date:	 Thu, 09 Jan 2014 11:58:37 -0500
>
> > On 2014-01-08 15:41, Aric wrote:
> > I am trying to use org-mode now with R code in it to write
> > manuscripts. That does unfortunately mean that it must be eventually
> > exported to some doc format. I have been able to export to markdown and
> > everything looks good in markdown (even previewed on github) with the
> > exception of latex code which is not converted. However, using pandoc to
> > convert the markdown to docx, the tables are not converted properly (all
> > a single column).
> 
> I'm not sure why you are using markdown as an intermediate file
> format. Org will export to latex, pdf (via latex) and openoffice odt
> (which can be exported from open/libre office to doc/docx.).
> 
> Both the above exporters are much more mature that the markdown
> exporter.
> 
> rick
> 

... which makes me wonder... Has anyone out there tried this for a
journal manuscript with figures, tables, and citations?

If I want go with pandoc, would I be ahead to do ...

org > latex > pandoc > docx ?

Thanks, George

Re: How to write medical journal articles with org-mode

[Jambunathan K]

regcl <regcl@channing.harvard.edu> writes:

> org > latex > pandoc > docx ?

Too many moving parts.  Each part coming from different manufacturers.

The components will rub against each other and the resulting heat may
vaporize the lubricant.

Pick a workflow that has minimum dependencies - even if that means
throwing Emacs out the Windows.

Re: How to write medical journal articles with org-mode

[Erik Hetzner]

At Mon, 20 Jan 2014 14:04:24 -0500,
regcl wrote:
> 
> Erik Hetzner <egh@e6h.org> writes:
> 
> > At Mon, 20 Jan 2014 02:54:08 -0500,
> > regcl wrote:
> >> 
> >> 3) How do I get references into MS word?
> >> 
> > Hi George,
> >
> > For question 3, you might have a look at pandoc
> > (http://johnmacfarlane.net/pandoc/), which can convert from markdown
> > to docx (MS Word) with citation support. You might find it simpler to
> > export from org-mode to markdown and use pandoc to produce your docx
> > files, thus saving some steps above.
> >
> > best, Erik
> 
> Hi Erik, Thank you for the suggestion.  
> 
> WRT this approach, I see that Rick Frankel has said ...
> 
> > From:	 Rick Frankel
> > Subject:	 Re: [O] Org Table Export to Markdown Table Question
> > Date:	 Thu, 09 Jan 2014 11:58:37 -0500
> >
> > > On 2014-01-08 15:41, Aric wrote:
> > > I am trying to use org-mode now with R code in it to write
> > > manuscripts. That does unfortunately mean that it must be eventually
> > > exported to some doc format. I have been able to export to markdown and
> > > everything looks good in markdown (even previewed on github) with the
> > > exception of latex code which is not converted. However, using pandoc to
> > > convert the markdown to docx, the tables are not converted properly (all
> > > a single column).
> > 
> > I'm not sure why you are using markdown as an intermediate file
> > format. Org will export to latex, pdf (via latex) and openoffice odt
> > (which can be exported from open/libre office to doc/docx.).
> > 
> > Both the above exporters are much more mature that the markdown
> > exporter.
> > 
> > rick
> > 
> 
> ... which makes me wonder... Has anyone out there tried this for a
> journal manuscript with figures, tables, and citations?
> 
> If I want go with pandoc, would I be ahead to do ...
> 
> org > latex > pandoc > docx ?
> 
> Thanks, George

Hi George,

pandoc has very rich citation citation support, much better than
org-mode as far as I know. If you are exporting to LaTeX you can use
BibTeX or BibLaTeX which of course work well, but pandoc can handle
citation export to docx, odt, etc. using any citation style supported
by citeproc.

The problem is that org-mode exports tables in markdown as HTML
tables, not pandoc tables. It should be possible to modify the ox-md
exporter to support pandoc tables, but it looks a little tricky.

pandoc’s standard input is markdown, so you’re probably best sticking
with that, but you might be able to get org -> latex -> pandoc -> docx
to work.

best, Erik

-- 
Sent from my free software system <http://fsf.org/>.

Re: How to write medical journal articles with org-mode

[Aric]

Jambunathan K <kjambunathan <at> gmail.com> writes:

> regcl <regcl <at> channing.harvard.edu> writes:
> 
> > org > latex > pandoc > docx ?
> 
> Too many moving parts.  

I agree. I tried this with a relatively simple export, albeit with tables and
figures and references,  and pandoc choked on the latex and I was not
able to figure out what the problem was.  

> Pick a workflow that has minimum dependencies - even if that means
> throwing Emacs out the Windows.

For collaboration it is actually easier to do just that. Keep all of your R
files and latex files in the directory and pound out the draft in odt/doc. 

Now trying org as a 'master' document to hold the latex (only tikz, no
other reason to use at this point) and R code.  I can easily produce draft
documents in odt -> doc for collaborators. The challenge will be the
references on a unix computer. For mac and windows I don't think it is
a problem at that point. 

A 'more mature' markdown exporter would help for medical writing.

Aric