Re: Organizing and taming hectic Academia work (faculty viewpoint)? Tips or a good guides sought after :)

[John Kitchin <jkitchin@andrew.cmu.edu>]

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I guess you could say I use it to manage my references. E.g. I add
references using the functions in doi-utils.el. I can search them using
helm-bibtex (which is not part of org-ref, we just use it because it is
awesome), and from that I can see groups of references with keywords,
etc... helm-bibtex provides the "table"view I think you are referring to as
a helm selection buffer. Alternatively in org-ref you could use the older
reftex interface.

When I click on a cite link, there actions available to do things like
open the entry, find related articles, etc...

(org-ref-build-full-bibliography) allows you to build a pdf version of a
bibtex file pretty conveniently.

the jmax-bibtex.el file in org-ref provides additional functionality to
clean up bibtex entries, etc...

so, it is fair to say emacs+org-ref+helm-bibtex is how I manage my
references, and use them in writing.

John

-----------------------------------
Professor John Kitchin
Doherty Hall A207F
Department of Chemical Engineering
Carnegie Mellon University
Pittsburgh, PA 15213
412-268-7803
@johnkitchin
http://kitchingroup.cheme.cmu.edu


On Sat, Jun 13, 2015 at 3:06 PM, Xebar Saram <zeltakc@gmail.com> wrote:

> Hi list and John
>
> Thank you all for all the great advice i will start incorporating them
> into my daily workflow
>
> John: org-ref looks great but is it also used for "managing" you
> references? that is searching for entries, grouping by keys, exporting them
> to html, adding etc. does it have a "table" view or other? if not what do
> you use for managing your references?
>
> best
>
> Z
>
> On Fri, Jun 12, 2015 at 5:02 PM, Ken Mankoff <mankoff@gmail.com> wrote:
>
>> Hi Julian,
>>
>> On 2015-06-10 at 10:16, Julian Burgos <julian@hafro.is> wrote:
>> > a) I first write in org-mode. Export to Word, either exporting first
>> > to ODT and then to Word, or to LaTex and then use pandoc to convert
>> > LaTex to Word. My coauthor can edit the document as he wishes, using
>> > the "Track changes" option. Then, I transcribe their edits back into
>> > the org-mode document. Advantage of this approach: your coauthor
>> > receives a clean word file, that could include figures, references,
>> > etc., and he/she uses the tools she likes to edit the file.
>> > Disadvantage: you have to manually incorporate the changes to the
>> > org-mode file each time there are edits.
>> >
>> > b) I write the manuscript in org-mode. Then I send the org-mode file
>> > to my coauthor. Because the org-mode file is just a text file, my
>> > coauthor can use Word to edit it. I ask him/her *not* to use "track
>> > changes" and to save the edited version also as a text file. Then,
>> > when I receive it I use ediff in emacs to compare both documents and
>> > incorporate the edits I want. Advantage of this approach: the merging
>> > of the documents is easy using ediff. Disadvantage: your coauthor has
>> > to edit a weird-looking document, with markup, code blocks, etc.
>>
>> It seems like with a bit of extra (scriptable?) work you could remove
>> both disadvantages.
>>
>> Why can't you use method (a) above, and then DOCX -> Org via pandoc (with
>> --accept-all option)?
>>
>> I know pandoc introduce some of its own changes to the Org syntax but not
>> the document itself. You can get around this. You can remove the
>> pandoc-generated changes automagically so that only co-author changes
>> appear in Org format, which you can then use with your (b) above and emacs
>> ediff.
>>
>> Original: Your Org source
>> A: Org -> DOCX for co-authors (using pandoc)
>> B: Org -> DOCX -> Org (using pandoc).
>> C: A -> Org (using pandoc and --accept-all-changes)
>> D: B-Original
>>
>> The difference between B and Original are pandoc-introduced changes that
>> you do not want. Ignore/remove these changes from C, call it D and then the
>> difference between D and the Original are your co-author comments. Now your
>> authors can edit DOCX with Track Changes and you can work on those edits
>> with Emacs ediff.
>>
>>   -k.
>>
>>
>

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