From mboxrd@z Thu Jan 1 00:00:00 1970 From: John Kitchin Subject: Re: Organizing and taming hectic Academia work (faculty viewpoint)? Tips or a good guides sought after :) Date: Sat, 13 Jun 2015 15:52:54 -0400 Message-ID: References: <7e093509.51e.14ddb300091.Coremail.chxp_moon@163.com> <161f0a5020b2f36c40a1e82a8af79089.squirrel@webmail.hafro.is> Mime-Version: 1.0 Content-Type: multipart/alternative; boundary=047d7b6d8d960e383205186b923e Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:40566) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1Z3rUA-0003PO-7b for emacs-orgmode@gnu.org; Sat, 13 Jun 2015 15:52:59 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1Z3rU8-0003r6-A2 for emacs-orgmode@gnu.org; Sat, 13 Jun 2015 15:52:58 -0400 Received: from mail-pa0-x231.google.com ([2607:f8b0:400e:c03::231]:34685) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1Z3rU7-0003qt-VN for emacs-orgmode@gnu.org; Sat, 13 Jun 2015 15:52:56 -0400 Received: by pacgb13 with SMTP id gb13so10725431pac.1 for ; Sat, 13 Jun 2015 12:52:54 -0700 (PDT) In-Reply-To: List-Id: "General discussions about Org-mode." List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: emacs-orgmode-bounces+geo-emacs-orgmode=m.gmane.org@gnu.org Sender: emacs-orgmode-bounces+geo-emacs-orgmode=m.gmane.org@gnu.org To: Xebar Saram Cc: Julian Burgos , emacs-orgmode , windy , Ken Mankoff , Holger Wenzel --047d7b6d8d960e383205186b923e Content-Type: text/plain; charset=UTF-8 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 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 wrote: > >> Hi Julian, >> >> On 2015-06-10 at 10:16, Julian Burgos 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. >> >> > --047d7b6d8d960e383205186b923e Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
I guess you could say I use it to manage my refe= rences. E.g. I add references using the functions in doi-utils.el. I can se= arch them using helm-bibtex (which is not part of org-ref, we just use it b= ecause it is awesome), and from that I can see groups of references with ke= ywords, etc... helm-bibtex provides the "table"view I think you a= re referring to as a helm selection buffer. Alternatively in org-ref you co= uld use the older reftex interface.

When I click on a cite lin= k, there actions available to do things like=C2=A0 open the entry, find rel= ated articles, etc...

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

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

so, it is fair to say emacs+o= rg-ref+helm-bibtex is how I manage my references, and use them in writing.<= br>

John

---= --------------------------------
Professor John Kitchin=C2=A0
Doherty= Hall A207F
Department of Chemical Engineering
Carnegie Mellon Univer= sity
Pittsburgh, PA 15213
412-268-7803

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

T= hank 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 fo= r entries, grouping by keys, exporting them to html, adding etc. does it ha= ve a "table" view or other? if not what do you use for managing y= our references?

best

Z

On Fri, = Jun 12, 2015 at 5:02 PM, Ken Mankoff <mankoff@gmail.com> wro= te:
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 b= ack 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 "tra= ck
> 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<= br> > of the documents is easy using ediff. Disadvantage: your coauthor has<= br> > to edit a weird-looking document, with markup, code blocks, etc.

It seems like with a bit of extra (scriptable?) work you coul= d 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 t= he document itself. You can get around this. You can remove the pandoc-gene= rated changes automagically so that only co-author changes appear in Org fo= rmat, 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 yo= u do not want. Ignore/remove these changes from C, call it D and then the d= ifference 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 wi= th Emacs ediff.

=C2=A0 -k.



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