December 12, 2013

emacs org-mode as outliner, bibliography and citation manager - working with zotero too

Well, for now I have regretfully given up on docear for writing papers - although it fantastic to be able to mindmap your ideas and citations, it still leads you into a dead-end when you want to actually get your paper finished - sadly, the export functions are not very pretty and you don’t get the actual citations in the export.

I have taken the plunge with emacs org-mode. Yes, emacs and orgmode are pretty frustrating for the first couple of days, but you get:

  • the only outliner which is better than Microsoft Word’s outline view, so while it isn’t mind-mapping, it isn’t far off
  • an insert citation” window which is way cleaner and more stable than, say, the zotero plug-in for your favourite word processor
  • plain text source documents so in the very worst case you aren’t going to end up with your work lost in some crashed .docx blob (looking at you, Word)
  • the ability to do lovely flowcharts and diagrams with the graphviz plugin
  • interact with R and other languages and include your results using ESS
  • most importantly, export to pdf via latex, beamer presentations, .odt, even to freemind mindmap format
  • it is emacs and orgmode, so it can make your tea and do your laundry for you too, really.

So my workflow is this:

  • Use PDFXchange to highlight and make notes. Why PDFXchange? Your highlighted passages can be read by zotero (see below) (and also by docear but this is not important for me now)
  • Use zotfile plug-in for zotero to extract the notes (you can do a whole folder-full of documents at once though that might take a while)
  • Use the zotero auto-exportplug-in to automatically export your entire library (or (sub)-collection) to a .bib file. I have this set up to export automatically as soon as I make any changes - though this might overheat your computer if you have a real lot of references, say over 1000
  • Write your paper in orgmode and tell it use the exported .bib file for its bibliography
  • Use the RefTeX functionality in orgmode to insert citations - it helpfully notices if your .bib file has been updated and reloads in an instant. From RefTeX you can see and if you wish copy your annotations too. Zotfile even includes the page numbers.
  • Export and feel proud.

reproducibleResearch zotero nerdvana


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