Workflow on Mac (Mountain Lion) for PhD Thesis

Posted by Dellu
Nov 7, 2012 at 01:40 AM

Hi Peter and Steve
I found your posts quite brilliant and helpful. I am also starting up my phd in linguistics, exactly in Peter’s situation. I tried almost all the apps you guys mentioned. Here are my observations so far.

1. I use Mendely for some preliminary works; to collect and rename my PDF files into a Dropbox folder. it is not the best reference manager; has a lot of flaws specially for Latex. But, the Watch Folder and Rename features are really helpful to cleanup my computer. I drop all my newly downloaded files into a dedicated folder, then Mendeley automatically sucks the papers in it, recognizes the metadata, rename and put it in another folder in dropbox. All my 2000 articles are beautifully renamed by Author-year-title format; easy to search them in Spotlight (alfred).
2. Bibdesk and Jabref are good enough for bibliography (I also don’t like Zotero), for Latex. But I use Papers for its Magic Manuscripts feature (amazing).
3. Devonthink is indispensable for its artificial intelligence; recommends related papers.
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4. Tinderbox is too complex. Plus, it has limited capability to import various file formats. I tried to import word files and Scrivener documents. It rips of the images in the files. It is poorly integrated with other applications, generally; seems to work best only with text files. Exporting to other format is also equally messy in Tinderbox.

5. There is one crucial feature that the Circus Ponies Notebook offers that all other note-taking applications, except Microsoft OneNote, don’t. The ability to tag (mark) points deep inside the text. When I am writing a long note, I always want some way of tagging some key points that I want to remember latter. All the note-taking tools could tag files, but never bullet points, or paragraphs. Notebook and OneNote can do that. It is called Keywords in the former and tags in the latter applications. Notebook also has a MultiIndex system, another way of finding your crucial points using keywords. If you like tagging your specific points in your extended notes, I think, there is a reason to use Notebook. I still am not satisfied how Notebook syncs with Devonthink. But, I think there is not better note-taking app right now, unless you want to use Scrivener for everything. Here is a good article on the difference between Scrivener and Notebook, http://www.organizingcreativity.com/2012/02/outliner-in-scrivener-vs-outliner-in-cpn-structure-scrivener-vs-content-cpn-outlines/.
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I am not still satisfied about the workflow; the sync between Devonthink and Notebook is so clumsy.

have you guys (specially Peter) developed a good workflow yet? Can you update us if you have come up with better solutions with the general workflow?