Workflow on Mac (Mountain Lion) for PhD Thesis

Posted by jamesofford
Aug 16, 2012 at 12:23 PM

Peter:

In looking at your later postings it looks like your approach is coalescing around a useful set of tools.
I don’t use Zotero, but I tried it out. It is a great piece of software. If I wasn’t running Papers 2, I would probably use it. Indeed, before the guys at Mekentosj released v 2 of Papers, I was looking at dropping the program and moving to Zotero.
Devonthink is also a good choice. You asked in an earlier posting how I use it, whether I export stuff from Devonthink, or just work within the program. I have tried exporting, but only to see what it can do. I use Devonthink on its own. I use it mostly for storing stuff I don’t want to lose. My databases have all kinds of stuff in them. Snippets from the web. Notes I have written. Copies of emails. I use it as an all purpose storage bin. I also use the collections functions to organize stuff. The easiest way is with a smart collection. Setup the smart collection, and whenever something goes into Devonthink that meets the criteria, it goes in there. Also being able to index individual folders is nice. Dump stuff into specific folder, run the index in Devonthink and presto-material is loaded in.
I don’t do much outlining(kind of an odd admission for someone who reads this group every day). I do use an outline if I am writing something like a paper or grant. In that case I usually do it with pen and paper first, then enter it either into Word, or sometimes I’ve used Notetaker. I am trying to get more in the swing of using Notetaker routinely.
As I said, I use Word when I write. This is mostly for two reasons. First, I have used Word since it was a DOS program, and I am comfortable with it. It’s big and bloated, but I know how it works. Second, it’s the standard. Journals want manuscripts submitted in Word format. Granting agencies want grants submitted in Word format. Exchanging documents with my colleagues I know they all have Word-either the Windows version or the Mac version. My university supplies either the Windows version or the Mac version for a substantial discount.
Still, the first draft of pretty much everything is done with pen and paper. My post-doc boss told me that I would never get anywhere until I learned how to compose on the computer. Well, I never managed it. And I have still been able to have a career in science, both industrial and academic.
Good luck.
Jim