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Workflow on Mac (Mountain Lion) for PhD Thesis

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Posted by Peter
Aug 14, 2012 at 05:48 PM


Thanks Steve, this is very helpful! The export feature you mention for Scrivener would certainly give it an advantage.

Just a quick update on how I see my workflow coming together, and a few questions:

Reference management/Annotation of PDFs
For now I will settle for Zotero but I am looking for reference manager that can sync with a shared folder such as dropbox. I believe Sente does this but I’ve been unable to find a way to export/sync my reference/PDFs from Zotero. Any advice here is helpful.

Data Management
Here I have settled on DevonThink, although Tinderbox is a strong contender.

Rather than using Circus Ponies Notebook, I am going to stick with Scrivener and a mind-mapping program. For notes I think I will try Notational Velocity or just create them inside DT.

On the Back Burner


Posted by Stephen Zeoli
Aug 15, 2012 at 10:51 AM


Peter wrote:
> Thanks Steve, this is very helpful! The export feature you mention for Scrivener would certainly give it an advantage.

This Tinderbox feature was hinted at on the Scrivener forum (I believe). There seems to be a lot of communication and cooperation between the two developers, so I am hopeful this is indeed in the works.

For me, one of the biggest drawbacks of Tinderbox remains its arcane (to me, anyway) export functionality. I’ve even had a communication with Mark Bernstein (the developer) about it and he assures me it is easy, just a matter of creating some export templates. Still, I can’t quite get my head around it. Fortunately, it is pretty easy to export to plain text and I can usually make do with this. Still, a dedicated Scrivener export would be brilliant and make the two applications a perfect match.

Steve Z.


Posted by Hugh
Aug 15, 2012 at 01:59 PM


A word about Tinderbox: although Tbx can be used for data management, such a use wouldn’t be playing to its strengths. In a workflow, I think it’s best used for either “creating by jotting down random notes to see what they add up to” or “analysis of what already exists to get a firmer handle on it”. But I think it does already successfully export to Scrivener - at least there’s a template in its file menu to allow it to do so, and I seem to remember a recent dialogue in the Tinderbox forums on this subject (do a Search on the term “Scrivener”).

Incidentally, Steve Z.‘s blogs on Tinderbox provide the quickest route I know (and I’ve done all the the tutorials, and I mean all!) to getting a decent grounding in the app.

A relatively cheap and simple mind-mapping programme for the Mac is MindNode Pro: http://mindnode.com/#!/mac. It exports via OPML to Scrivener.

A word about DevonThink. It’s a magnificent application, but you have to get used to its quirks. Personally, I wouldn’t tag anything that I index or import into it; tagging complicates what you can do, and in the DevonThink context it has a slightly special meaning and takes a while to learn and understand. The other methods of finding documents in DT, or filing them away in the first place are sufficiently sophisticated that you don’t really require tagging (although plenty of people would disagree with that). Personally also I would start off by importing rather than indexing, again for reasons of keeping everything simple. With indexing, you have two databases to worry about - the Finder’s and DevonThink’s own; with importing, effectively only one. You can always re-export what you’ve imported, and then index, when you’ve got the hang of the application. (Again, others may disagree.) And I certainly wouldn’t mix both importing and indexing, at least to begin with.

I imagine that DT Pro would be enough for your purposes, unless you plan to scan material in, when DTPO would useful.

Generally Scrivener, Tinderbox and DevonThink do all play very well together. Good luck!


Posted by Hugh
Aug 15, 2012 at 06:16 PM


Peter wrote:
>I would be interested in
>posts that detail the challenges and promises as one navigates, imports-exports
>(and when) across such tools in their workflow!
> >Cheers,

I’ve never written a thesis as such, but I have written various long-form factual pieces. This is the sort of workflow I recommend (distilled from the advice of many others):

Structuring > Drafting > Formatting/polishing, plus Data Managing and Storage, Citing and On-the-fly Note-taking:

- Structuring: Tinderbox, OmniOutliner Pro, Neo, or a mind-map programme (apart from MindNode, there are several others including NovaMind, MindManager for the Mac and the new/old champ, Inspiration). Curio is excellent as a virtual whiteboard, but better for fiction than fact (as are SuperNoteCard and Blake Snyder’s Save the Cat software - though I’d love to try using it for a dissertation!). Scrivener’s outliner plus corkboard is also a candidate. Export via OPML to…

- Drafting: Scrivener. Export via Scrivener’s .rtf or .docx exporters to…

- Formatting/polishing: MS Word (better on Windows than the Mac), or, on the Mac, Nisus Writer Pro or Mellel (both of them favourites with academics, so I’m told). I don’t think Apple’s Pages is regarded as appropriate for academic use.

- Data Management and Storage: DevonThink (best for large volumes of data, and for filing, searching and simply getting the data in), Eaglefiler or Together. DT seems to be the choice of academics.

- Citing: Bookends, Zotero, EndNotes, Sente etc. It’s well-worth consulting the Scrivener forum for this: there are several threads on this topic and posters there who’ve recently finished their dissertations, and as far as I can see Bookends and Endnotes are their favourites. Whatever you use, it needs to play well with Scrivener. I should also experiment.

- On-the-fly Note-taking: my favourite is nvAlt too (although there’s a Scrivener scratchpad).

There’s a running debate about how, in the middle of drafting a thesis with Scrivener, you send individual chapters to your supervisor, and then receive back comments and embody any amendments demanded. It’s well written up in several threads on the Scrivener forums. Some people evidently round-trip Scrivener > Word > Scrivener, and some even apparently manage to “sell” Scrivener to their supervisors. But others make major supervisor-induced changes in Scrivener using its dual-editor feature, and then move over entirely to Word (or equivalent word processor) for final detail and polishing. For these purposes, MS Word’s “Track Changes” and “Comments” are powerful features, although Scrivener has two types of comments and footnotes and I’ve read that Word “Comments” can be imported into Scrivener; personally I’ve never tried to do this.

I hope all this is useful.


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



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.


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