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Workflow on Mac (Mountain Lion) for PhD Thesis

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Posted by Stephen Zeoli
Aug 13, 2012 at 11:21 AM


Peter wrote:
>Steve, the point about tagging outside of DevonThink is that DT only searches within it’s database, not the drive(s). With a simple tagger app Spotlight (like Windows Search) can be used to narrow searches outside of DT. Tagger (and I suppose Tags) also permits Boolean searches. I guess it’s a bit like advanced googling for your computer.

You can “index” files using DevonThink, which means DT will have an avatar like item in its database that is a link to the actual file outside that database. You can then create tags and add Spotlight comments right within DT. Indexing is a piece of cake. Just use the Index command from under the File menu and then select the folders you want to Index.

I just Indexed a folder of Scrivener projects as a test. Here’s a screenshot of what I got:


There’s a tutorial for doing this, which you can access under the “tutorials” listing of the Help menu. The tutorial is called Importing Data.

Anyway, I’m not necessarily saying this will be more effective than having a separate tagging program, but if it works to your satisfaction it will have to be a simpler solution if you’re already using DT for other information chores.

Steve Z.


Posted by Peter
Aug 13, 2012 at 12:30 PM


Hi Steve,

Thanks! Looks like it must be possible. I must admit I haven’t started using DT yet but fascinated by what I hear/see. Unfortunately there are very few screencasts of it being used in action, a bit strange given it’s popularity. The DT tutorials are okay but the narrator has an annoying “marketing’ kind of tone that puts me off. About the only thing I’ve found, along these lines, is this: http://www.youtube.com/watch?v=UH2L6WSA0UY - but it’s from 2009. If you ever felt like doing a screencast of how you use it I would be an eager audience! (Here I can recommend the free app Jing http://www.techsmith.com/jing.html.

One question I have is how you distinguish/integrate your workflow across different apps like DT and other things like Tinderbox, Scrivener. In other words, the importing and exporting and flow of information (keeping in mind the different file formats). Do you start with TBX first or DT or perhaps S or a mind mapping? Does this different for the kind of project you have in mind (like a thesis hint hint)?

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!



Posted by jamesofford
Aug 13, 2012 at 01:42 PM


It’s been many years since I wrote my dissertation. So many that none of the programs that you mention were available. I suspect that the people who wrote them may not even have been born when I was in Grad School. Indeed, I was one of the first people in my department to write my dissertation on a computer. I used Microsoft Word. Not the Windows version or the Mac version-the DOS version.
However, I have stayed in the business since then. First as a Post-Doc, and then as a researcher at a pharmaceutical company. Now I am back in academia.
In each of those different jobs I have had a similar set of tasks to the ones that you have. Assemble information. Put it someplace I can find it when I need it. Come up with a way to write about it. Come up with a convenient way to cite it when I write. This is an unending set of tasks that will always be there.
You will probably find that any system that you come up with is unique to you. Try a few things. If they help, keep using them. If they don’t, dump them. Don’t worry about what has worked for someone else. We all think and work differently. That being said, it is always good to have someone say “I tried program X and it worked to do Y.” If you need to do Y, then give it a try. But just because someone else found it useful, that doesn’t mean that you will. You found your way to a good place here. The people here have tried a lot of different things and write about them. Good place to find stuff to use.
What I have found works for me is four things. Devonthink Pro Office. Papers. Evernote. Endnote.
I use Devonthink for keeping a lot of the junk that I accumulate in a kind of order. I have a series of folders that Devonthink watches over and from which it sucks files. I have sets of smart collections and sets of manual collections that things get put into as well as some databases that just have stuff in it. Papers is invaluable to me for dealing with PDFs. Up until version 2 it wasn’t that useful. Now it does most of the things I need. Highly recommended. Evernote is what I use for sharing stuff that I find with others. I could use Devonthink for this, but Evernote is easier and cross-platform. Finally Endnote. I don’t really like Endnote, but it is the standard when it comes to sharing bibliographies and when you are writing.
Oh, I should also add, I use a Mac. Not that I have any sort of dislike of Windows machines. The software above runs on Macs, so I use a Mac. Also, I do my first drafts with pen and paper, then move them to the computer.
Finally a comment about writing-Just write.  I found that the hardest part of the dissertation was simply sitting down and entering the words. I’ll leave you with a quote from E. L. Doctorow: Planning to write is not writing. Outlining, researching, talking to people about what you’re doing, none of that is writing. Writing is writing.

Good luck.


Posted by Peter
Aug 13, 2012 at 03:02 PM


Jim, thanks for those words of wisdom. It’s easy to get carried away with all the new tech out there. By and large I’ve felt my current workflow is sufficient for smaller projects (mainly Word and textedit) but the thesis has me a bit concerned. So many good ideas written down, but where did I put them? With my dissertation deadline approaching I’ve frozen a bit, like a dear in the headlights. I thought I would take another dip into the sea of apps after a few years of abstinence.The pencil and paper are under-estimated, so thanks for the reminder. My problem is that I tend to loose them.

A question about your use of DT: do you export anything when writing or just leave it all your DT databases for inspiration? (You didn’t mention what word processor you use.) I wonder because I’m still a little unclear how best to integrate it into my process. I’m pretty clear now on the reference management, outlining/word-processing bits.

BTW I was a diehard Windows guy up to this past year and then finally broke down and got a Mac. I have Parallels with Win 7 installed as but its really more of a security blanket than anything else as I make the transition.


Posted by Stephen Zeoli
Aug 14, 2012 at 11:37 AM



Have you read Steven Berlin Johnson’s article about how he uses DevonThink? It’s insightful:


If you haven’t explored its export capabilities, you’ll find that it is extremely easy to export data from DT for use in Scrivener.

Regarding Tinderbox, I find it a great resource when I feel a little lost in my data. You can use it to create a road map of your project, and not even worry about putting any of your research in it. (Note: I’ve never had a project as research-heavy or rigorous as a Ph.D. thesis, so I can’t comment about how all these tools work when you delve into a job like that.) Tinderbox can now import a Scrivener project directly, which is nice; but it will be especially nice when and if the promised export TO a Scrivener project is ready. That will make for Tinderbox/Scrivener nirvana.

Steve Z.


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