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Academic Workflow (Revisited) (Read 26244 times)
Mark Cubberley
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Re: Academic Workflow (Revisited)
Reply #15 - May 20th, 2009, 1:35pm
 
Quote:
As you mull over the interrelations of applications, just keep in mind that getting back to the original document, citation, etc., for me at least, is pretty important. No need to move stuff into an application if you don't intend to manipulate it there, but if you want to refer to it, how can you make that happen?


Getting back to the original document is important to me as well.  It's easy enough to create a link between TBX and Bookends.  (Dragging and dropping a citation in Bookends into TBX while holding option and command creates a note in TBX that has the article title as the name with an associated URL to the article citation in my local Bookends database.)  If this note is a container for my highlights and annotations, it would seem to be possible to use an agent in TBX to attach this Bookends URL to any notes in this container.  In this way, I could manipulate quotes and annotations in TBX without losing their source.

I'm guess I'm curious about your own workflow, Charles (or anyone else's for that matter).  If you could elaborate a bit on your moving pieces (Skim, TBX, DEVONThink, etc.) and how you translate/organize information, thoughts, etc. from one to another (using Applescript, if needed), I think this would be helpful.  (This could happen outside of this forum if more appropriate.)  I've been leaning on Mark A.'s expertise for the mechanical side of things, but I'm willing to explore Applescript if needed.  (I definitely need to delve more into TBX's syntax as well.)

Mark
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Jean Goodwin
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Re: Academic Workflow (Revisited)
Reply #16 - May 20th, 2009, 11:31pm
 
Hi, Mark:  Looking back at your original post, I was struck by your wish to turn from a "product" to a "process" writer.  That's a pretty good summary of the main message of Robert Boice's Professors As Writers--the best book on academic productivity I've ever come across.  It doesn't tell you how to write well--it just tells you, write!  Get stuff down on paper!  Worry about it later!

Anyhow, I suspect from everything you've said that you have a very well-developed workflow already going, with good habits of note-taking, bibliography building etc.  (Better than me, at least;  I'm lazy about adding citations to my database.)  One possibility would be to use Tinderbox to help you turn these good habits just a few degrees towards more "process."

For example, let's assume that the Skim-to-Tinderbox technique is perfected.  That's cool!  As you use Skim to mark up an article, maybe some vague or specific or utterly innovative idea occurs to you about your own projects.  Since you're in Skim anyhow, capture the idea as a note, and include some tag along with it--like
•BigIdea
After you pour your Skim notes into Tinderbox, you can easily search for the tag and harvest these idea notes.  (That could be automated too, if you find you're doing it regularly.*)  Stick all of them in a container, and start playing with them--in map or outline view, depending on your style.  Find bits of order, and write more notes to glue the bits together.

In the long run, 90% may be useless, and the process won't produce great prose.  But it could produce the vital first rough draft of a few pages, without much more work than you're doing now anyways.

Good luck!

*(p.s.) The "smart" adornments new to 4.6.3 are going to make this very easy.
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« Last Edit: May 20th, 2009, 11:48pm by Jean Goodwin »  
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Charles Turner
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Re: Academic Workflow (Revisited)
Reply #17 - May 21st, 2009, 2:05pm
 
Hi Mark-

Well, Jean had a great response. I don't think my response will be as useful as hers...

One issue your post brings up for me is, and this is not directed to you in particular, how many folks are obsessed with linkages to citation managers like EndNote, Bookends and Sente. I just don't see what they bring to the table concerning a view of your content. At best, they relate about 6 items of information to a PDF. I think if academics weren't so attached to MS Word-like text processing, these applications wouldn't have much traction.

Bookends is a well maintained product, but hard to reorganize. The Sente folks seem a bit too flaky for my taste. As I'm committed to Latex, BibDesk is a far better choice due to its Applescript-ability.

My current work with Tbox concerns a database of about 5000 newspaper articles that mention 5 different people. It's for my dissertation, and the information is both factual and critical. It's a perfect "bottom-up" kind of project, trying to discover relationship and significance in the material.

The articles are in a DEVONthink database as OCR'ed PDFs, and I have an Applescript that will export Skim hilites as text with the DTPO link included. So I read and hilite the material in Skim, then export text that goes into Tbox. The link allows me to refer back to the DTPO source whenever I'd like.

My script isn't very automated, much less sophisticated than what Mark A. has been working on. The OCRs, plus a multicolumn format, are just too messy to script reliably. So I post-process a bit in TextMate and Tbox. I see this as another opportunity to make contact with the material, and I find it quite useful.

I've been titling my notes, which correspond to a newspaper article apiece (ie no "exploding"), with really long display names. Effectively, the name encapsulate about 4-5 Tbox attributes, and I may convert them. But right now they are really informative about the content of each article, and they are tremendously stimulating to read by themselves.

So I really have two linked views of my data: Tbox and DTPO, and I'm glad they are logically separate. DTPO offers a different way to search the material with both a concordance and proximity searches (like: "Boulez NEAR Philharmonic") where Tbox offer a regular expression search (like: "b[ao]bbit+"). DTPO has everything, and Tbox has my distillation.

One thing I'm contemplating is how to adapt qualitative data analysis to Tbox:

http://www.vze26m98.net/tbx/Qualitative%20Research%20For%20Beginners.pdf

That's from the TAMS application: http://tamsys.sourceforge.net/. Conceptual tagging of passages in my texts seems very interesting, but it falls below the atomic level of the "note" in Tbox. Aside from table expressions, I'm not sure how I'd approach QDA with Tbox. I know I could break up my texts into children of a master-article note, but right now I'm a bit loath to do that: I think I'd lose the overall thought in each one that way.

Something to ponder, though...

Best, Charles

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Charles Turner
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Re: Academic Workflow (Revisited)
Reply #18 - May 21st, 2009, 2:43pm
 
I got some requests for the Skim scripts I mentioned above. You can find them here: http://www.vze26m98.net/tbx/skim-applescripts.zip
The Zip-file contains a script to export selected, Skimmed, PDFs from DTPO as textfiles; and also a script to make Skim backups from a selected group of PDFs in DTPO.

On the Tbox side, you'll need an agent like this

query:   Text((<ln>)(.+)(</ln>))
action:  URL=$2

to get the tagged "x-devonthink-item://" into the correct attribute.

I'm not sure how much support I want to provide for these, and whether it should take up Tbox forum space. Email me if you want, and remember that you screwed up your data, not me.

;-)

Enjoy! Charles

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« Last Edit: May 21st, 2009, 4:52pm by Charles Turner »  
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Jean Goodwin
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Re: Academic Workflow (Revisited)
Reply #19 - May 22nd, 2009, 9:40am
 
Charles, your research set-up is truly impressive.  As you figure out how Tinderbox is going to help, don't be shy: continue post your ideas to the Forum.  In graduate school, there's a lot of discussion of methodology, but much less of productivity, and so I suspect I'm not the only one curious about how other researchers get things done.  (You lurkers out there--come forward, too!)

I particularly liked the way you're leaving your data a bit messy, with overburdened note names and hand-massaging of fragmented items. When I get stressed, I start dreaming of a tidy and streamlined work environment, physical and virtual, with every item in a place and moving without effort from one place to another.  Then, I imagine, it'd be easy to accomplish 1,000 things at once. So I re-arrange the piles in my office and buy a license to Things (or whatever). But in fact, we probably function better in environments that are somewhat complex and chaotic.  They engage us, which is what makes for productivity in real, as opposed to dream, life. Within a few weeks I'm supplementing whatever new software with scraps of paper, and within a few months I've abandoned it.  

That's one of the great things about Tinderbox:  it patiently endures my brief fits of 'productivity' and automation, and keeps all my notes safe so they'll still be there when I recover.
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Paul Walters
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Re: Academic Workflow (Revisited)
Reply #20 - May 23rd, 2009, 9:23am
 
I made a BBEdit text factory that converts a file of Skim annotations that have been exported as a text file to an OPML file, which can be imported into Tinderbox.  (This is my weekend for making text factories).  It is not a canonical OPML file, but is good enough for Tinderbox use.  Send me a note if you want a copy.

Paul
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« Last Edit: May 23rd, 2009, 9:25am by Paul Walters »  
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frankiben123
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Re: Academic Workflow (Revisited)
Reply #21 - Jun 29th, 2009, 11:09am
 
thanks.......for such a nice post......

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« Last Edit: Jun 29th, 2009, 11:10am by frankiben123 »  
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