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Message started by Lew Friedland on Jun 30th, 2012, 10:29am

Title: Tinderbox for Academic and Nonfiction Writers
Post by Lew Friedland on Jun 30th, 2012, 10:29am

Hello all. Am launching a topic here for those of us who (mostly) write in an academic mode, use Tinderbox, Scrivener, some other bibliography manager (Endnote, Bookends, Zotero, Sente, etc.) and often/sometimes a database like Devonthink.  There have been a number of great threads here on academic note taking, organizing/writing a Ph.D., with great contributors like Derek, Jean, Russ, and of course Marks A and B.  

I anticipate three kinds of discussions here that have floated through academic writers' questions on the forum.

First, the basic issues about tools and organizations: which ones, how do they work together.  The new Scrivener integration is a huge advance for many of us, but, for example, those of us who use Zotero because of its openness to the web and groups might want to figure out how to get the same or similar drag and drop capabilities that are now built into Bookends (at least I would).

A similar question, one that's been scattered through bits of the forum: how do people manage PDFs, other files, and how to link them in a TBX document?  For example,  I add new PDFs to Devonthink, use this for storage and exploration, but when I actually start to write notes and use them, these go in TBX. What is the simplest way to link notes in TBX to a document elsewhere?

The second kinds of questions have to do with the kinds of code use issues that crop up among many of us.  What are the most important bits of code to learn to unlock Tinderbox's full capabilities?  This is, of course, as much a question of how to organize academic files in TBX and take notes as it is one of the "right" codes. But that's the point: these issues get tangled up and sometimes it takes someone writing in a similar vein to help untangle them.  

Finally, there are other basic questions of note taking and writing craft. For example, how to other users take notes on books and longer documents?  Do you use a single container for a book and then go "vertical" with containers within containers for chapters?  How to avoid losing one's place if notes on books become buried (note to Marks, I do know that agents search deeply, etc. But I use a lot of maps so having first level display is part of how I use TBX which is an ongoing paradox).
Or, I have at least 75 Tinderbox files.  Does it make sense to consolidate those that are substantively related for a larger project? If so, what's the best way to do this?

So, fellow academics and non-fiction writer, let me know if this is a thread that seems useful or not and we'll see if it's worth continuing.

I'll throw out two starting questions: how do you link Zotero or other bibliographic DBs entries in TBX files?

How do you use TBX with PDFs?

Title: Re: Tinderbox for Academic and Nonfiction Writers
Post by Mark Bernstein on Jun 30th, 2012, 11:19am

An excellent topic!

On reference managers: Under the hood, the Bookends/Tinderbox connection understands RIS, one of the major bibliographic interchange formats.  This support could probably be used for other reference managers; people interested in this could contact us. But Bookends is terrific and not very costly, and it imports data from all sorts of places.

I'm VERY interested in the role of Tinderbox for structural edits, especially of larger work or complex narratives.

[edit]admin: Mark A added link to RIS format to RIS reference[/edit]

Title: Re: Tinderbox for Academic and Nonfiction Writers
Post by Lew Friedland on Jun 30th, 2012, 11:46am

Mark, thank you. Already very useful.  I have used Bookends and like it. But Zotero has a large open source community, is very flexible at downloading data from web, etc. Mostly good for collaboration.
Main point is that if there is a way to adapt an RIS solution more generally, I would be interested in helping out (although not sure what I could do).

But yes, one focus of this group should be relatively large projects over time.  So hopefully a discussion of emergent note taking strategies from multiple sources.

Title: Re: Tinderbox for Academic and Nonfiction Writers
Post by Lew Friedland on Jun 30th, 2012, 11:49am

For those interested here's a link to an RIS thread on the Zotero forum:

Title: Re: Tinderbox for Academic and Nonfiction Writers
Post by Mark Anderson on Jun 30th, 2012, 1:59pm

So as not to derail the thread, I've branched to a new thread some issues on the simple mechanics of inter-app linking.

Reading further into RIS, I can across this, which seems to be a map of the RIS tag list which is big, some 57 tags. Full RIS might mean adding 57 new attributes to you TBX. TB doesn't mind that many attributes, but do you actually want all that info in TB? If not, IMO it's it best to let the full reference reside in your reference manager and use a 'shallow' reference in TB. It's in our nature to just want one tool for everything but it would be a very complex one.

Title: Re: Tinderbox for Academic and Nonfiction Writers
Post by Lew Friedland on Jun 30th, 2012, 2:47pm

Thanks Mark. If you drag a zotero reference into TBX it shows up as a note (obviously) with all information (author, title, etc.) but just as a text string. Is there a way to set up a note (e.g. I have bibliographic prototypes) so that it would recognize the RIS fields and create a note in prototype format, rather than as text?

Title: Re: Tinderbox for Academic and Nonfiction Writers
Post by Mark Anderson on Jun 30th, 2012, 7:33pm

That drag and drop so often just works tends to make it appear simple.  The problem seems to be (I am not a software engineer!) as to how/if the receiving app can correctly deduce the structure/type of the data being passed.  In other words, it the originating app sends incorrect info, the receiving app can't identify it or has to build costly/fragile workarounds to accommodate the problem.

I'd assume (again I'm not a coder - Mark B's better placed to comment) that now TB can understand RIS data from Bookends, it can likely understand RIS from Zotero. But, does Zotero actually pass RIS-foratted data via drag-drop? If not, the place to fix this is at the Zotero end rather than the TB end.

Looking the other way along the inter-app linking, note the question in my side thread - can you link *into* Zotero? How else does TB open a Zotero reference (as opposed to simply opening the referenced s
document or resource.

Title: Re: Tinderbox for Academic and Nonfiction Writers
Post by pierfranco on Jul 1st, 2012, 8:13am

I find it a great discussion thread. I too am interested in making Tindebox interoperable with Zotero.
As to the question whether Zotero can export via drag and drop a bibliographic reference formatted in the RIS format the answer is Yes: the result in Tinderbox is a new note which contains the reference duly formatted as RIS.
As to the use of Bookends: for those who use Zotero it doesn't seem for obvious reasons a good solution to export periodically from Zotero to Bookends so as to exploit the direct linking capabilities of Bookends. Above all, even if we exported periodically bibliographic references from Zotero to Bookends, the file which often accompanies bibliographic references in Zotero and which can be an html file or a PDF etc. would remain in Zotero and no direct link to the file is put in whatever field of a RIS export from Zotero. So Bookends can't be of any help when you need to open the file, which instead is a very easy action in Zotero.

Title: Re: Tinderbox for Academic and Nonfiction Writers
Post by Lew Friedland on Jul 1st, 2012, 11:07am

Pierfranco, thanks for joining the thread. I'm afraid I have gotten us off to more of a "tools" based discussion than I had intended. But now we might as well run the issue to ground. Please tell us how you drag and drop from Zotero retaining RIS information. It is not as simple as just dragging a cite. That's what I do, and get a note that is just a text string. Is there some other intermediate step? Must be.

As to your second issue re Zotero, I think that is a big issue for many of us in this area. How to manage PDFs, etc. without absurd duplication (e.g. put PDFs in Zotero, Devon, links in TBX (which I actually don't know how to do if not on web).  So organizing PDF workflows is probably a major topic.  Any more thoughts on how you (or others) do this would be welcome.

Title: Re: Tinderbox for Academic and Nonfiction Writers
Post by pierfranco on Jul 1st, 2012, 12:01pm

Dear Lew,

in order to drag a bibliographic reference from Zotero to Tinderbox in the RIS format you should firstly open the Zotero Preferences and select the Export tab: from here select the RIS format in the dropdown menu.
As to the attached files: they are not only PDFs but also HTML files: for example when you use Zotero for saving a screenshot of an electronic article which only exists as a web page.
In these cases Zotero save files in his directory which is part of your file system and only Firefox is able to open a file which receives from Zotero a specific address. So for example, if I use Zotero for storing both the bibliographic data and the screenshot of the article at:
then Zotero creates for the screesnhot this address:
But actually, in my file system the right path to the subdirectory contained in the main Zotero directory and which contains the main html file, together with the CSS file, images and so on, is the following:
Once Zotero has saved all the files connected to this web page in a specific subdirectory, I am able to view it even when I am offline in their original and complete form.
Unfortunately, Zotero exports neither the address created for any attached file, nor the full path. So no export from Zotero can be used to point to the files saved in the Zotero directory. This makes it impossible to use other applications for pointing to files saved in the Zotero directory, which is part of your file system.
The important thing to point at is that Zotero is not only a bibliographic manager but also a file manager and it would be totally cumbersome to use another application for duplicating this work which is perfectly done by Zotero and no other application can do so well.
So for those willing to use both Zotero and Tinderbox, the problems are 2:
1) how to effectively import in Tinderbox the bibliographic references from Zotero
2) how to point to the attachments: the file HTML or PDF etc, stored in your file system.


Title: Re: Tinderbox for Academic and Nonfiction Writers
Post by Lew Friedland on Jul 1st, 2012, 12:26pm

Thank you very helpful.  So now I have a note that reads (as a text string):
ID  - 252
T1  - The new urban America : growth and politics in Sunbelt cities
CY  - Chapel Hill
A1  - Abbott,Carl
PB  - University of North Carolina Press
PY  - 1987///
N1  - 86040490
Carl Abbott.
Bibliography: p. [291]-327.
Includes index.
KW  - Cities and towns Sunbelt States Growth.
KW  - Metropolitan areas Sunbelt States.
KW  - Regional planning Sunbelt States.
SN  - 0807841803 (pbk.)
ER  -
I am assuming that one must set up a specific TBX bibliographic prototype that matches the fields of RIS precisely?   If so, can you point to how?

Title: Re: Tinderbox for Academic and Nonfiction Writers
Post by Mark Bernstein on Jul 1st, 2012, 12:49pm

Let's move all this discussion of Zotero vs Bookends vs whatever to a separate thread -- Mark Anderson has already made a thread for this -- and return this thread to a general discussion of Tinderbox for Academic and Nonfiction Writers.

There's a lot more to writing nonfiction than wrangling over whether we happen to prefer Zotero or Bookends.  

Title: Re: Tinderbox for Academic and Nonfiction Writers
Post by Lew Friedland on Jul 1st, 2012, 1:38pm

Yes, happy to do that.  Although much discussion of academic writing on the forum migrates back to workflow.  The larger problem here is bibliographic management in/with Tinderbox, how much sync do we need between tools. When 50% plus of all notes refer to sources (and for most of us the threshold is closer to 80%) then this is a real problem that crops up repeatedly. As you point out, the specifics of tool management we should move elsewhere, the problems of flow, perhaps not?

Title: Re: Tinderbox for Academic and Nonfiction Writers
Post by Derek Van Ittersum on Jul 2nd, 2012, 9:01am

I use Zotero, DevonThink, Skim, Tinderbox as well, but don't find the PDF management to be an issue really. Basically, all my PDFs are in a single dropbox folder with filenames matching this pattern:

author - title - year.pdf

Then, reading notes for each PDF gets their own folder in DevonThink named through the same pattern. PDFs are not stored in DevonThink, but they are indexed by it.

Then, when notes in DevonThink migrate to a tinderbox file (for a specific project), I have recently been using bibdesk to approximate the same function that is now possible with Bookends/Tinderbox. But even before I was doing that, I found it trivial to create a prototype for each source that populated author/title/year KeyAttributes.

Under this system, I don't have "links" that can take me to each source with a click, but I find it trivial to simply navigate to the source I want in whatever application (Finder, Devonthink, etc.).

For me, everything that ends up in Tinderbox is put there deliberately, which helps me use it as a thinking place, rather than a giant inbox (like DT). So, even if I'm using some reading notes from a source in a project, I won't dump all the notes from DT into TBX, just the ones that seem useful at the moment. Given the low volume of sources I'm working with (relatively I suppose, we're not talking more than 30 sources per project at this point) I don't see the value of clickable links for PDFs for my working practices.

Title: Re: Tinderbox for Academic and Nonfiction Writers
Post by Christian Tagsold on Jul 2nd, 2012, 10:19am

Very much like Derek I do not depend on linking to pdfs and so on very much.
Pdfs go into DevonThink, Bookends is purely for creating bibliographies in the end while I write my papers in Scrivener.
I put all my excracts of what I have read the last 10 years into one single Tinderbox file just weeks before the possibility of drag & drop from Bookends. However, it was also ok to manage the task by exporting all relevant bibliographic information via a numbers document from Bookends and back into Tinderbox. The extracts came from rtfs which had lived in DT. Lately I have been arranging notes on what I have read in mindmaps in Tinderbox. This makes the information much more accessible for me even after memory has blurred on what I have read excactly.

So Tinderbox does mainly three things for my writing:
1. a repository for extracts from papers, books and archival stuff
2. a bucket for all sorts of ideas which come across my mind for future projects and papers (mostly a list sometimes evolving into some sort of map)
3. a mindmap for carving out the actual structure for what I want to write which then moves into Scrivener when done

These three things happen in different documents however and I have not yet found a compelling way to bring them together in one. Hence they are not linked very well. I even don't know wether it makes sense to streamline this process into one document… which might become extremly bulky anyway since it would hold probably about 10.000 single notes.

Title: Re: Tinderbox for Academic and Nonfiction Writers
Post by Lew Friedland on Jul 3rd, 2012, 9:23am

Very useful Derek and Christian. A few questions.
Derek, you take your notes in Devon Think rather than Tinderbox. Can I ask why?
Christian, you keep separate files for extracts etc, ideas, and mind maps for specific writing you are working on. I assume you move material from one file to another in a kind of sifting process as you go.

Another question.  How do you all take notes on books? At first glance, this seems fairly obvious.  Take notes on passages that interest you. But for many of us, a book is a system of arguments as much or more than facts.  These are linked, of course, in a logical order, and build on each other. One option is setting up a prototype or OnAdd in a container and taking notes by chapter.  However this doesn't necessarily preserve logical threads.  Another is linking notes. How do you take notes on books with complex arguments stretching over multiple chapters?

Title: Re: Tinderbox for Academic and Nonfiction Writers
Post by Derek Van Ittersum on Jul 3rd, 2012, 10:07am

I keep my notes in DevonThink because I think its artificial intelligence (fuzzy searching) capabilities are very useful (just Google the Steven Johnson NYT piece and blog pieces about DevonThink for more on how this works). I keep one head note as a summary about the book's main arguments, points, interesting features. Then, each book/article has many  subsequent notes that contain 1 - 4 pull out quotes or summaries and then my own commentary. DevonThink supports links between notes, so I'll often add hyperlinks to related notes (within books and amongst several books).

I can then create a new tinderbox file for an upcoming project, copy over notes from DevonThink that I know will be relevant, then use the fuzzy searching in DevonThink from those notes to find other connections and links. I copy all these over to Tinderbox in the map view and just start making connections and "emergent structure" with adornments and so forth.

After working with this system for some time, I find it very sustainable. DevonThink, I believe, is just better suited for my long-term database/archival note keeping needs, and TBX is better suited for individual project development and analysis.

Title: Re: Tinderbox for Academic and Nonfiction Writers
Post by Ted Goranson on Jul 3rd, 2012, 10:30am

Replying to the original post here...

I have an ambitious non-fiction project that I originally started using TBx, Bookends and EagleFiler, authoring in BBedit.

I own many other applications, including Yojimbo and DevonThink Pro but they just don't work for me in this context.

However, once I got going, I am finding that I am making a very heavy investment in Filemaker. I also expect to move some of the writing to Scrivener with Aeon Timeline, though I have not started this yet.

The integration between TBx and Filemaker seems to be easier than supposed, as each is published to the web, and each can read from the other's published pages.

-- Ted

Title: Re: Tinderbox for Academic and Nonfiction Writers
Post by Mark Anderson on Jul 3rd, 2012, 11:26am

However this doesn't necessarily preserve logical threads.

Not necessarily. If you link each note to the next sequential logical nugget - which may not be next in map position/outline location then you can walk the path either via Roadmap view:

Or in maps only, via link enactment. Note how only outbound links from the selected note(s) are active. They're actually animated on screen, though you can see that in this grab:

If some of the originals aren't on the same map, consider creating aliases of them on the current map so the entire logic chain can be viewed as a visible path.

Not a map user? Don't like links?  Use 'tags' - custom attributes of your own design - to mark notes that are part of a thread. Use an agent (or Find) to recover the notes using a given tag. There's no reason that you can't use both tags and links if so desired.

At the analysis stage, what's best is likely what best fits your personal style of work and how each user likes to interact with data (very visually, or more abstract). As/if/when you move to needing to share the data or export it you may find it pays to use methods that help with export, for instance restructuring flat maps to a more hierarchical outline.

There's no specific right or wrong way to do all this, which probably reflects why very broad-based topics like this are hard to respond to.

Title: Re: Tinderbox for Academic and Nonfiction Writers
Post by PW on Jul 3rd, 2012, 1:27pm

Ted Goranson wrote:

"The integration between TBx and Filemaker seems to be easier than supposed, as each is published to the web, and each can read from the other's published pages."

@Ted, I'd be interested in hearing more about your approach to TBX/FileMaker integration -- maybe as a separate thread since it's a sidebar to this thread.

Title: Re: Tinderbox for Academic and Nonfiction Writers
Post by Steve Thorpe on Sep 27th, 2012, 11:26am

My workflow is based on Skim and Goodreader for reading and annotation, DevonThink to store my pdf's and notes, Zotero for bibliographies, TBX for thinking through specific writing projects and Scrivener for the actual writing. It all works fairly well so far, but I would love some integration between TBX and Zotero. This could potentially change the way I work completely and allow me to use TBX more effectively.

The way I use TBX for a project is fairly simple. I keep meaning to get deeper into TBX functionality, and can see where it would help a lot, but I have yet to get any deeper into the mechanics of the thing. My TBX document includes a list of articles and within each container article I keep my notes. As I map out my ideas I replicate relevant notes and place them in a map, that way keeping links back to the article. Each note  then becomes quite a complex object which can be used with agents to look for patterns that I might have missed.

My approach is a work in progress, and certainly needs much more thought. But I do hope this contributes something to the discussion.

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