I began using a program called Tinderbox many years ago. Although I understood the program was very powerful, I never took the time to dig into its many features. Over the last six months I've been incorporating Tinderbox into my Writing and have been extremely impressed at the depth of features and the incredible capabilities it adds to my workflow.

Don’t feel badly if you haven’t heard of Tinderbox—It’s a bit hard to explain. One might call it a hypertext personal information management tool—but that description really doesn’t do it justice. If you’re interested and would like to orient yourself to what Tinderbox is, try this Macworld review of Tinderbox 5 (the current version is 7).

An increasing amount of my time is now spent thinking about the rapidly evolving information on the human microbiome. I have read hundreds of papers in this domain, but, like most academicians, I struggle to keep track of the things I’ve Taken in, and how it connects to past and future information. I decided microbiome information was the perfect use case for Tinderbox and finally bit the bullet. To say I’ve been impressed would be an understatement.

The first step was getting the abstracts and metadata from Papers into Tinderbox. I used Keyboard Maestro to build a script to automate the process. The script uses TextEdit to build a document that includes the title, authors, abstract, Pubmed link, Papers link, and Papers citation.

Once the information is assembled in Textedit, the whole note is copied to Tinderbox.

I then put together an assortment of agents that search across the entirety of the imported information and aggregate information similar information under a single heading.

The result is the ability to rapidly find related Information, in an organized fashion, on virtually any topic I’ve read. As I digest new information, I add the abstract and metadata to my Tinderbox Inbox and the agents do the rest—duplicating the abstract into the relevent topics throughout my outline.

I have been using the collection of abstracts as the starting place for writing manuscripts and grants. Tinderbox can export Individual items, or the entire document outline as OPML—making it easy to import into OmniOutliner, or more commonly for me, Scrivener. I’ve found myself starting with Tinderbox, then making queries in Devonthink as the idea evolves.

Although it has taken a significant amount of time inputting the abstracts into Tinderbox, I am already reaping rewards. It worked so well with the microbiome, I’m using the same method (and scripts) with each of the major areas of my academic life: simulation, integrative medicine, and the microbiome.

Tinderbox has an incredible feature set, but it has a very steep learning curve. That is where the User Forums come in. There is an active and friendly group of Tinderbox experts more than willing to answer even the most basic question. I have found digging through both the new and old forums incredibly useful while learning to use this incredible piece of software.

Although I spend the majority of my time in the outline mode, Tinderbox offers the opportunity to visualize information in a variety of different ways including basic maps, tree maps, and a whole host of other methods. These options add many other possibilities,. There are hundreds of features I have not covered in this entry but will in future entries. The program is so feature-rich, I’ve only begun to wrap my mind around the many ways Tinderbox can be used.

A few caveats with my Keyboard Maestro script:

  • The item you wish to extract must be highlighted within Papers
  • TextEdit must be running.
  • Keyboard Maestro is wonky when it comes to adding carriage returns—when typing the metadata I have to manually place carriage returns to separate information. I deliberately put a two second delay between each paste to give me time to press the return key.
  • Do not interrupt the macro-interruption may result in data-overwrite or loss.
  • The script gets the reference information from Papers—and prepends a “1. “ before the actual reference. This is both a bug and a feature—because of this, the new reference bubbles up to the top of the information (sorted by title name), but has to be manually removed.

Overall I have been incredibly impressed with Tinderbox and wished I had learned more about it years ago. My investment of time is already paying dividends. I’m currently using Tinderbox to draft a manuscript and a grant proposal. I will continue to blog about features as I learn more about the program. Enjoy.

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8 Responses to Sense-making of Academic Literature using Tinderbox

  1. Interesting. I recently purchased Tinderbox. It’s an incredibly powerful environment for exploring ideas/notes and their relationships. I have been using it in a similar way to you (without the automation): one note per paper including metadata, abstract, and annotations that I extract manually. I also have been using agents to classify notes. However, if the same notes are entered into DevonThink, I find DT finds related data more efficiently and picks out relationships that my narrower keyword searches would miss. So, I’m less convinced that I’m using TB to its full potential in this way.

    I’m curious to hear about how you’re using TB for writing.

  2. Andy says:

    I own TB but have never really explored its potential. Like Steve above, I’ve always found DT gets me going quite well in terms of finding relationships and developing papers. I’d love to hear how TB is more effective /efficient.

  3. Frank says:

    Hallo, since last Christmas I´m learning how to use Tinderbox and think it is an amazing tool with lots of functionality. It is ver powerful but YOU have to have a concept how to use it.
    Could you tell more about your agents? What exactly do they do?

  4. Mateusz says:

    Hello Sir, it’s been a pleasure to read the post. I was wondering if TextSoap could be used to clean the imported information into TexEdit. One could build the appropriate filter and maybe even apply it as the last step in KM macro. Just thinking aloud. I look forward to hearing more about your Tinderbox use. As probably all other TB users scratching their heads and trying to love the (lets face it) pretty expensive software they have invested in.
    Greetings from rainy Kraków, Poland

  5. rickla says:

    I’m wondering whether your need to use Tinderbox might be seen as indicating an interface problem with DevonThink? I think that, just talking about the functions offered by the applications, the kind of system you’ve built in Tinderbox basically duplicates what DevonThink offers out of the box—minus the AI bits, perhaps. But something about DevonThink makes you—and many other people, including me—want to venture out into something like Tinderbox. I don’t know what adjectives best apply here, but Tinderbox might be called “warm” or “organic” or something of the sort, while DevonThink feels like a database application…perhaps more “mechanical”?

    More specifically, while See Related Text is arguably DevonThink’s most powerful command, if you actually follow the links it’s very easy to lose track of where you were before. Perhaps Tinderbox’s strength is that you can see related text while simultaneously seeing the “original” text, arranged in a visually attractive way.

    I wonder whether it would be possible for DevonThink to incorporate a more visual metaphor, or whether that lack is simply part of the intrinsic nature of the software. Another software that is interesting to compare with DevonThink and Tinderbox is Atlas.ti, which appears to me to incorporate something of both programs.

    • It’s definitely about the interface for me. I track a large number of manuscripts in a rapidly developing field. The outline view in Tinderbox organizes the information quite well and allows me to make rapid visual connections. Although Devontthink is able to perform the same queries, the folder paradigm does not work for me–especially in the early phases of writing.

      I’ve been using Tinderbox to keep my abstracts organized and for making an initial outline in Scrivener. I then use Devonthink to put flesh on the bones.

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