Tinderbox Forum

Medical research start

Yup, I don’t disagree with you Paul.

For me learning is messy and I do better by learning with others, rather than alone. At least, that is my style. I like running to the edges even if I don’t fully understand it, like with this hyperbolic link map, and then pulling back and seeing where I am now and then figuring out all the paths to get back and finding creative ways to refine the path (new ways to use the tool or new feature suggestions for Eastgate) and to have fun along the way.

To those that may find some of my examples or explanations confusing, that is not my goal. I ask for your help. Like you, I’m exploring this wonderful tool and learning how to create knowledge through the 4Cs (collect, curate, create, contribute). I’d welcome your feedback. Please let me know now,

  • what is working for you
  • what is not working for you
  • what would work better for you

That way I can learn what I should,

  • keep doing
  • stop doing
  • do differently

I’m grateful for Eastgate, Tinderbox, and this community. Thanks, all.

1 Like

Me+100. We all know different things. I the less interact with people who know things I don’t, or as important have a different perspective of the same data, the less I learn. I treat every day as ‘school day’. I love finding out things I never knew, it is what keeps me engaged here.

Social media has nerfed interaction into the yaa—boo of binary outcomes. Who cares? We all have different needs and outcomes. what works for me probably doesn’t work for others, but it might in a differing context. We don’t have to agree or all do the same thing. The joy for me is being able to contribute to a context I’ve often never met before.

Happy <$DeityFest> to all!

1 Like

I think there are two different uses of visualization, and that these are easily confused.

First, we may want to view information in order to see what’s there, to examine what sort of relationships it may contain or what trends it may represent.

Second, knowing (perhaps imperfectly) about some relationships that the data demonstrate. we may want to demonstrate those relationships to others.

Michael Becker here is, I think, exploring the first. Tufte’s customary terrain is the second.


Yes! The differences possibly being “exploratory” vs “explanatory.” @eastgate. Thanks for the revelation.

Yes, of course. I was overly prescriptive.

Learned something new from you post(s). Am grateful.

@dr.cox as promised, here are two trainings on how to bring media files into your Tinderbox.


Hi Michael,

happy new year. Just bookmarked your youtube video page and will start checking them out. Thanks for putting the effort in! Cheers, stay safe, get vaccinated!!! J.

1 Like

We have many academic users of TBX in the community. I’m an MD, PhD Neurologists and have been using Tinderbox for years as an “idea processor”. I just read through this conversation and just wanted to mention that many of use other specific programs in an academic workflow like Bookends to catalog references, various PDF viewers to read and annotate and Tinderbox for the note taking and connection process.
These days I keep my reference database of annotated PDFs in Bookends and drag references into Tinderbox where I expand their notes and create summary notes that link to references and various ideas in the references.
It’s great for constructing review articles and seminar presentations.


Hi James,

Thanks for chiming in. This us what I was hoping to achieve.
Any chance you can elaborate on how you do that? Maybe a screenshot or two? I own bookends and goodreader as well as devonthink. Tried highlightsapp but wasn‘t convinced. Also, I loathe subscription licensing.

Stay safe and thanks again.

Cheers, Johannes

Here’s a screenshot of a file I’m working on now, teaching myself about recent fMRI exploration of brain networks. This top layer right now is scattered thoughts and notes, all my own ideas or summaries like the Zettels people talk about now. Then there’s a container with references that I dragged from Bookends with option-cmd which carries over key information. I have a stamp to pull the backlink out of the attributes by. the way so I can click to get back to references. Notes specifically about that paper are composites with the reference itself. When I write about the reference, I link back to the reference because I’m trying t create a level of abstraction from the paper itself.

The funny thing is this is the way I worked as a graduate student 30 years ago. I would copy papers and with a yellow legal pad, put the authors and year at the top of the page and then take notes on the paper, putting findings into my own words. I’ve always used brackets to denote my thoughts that aren’t in the paper if I interpret finding or contrast. But then I would start topical pages from the pad where I summarized my thoughts and the findings. And then its a matter of putting those summary notes in the right order and you have a review paper or presentation.

No one taught me this, but I’ve run across a few similar workflows over the years, so it must be a pretty common solution to going from primary literature to review.
And I never review my notes ever again, I look at my finished work, so I’m always starting new Tinderbox files for a specific project. For me, the Zettelkasten or Wiki idea just turns into a rats nest of links and repetition. But that’s me.


That works brilliantly. Love it. Can you tell me how to use the stamp to automatically create the back-link, please. I was hoping to have the highlights and notes be part of that dragging export as well but somehow that doesn‘t happen. I was maybe hoping to explode (need to figure out hiw that works as well) that the.

That I don‘t quite understand… do you mean you create a single note per Single thought / idea and link it? If the refs are in a container will that not be quite an overwhelming look with all the lines linking back?

Thanks for taking the time!


The stamp is just
$Text = $Text + "\r\r" + $URL + " \r\r"

I’ve tried putting an action in the prototype, but I haven’t got that working. The $URL attribute isn’t an active link, so I find it easier to just stamp it into the text.

So in my workflow, I’ve never been one to highlight and note in PDFs because I tend to never see them again until I actually pull the paper up. If I do take notes in Highlights or Preview I’ll just drag them in and process in Tinderbox anyway.

One of the nice features that’s evolved in Tinderbox is that when the links are to another level, you just see a number not a spaghetti graph of lines. So the links to back to the references that support ideas are displayed in the note itself, and don’t clutter the map. My linking between notes is kind of limited unless it makes graphical sense. I tend to use adornments and containers if it’s getting complex enough that you can’t take in the whole on a single map level. Big hi res monitors help here. And my notes usually are usually enough to fill the text area. Much longer than that and I’ll split and start a new note. That’s around 250 words which is a text page of a book anyway. Once you have a document with 200 notes of that length, you’ve written a book!

The other useful feature is that when I look at the reference note, I see all of the links displayed, so I can see where the reference has been used.

The $URL in the reference points to the source (i.e. the Bookends record) whereas the $ReferenceURL points to the source $URL (if any) for the reference.

Tinderbox’s default ‘Reference’ prototype shows $ReferenceURL in its Displayed Attributes but not $URL. However, it is easy to edit the prototype to add $URL to the Displayed Attributes to get this:

Note for Big Sur users: an OS-related glitch means that as at v8.9.1, the globe icons (and other Displayed Attributes icons do not show. They are still there and you can click them, there is just no visible artwork. Te cause is being investigated for a fix.


I forgot I had to do that to the prototype to show the URL.
Since I added Bookends and the $URL since moving to Big Sur, I didn’t realize that the globe was missing to click. So my stamp is only needed if I want the link in the text.

But that backlink to the PDF is what really moved me to Bookends for doing this.

1 Like