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.

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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!

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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.

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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.

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Dear Forum,

I finally got started on my first TB project properly. I need to get my head around a new area of research while also collecting background and relevent quotes / references for future writing. thus, I collect references from Bookends and sort them through adornments in a reference folder, I also export the highlights from Bookends and have them within the exported reference note. sometimes I explode key pharses or notes along with cited sources. that way, I hope to recap certain areas while writing pieces of new research and have it all in one place. (sound good so far?)

I the long rund, I want to map out certain concepts an relationships in the top view that I will supply with key quotes and key references to have relationships visible while still being able to access the underlying research / proof / related ides.

not terribly smooth, but still a lot of fun discovering and also a nifty excuse to plough through more papers… :wink:

no back to you guys a couple of questions:

  1. any suggestions and pointers how to use and choose attributes to make sorting through the growing note collection more accessible?

  2. do you reckon simple $text.contains agents are enough?

  3. can you search for text phrases or words and TB gives you not verbatim matches but suggests similar stuff similar to DTPO

  4. is it more advisable to explode the note collections for individual papers and have single statement in the title notes or should I leave it in one big note?

  5. lastly, links! when I use [[ links, I like the suggested notes drop down list… (how) can I
    a) make the link in the text have a different name than the note… i.e. linke to “terribly long note name”-links becomes “short-name”-link
    b) can I make the destination note have a reverse clickable link at the same time?

I know that were a load of questions and I sometimes take some time to post on (sorry for that but I don’t have protected time for my research so it is a free time hobby like for many…) but your input is highly appreciated. if I should open different topics for all the questions, please let me know.

all the best, stay safe, cheers,


Yes, you have a ton in this post. There are many ways to accomplish what you want to achieve in the fine points. Let me response to this one.

Check out:

You can use the pipe element with a ziplink to create a different anchor from the name, e.g.


NOTENAME = the name of your note
ANCHORNAME = the name you want to give the anchor
| = the pipe, the instruction to Tinderbox to use an anchor name and not the note name.

To make the is work enter [[ start typing your note name and then click and hold done the opt ⌥ key; then enter the | and you anchor.

I’ve got to go walk the dog…will put more thought to your questions. Perhaps you can join on of the Wed. or Saturday meetups and we can all review your project together and work through options for yo.

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Have you watch my wrapping your head around attributes video? This might be a good place to start: Tinderbox Training Video 05 - Getting started and wrapping your head around attributes - #6 by pmaheshwari.

REMEMBER: You can create user attributes, make them anything that you’d like. Also, the type of attribute will mater in your search. For example, if your’e searching on a list or set attribute you’d want to use “$MyList.format(”;“).icontains(”“)”. This is explained in this video: Tinderbox Training Video 14 - Searching sets: understanding the .format dot operator.

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The answer to this question is that it depends; it all depends on on your goals and intentions and how you plan to curate your notes for future creation and contribution. Personally, I like breaking notes down to their atomic essence, and the to cite them individually. This works for me as I use and use my atomic notes in a lot of different applications.

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I’d accord with the last answer above. See what others do, but don’t let their process override your style of work unless you can see a benefit.

It is a start, but it scales messily, IMO. Once you know a term or relationship, capture the fact in $Tags or a user attribute, or make a link. The information in these attributes becomes metadata (annotations!) on your notes but is more easily searchable if you annotate with care. Rather than search every note’s text ($Text) for the term pulmonary, when doing initial ingest/review of notes, you could add the term ‘pulmonary’ to the $Tags of relevant notes (or use some user attribute of your choice). Now you can search $Tags for notes that include the ‘pulmonary’ tag. It’s still a wide search, but it’s processing less overall data than all the $Text or all the notes. Plus, the word ‘pulmonary’ might occur in general text but where it is not germane to finding notes on that topic. In such circumstances you would not tag that note, thereby excluding a note from a $Tags search that a $Text search would find.

For me (others will vary), as time goes by with a project, if I have to use $Text.contains() for more than occasional or unusual things, I take it as an indication I’m not being effective with identifying key terms and ideas and extracting them into attributes. This arc applies for new notes added to a project. Initially, I may need to use some $Text searches just to get familiar with the new content but with some extraction structure (existing attributes) already in place the move from only $Text to a more nuanced set of information gets faster.

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