Tinderbox Forum

Organizing notes, Tinderbox?

I’m getting started on studying for my PhD qualifying exams, and I’ll be reading somewhere around 100 books and probably hundreds of .pdf articles. I’ll also be taking notes on most of those books, articles, and random thoughts related to both.

So, I’m thinking I might need to do more than keep just my usual simple word/pages files, and I’ve been kicking around the web looking at possible applications that might help with this. I was wondering if you all had any opinions about the following apps, or if you all had better recommendations for things I should look at.

  1. Scrivener. This looks simple enough to use, but not all that powerful or flexible. Good for notes, bad for pdf’s and not sure how it is for organizing thoughts. The price is good, though.

  2. DevonNotes/Think/etc. Haven’t tried this yet, but it looks useful–particularly like the fact that it can organize pdf’s. Not too expensive.

  3. Ulysses. I can’t see a reason to use this over 1 or 2, honestly.

  4. Tinderbox. Ok, now this I don’t understand at all, but I’ve been playing with the demo and it seems powerful, flexible, intuitive, and almost perfect. BUT, Oh dear lord is it expensive. $220??? It better come with a guarantee that I’ll pass…

So, any thoughts? Any experiences with these? Will I regret not getting tinderbox? Am I forgetting something equally as good as the others?

To recap, I want to keep notes, pdf’s (or links thereto), and be able to organize them hierarchically and visually by author, subject, thesis, etc, etc. I’m doing an exam in literature, by the way, if that matters at all. So lots of authors, lots of books, lots of criticism, lots to organize.

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I believe you have two tasks that might benefit from two types of software. Organizing the source documents (PDFs), and capturing and working with your notes.

Document organization: the options I would consider (in order) are Finder, DEVONthink, Keep It, and Eagle Filer.

  • Finder obviously is free, and the ability to create hierarchical organization, along with tags, and smart searches, can do exactly what you want. Integration of Finder on macOS with iOS is not possible (if you want to use an iPad as a tool), but you could achieve that with Dropbox. Tinderbox works well with Finder, see below.
  • DEVONthink has a price (get the Pro Office version because of its integration with scanning, etc.), and has the DEVONthink to Go companion for iOS. There are many many blogs, and discussions in the DEVONthink forum, from academics who successfully use DEVONthink for document organization and note taking. I wouldn’t want to repeat all of that – go to their forum and start asking. DEVONthink (on macOS) works well with Tinderbox, see below.
  • Keep It is a simpler app than DEVONthink, has an iOS companion, is far less capable for hierarchical organization than Finder or DEVONthink. Moderately OK at note taking. Does not integrate well with Tinderbox without doing continual gyrations via Finder.
  • Eagle Filer similar to Keep It. No iOS app, but files can be accessed on iOS via Dropbox, etc. Also does not integrate with Tinderbox without fiddling with Finder.

Summary: I suggest getting the DEVONthink trial – the developers are very generous about extensions. Read up on DEVONthink work processes. First, though, I would work up your rules for document filing in Finder – whatever you do there can be imported to DEVONthink if you choose that route, or kept in Finder and indexed in DEVONthink. (Indexing is a method by which DEVONthink knows about the documents and their content, but the documents themselves are stored outside the DEVONthink database.)


Tinderbox. I think nothing exceeds Tinderbox in note taking, and, especially, the ability of Tinderbox to help you worth with your notes to discover relations or links, organize them, and expand with references, visual maps, etc. Again, Eastgate is very generous in helping folks in your situation with the trial, advice, etc. A recent series from user @beck Tench is a fantastic intro to the kind of process that you are looking to build. You can see the videos on Beck’s site.
Scrivener although many people use Scrivener for academic note taking, and to some extent, document organization, it’s not the best choice, in my opinion. Scrivener is a fantastic tool for writing – research articles, non-fiction, fiction, whatever --and should be part of your stable as you prepare for submitting your research or writing articles. macOS and iOS. Tinderbox and Scrivener have some integration features too.
Ulysses is pretty good for writing markdown notes. It doesn’t really play all that well with DEVONthink without fiddling via Finder. macOS and iOS. Fourteen day trial, then you’re stuck with a subscription – separate cost on both OS.

Summary: I’m biased toward Tinderbox (you did ask in the Tinderbox forum, after all :slight_smile: ). Please read deeper in this forum articles from the master of using Tinderbox for PhD work, Mark Anderson – @mwra. Find and watch Dominque Renauld’s videos on YouTube (links here from @dominiquerenauld). Jim Fallow’s discussions of using Tinderbox to support his note taking for his award-winning writing and journalism (@JFallows), and many others I don’t want to insult by not mentioning them.

If I were doing this, I would get the DEVONthink trial, the Tinderbox trial and set for myself a defined research task utilizing 10 or 15 articles stored in DEVONthink. Use DEVONthink’s annotation feature to make notes that you save in a folder (group) there. Use the Tinderbox / DEVONthink integration to “watch” that group in DEVONthink to view the notes in Tinderbox. Organize the notes with agents, maps, other features of Tinderbox, to get a good idea of how you would use Tinderbox to extract meaning and linkages between those notes.


I wrote my doctoral thesis using Tinderbox and Scrivener: this one to re-re-re-(…)write the body of my thesis; that one to take notes, searching into my notes, brainstorming and visualizing my notes as you can do in a kaleidoscope. You can easily use Scrivener in order to store and read pdf files especially if you split your screen between your writings and your pdf files. DEVONthink Pro is also a good choice, but, as @PaulWalters said, the Finder and its tags can also help you organize your pdfs. When I was writing some parts of my thesis, I used to export them from Scrivener to Tinderbox and reorganized them with Chart View which is very convenient. @beck Tench made some great tutorials about how she uses Tinderbox to think and write and @SteveZ wrote interesting articles about that subject. Good luck for your phd!

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This ^^^ 100%. There is on one-single-tool for study and noting

I use Tinderbox for notes and for mixed-methods qualitative research. It’s peerless for painless investigation of data where the structure is not clear at outset and/or you don’t want your intellectual insight cramped by someone else’s concept of how to investigate things. I also use DTPro as an everything bucket though (folk here like @PaulWalters are much more expert in their use of it). Scrivener is good. I have it (and Scapple too), I like it and it it weren’t for the fact I’m using LaTeX for my thesis I’d be writing in it. Apparently you can export to LaTeX from Scrivener but it’s not ‘in the box’ and I lack the time/skillz to figure it out. A shame as it would be a killer feature for academic use, but I think the core scrivener users is authors/would-be-authors and LaTeX is probably something they’ll never touch.

Missing also in this is a reference manager. Let’s be honest, even publishers of papers do a very variable job in helping good citation. If you care about your craft, you’ll get a reference manager. Apart from cleaning poorly formatted references (from papers, and publishers’ websites) you’ll find that most journals/conferences have an idiosyncratic mandated reference style. A good reference manager (disclaimer - I use Bookends, but other free and pay-for options abound) is a vital part of your PhD toolset IME. Academics seem embarrassed to discuss such tools as I think the dirty secret is in many papers that list of refs at the end isn’t always too useful to fellow scholars (<\rant>).

Cost. Many of the tools discussed here are small shops, with user-size far below the Apple/Google size and software makers, like PhD students, need to put food on the table. Many of the tools like Tinderbox and DEVONthink tends to have Winter/Summer sales (sadly you’ve just missed the winter sale) with discounted pricing. Some apps (Scrivener, IIRC but ? others too) also offer Edu pricing. So do shop around. As a fellow PhD student, I recognise intent/desire and budget don’t always match. I can say as a long-term user of some of them that the investment is worthwhile, especially if you’re relaxed enough to work with, rather than against, the design paradigms of each. Put another way, don’t privilege your assumptions about how tools ought to work - go with the way they were designed to work (unless you want to go build your own).

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I used many of the tools mentioned above to complete my dissertation in May 2017. Tinderbox for contextual analysis. Bookends for PDF storage, reference, smart group creation and color coding. As I came closer to writing my research findings, I leaned heavily on OminiOutliner to link notes specific to each reference that I used. Tinderbox also has the ability to link references to notes, but for me, maintaining the structure of the reference in relation to my notes was important. For example, after I completed taking notes on Reference A, I could use OmniOutliner’s export function to push all of my notes on Reference A into WorkFlowy where I could manipulate notes even further. Pushing all my reference notes into Workflowy gave me portability and the ability to print nicely formatted notes documents at any topic level of my choosing.

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Much to my dismay, I discovered Tinderbox after I was finished writing my dissertation (comparative lit.). It would have been a real help.

For me there were actually three tasks at play in my PhD:

  1. Managing Research: I relied on the finder and then later a combination of DevonThink, a reference manager and some good PDF tools.
  2. Writing: I used Scrivener 1.x and can’t imagine how I’d have written without it. Simple word processors are like clay tablets in comparison.
  3. …that unsettling middle-ground–call it thinking–when I knew tons of stuff but didn’t have anything to write and just needed to sit, sometimes for hours, doodling, thinking, flipping through material, and just figuring things out. I used paper and pencil for this but I wish I’d had Tinderbox. Working with the trial will show off a lot of its potential for this kind of meaningful work, but honestly, it’s a tool that functions like an instrument: the more you play with it and the better you get at using it, the more powerful and useful it becomes.

My final thought: the initial price is steep, but after a year when your updates run out, TBX still works for as long as you want it to, even if you don’t upgrade every year. And the current version is stable, flexible and very powerful. That doesn’t mean it’s the right tool for you. It’s just a way of saying, the sticker shock isn’t necessarily as big as it seems if you consider that postponing upgrades is a viable option (that isn’t always the case elsewhere).


While an amazing tool, the learning curve on Tbx is steep, at least it is for me, and I’m not clueless. You may not have enough time to master it. For shorter flashcard-type notes, I really liked using Brainscape to study for the PMP exam.

Oh, and remember: when the day comes, it’s just another Tuesday at work for the committee members; that really helped me what is now a long time ago.

+1 @beck’s videos, they were what convinced me to dive into Tinderbox. Very à propos your question.

I concur with most of the suggestions made, but I’d add another use case.

While writing rather than researching, I often had ideas that were related to other parts of my thesis. I noted these down as I went and dropped them in “buckets” for later processing. In the early stages, the buckets identified different themes, arguments, or areas of exposition in my research. In the later stages, each bucket corresponded to a chapter in progress. For example, if I thought a cross-reference would be needed, I’d make a note and drop it in the right chapter buckets. That allowed me to save the idea and return to writing directly. Part of my process was to turn to a new chapter and then review the notes in the bucket for that chapter. Over and over again.

It was long enough ago that I did not use Tinderbox. I think I used the now-non-existent iOrganizeX which was rather limited to a flat hierarchy of buckets. Tinderbox would have fulfilled the role that I needed and much more, because I could have put the notes in several “buckets” at once using attributes or links or containers. With the use of agents, my process could then have been directed through any grouping that corresponded to whatever I was working on, whether a chapter revision, an argument revision, an augmentation based on new literature and so on. It is trite, but Tinderbox could be a game changer for you.

For what it is worth, I wrote the first full draft of each chapter in Mellel—an excellent, affordable word processor with every feature academic writing could need. Then I ported the full draft to LaTeX using BibTeX for references. I would recommend Mellel. However, I would not recommend LaTeX for work in the humanities unless you have considerable computing experience. It is a lot of extra work and you can get everything it offers in other tools now more or less (the sole exception that comes to mind is an automatic analytical table of contents and a names-referenced index).

Again, generally speaking I now do academic work using these tools:

  • DevonThink Pro for storing PDFs and the like. (I have also used EagleFiler.)
  • FoxTrot Pro for searching local PDFs and the like.
  • Ulysses for drafting articles.
  • Mellel for final drafts for submission.
  • Bookends for managing references.

And for the last almost two years I do my “thinking” and note-taking in Tinderbox. I would not want now to be without it, even though I feel I am still learning how best to use the software to support my work. It is exciting to feel that a tool has unplumbed depths and that it is so flexible that as my working changes, it can change too.

I’ve tried Scrivener many times and written a few things in it. My experience was that storing the materials in the project was very convenient for keepng things together, but that in practice having them all in the same app made it harder to use, complicating window management. I like the idea, and the company, and the software, but it has never actually suited my work. An extra 2¢.

I hope that is some help.



Too late to be much use to the original poster, but here is my version of the above. Since you’re already on a Tinderbox forum, I’m going to assume you already have some knowledge of the software and/or immediate access to such knowledge.

Document organization and reference management:

  • DEVONthink
  • Bookends

Neither of these is difficult software, but a bit of time spent looking around the forums will repay itself by helping you to learn the deeper functionality of each application as well as their integration.
Bookends tip: If you tend to obtain a lot of papers that may end up not being useful for your thesis, keep two databases, calling them Thesis and Other, or something equally imaginative. With Other, don’t spend time filling in any missing bibliographic data. When you decide that an item in Other is useful, do take the time to make sure the metadata are complete and drag the item into the Thesis database. (Caveat: This goes against popular advice that you should keep everything in one database and use Static or Smart Groups to organize them.)


  • Scrivener: Use it to structure and plan specific pieces of writing. I would avoid pulling in complete PDFs, but pull in key quotes and relevant anchored and unanchored notes that you have written in Bookends, DEVONthink, and elsewhere. Export to a word processor (see below) when you’ve finished the first draft.
    If you really like DEVONthink and find yourself drawn to using it, and especially if you want to save money, then you could do all of the above in DEVONthink.

  • OmniOutliner: As a dedicated outlining application, OmniOutliner has unlimited hierarchy, which means you could use it to structure a whole thesis (, etc.). It also has columns as well as a hideable notes field for each outline item. That makes it very usable for writing: In the main column, you could write your initial thoughts on a part of your thesis or the paper you are writing, adding relevant references (exported from Bookends) in the rightmost column, and quotes or notes from those references (also exported from Bookends) in a middle column. As you refine your writing, you can move items around if necessary if you decide to restructure the paper.
    As with Scrivener, export to a word processor once your draft is ready.

  • (Mellel or Nisus Writer Pro): Both of these are more pleasant to use than Word. I’ve placed them in parentheses because Word is fine if you already own it, are used to using it, and don’t actively dislike it. Similarly, although both have most of the functions you need, there may be one key Word function you need that the other applications don’t have, in which case your choice is made.


This is the most difficult one to decide on. As has been noted, Tinderbox has the greatest potential but the most demanding learning curve. If it seems a bit forbidding, there are several alternatives:

  • DEVONthink: Again, if you find yourself comfortable using DEVONthink, you might as well leverage it to the full.

  • Keep It: This is a very pleasant application to use, with some nice organization features. You can drag items into DEVONthink as needed. If for some reason you don’t like DEVONthink or think it is overkill, you could replace it with Keep It, though you’ll lose the AI functionality and a lot of the integration with other applications.

  • EagleFiler: This doesn’t look as nice as Keep It but it has two differences that you may find to be advantages. Firstly, it allows multiple databases. Secondly, it stores everything in user-accessible Finder folders. So, unless your computer breaks and you don’t have any backups, you’re very unlikely to lose any data. (The same is basically true of DEVONthink.)

  • Day One: If your notes are basically just text, if you think chronologically, and if you value the discipline-enhancing effects of a date-based application, this may be a good choice. It has tags for organization and good exporting functions.


You may not need to do this, but if you do Tinderbox is an obvious choice. Alternatives are:

  • MindNode: This is a conventional mindmapping software. It syncs over iCloud. There is an info pane for each node, where you can put info that wouldn’t fit in the map. An obvious thing to put in there if, for example, you’re mapping out your thesis or a part of it or a separate paper is a formatted reference (or a Bookends or DEVONthink link) to any paper/book that you refer to.

  • If you prefer to escape from the hierarchy of mindmaps, Scapple (also referenced above, and from the makers of Scrivener) is a wonderfully original alternative.

Finder-centered workflows:

  • If you would prefer to use the Finder for as much of this as possible (potentially replacing everything except Bookends), I would suggest getting Yep. Without moving anything around or creating a proprietary database, it gives you alternative and optionally hierarchy-bridging views of your files as well as tagging and tag-browsing functions.

  • HoudahSpot or Foxtrot Pro for searching for things that you’ve mislaid. I bought HoudahSpot in a special deal so I’ve continued to use it, but I understand that Foxtrot Pro is even more powerful. Also, I believe that, if you want to take the time to learn how, you can do everything in Spotlight that HoudahSpot does.


Very generous posting, @rickdude. Spot on.

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Can I quickly butt in and ask you about Nisus and Mellel. I own Mellel and did one project with it which went ok. Bookends live ref list was nice to have but the rest was nit mega smooth. How is Nisus pro behaving in comparison? Is it worth to shell out for it? All of
My colleagues use Word and track changes. (As a note, I own Word but don’t like it.) Nisus claims thezy are compatible with tracking changes. Is it worth for just simple 10-12 page research papers to buy it? Or should I just get more proficient at Mellel / suck it up and cope with Word?

As to the original wuestion: DTPO is brilliant. I am well underutlilizing it but would not want to be without. Bookends is a must as well for research. Very powerful. 10€ is worth it for wifi sync/year.



I’ve always been impressed with the craftsmanship behind Nisus. I’m newer to Mellel, but it’s an achievement, and I understand its language support is unsurpassed.

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So, jury on which comes out on top is still out?

Clearly, I’m late to the game on this thread.

For those that use Devon think, I rekindled the DevonThink annotations export discussion a few weeks ago: Revisiting Devonthink Annotations to Tinderbox.

@Pete came to the rescue and build an Apple Script for the community. See the post. You can now pull highlighted annotations out of your DevonThink PDFs and get them into Tinderbox. It works great.

If the question the jury is considering is Mellel versus Nisus, then in my opinion Mellel comes out on top. I was a Nisus user for many, many years until they botched the OS X transition (in brief: long transition, weak debut, slow development). I moved to Mellel and checked in on Nisus from time to time. I always preferred the approach in Mellel which seemed to me oriented to the professional writer. I’ve prepared several book manuscripts in Mellel and the control over consistency of style (in every aspect) is tremendous. The integration with Bookends is very strong too. I have found that they get the UI better for advanced features, for example separate note streams (e.g. footnotes in an original text, and editors’ footnotes) or cross references. It approaches LaTeX in power but with a GUI. There are a lot of other little details such as support for OpenType optional glyphs. Language support is amazing.

In short, Mellel is a powerhouse at a great price. The company is very responsive too.

Your question appeared to relate to the track changes functionality in Word. Mellel claims to support that, though I admit I do not use it much. I have made extensive use of the feature allied to track changes, which is Word’s comments feature. I’ve used it for back and forth with lawyers as well as very close collaborative editing. I’ve tried most everything for this.

Lately, my go-to is Pages for working on comments. I think it has the most clear UI for this kind of work and it prints the comments out particularly well. So sometimes my workflow is to receive comments, edit the comments with my responses, then print the document with comments showing to PDF. My collaborator(s) and I then work from the PDF with one person making agreed edits to a master copy as we go.

In fact since this is the Tinderbox forum, my workflow often begins with export from TB to Word, send to collaborator, collaborator comments in Word, sends it to me, I put it into Pages and then proceed as I described above.


I enjoy working in Pages more than any alternative – especially that I now have a choice after decades of being required to use Word by corporate diktat. If only Apple would apply the design and relevanat features of Pages to make PDF annotation software.

I agree. It is remarkable how lame the user interfaces are on PDF annotation software. I have the sense that no one who has used them at the sharp end of pairwise or small-team collaboration is ever the product lead for them. They’re either for finance departments, government-style bureaucracy or very lightweight application.

My most common approach to heavy markup, editing or comment is still print it out; scribble over it in pen; drop it in ScanSnap (or use my phone).

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My two cents on this. I use Nisuswriter pro over Mellel after their v3, and used Mellel before. Both are refreshing, but NW feels better. I write many short (fewer than 10 page) documents for work and use it exclusively, either exporting to PDF or Word. It integrates well with Omnigraffle via Linkback (which they invented) and Bookends. I seldom need it, but their macro system is amazing. I have four workflows. In order of actual use: Nisuswriter/Bookends/Omnigraffle/Keynote is one; Tinderbox, Devonthink/agent and host of support tools are the second. Ulysses and Scrivener/Aeon are the other two: each dedicated to a single long term project shared on an iPad.

Because the original question was about Tinderbox, I will recommend you try it. I used it for a huge project some years ago, and am well into a second large one now. The first project was fully designed before I started and did not use map much. It was agent/action heavy; had an amazing degree of visual customisation; and exported to complex html.

This new project is probably more ambitious, but I just started without knowing where I’m going with it, trusting the tool can be made to adapt once I know what I am doing. Also, this one is map-centric. I recommend starting with maps and spatial thinking.

If what you want is just reference notes on books and papers, it may not be much better than Devonthink, or the others for that matter. But if you think you will be using the notes to synthesise new insights and recognise structure in the space, you need a tool like TBx for that emergent work.

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