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.
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.
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.
Ulysses. I can’t see a reason to use this over 1 or 2, honestly.
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.
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 ). 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!
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).
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.
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:
Managing Research: I relied on the finder and then later a combination of DevonThink, a reference manager and some good PDF tools.
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.
…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.
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¢.