Tinderbox User-to-User Forum (for formal tech support please email: info@eastgate.com)
Tinderbox Users >> Tinderbox applications >> Academic Note-taking

Message started by Barbara on Sep 26th, 2011, 3:43pm

Title: Academic Note-taking
Post by Barbara on Sep 26th, 2011, 3:43pm


I am currently working on my dissertation and have considered buying either Tinderbox or Twig as a Note-taking tool.  I've experimented in the trial program read through some of the forums, and case studies but still find this confusing. Mark Bernstein has been super in answering questions I have about how I might set this and suggested that I ask those in the forum who might have insight in applying TBX to academic note-taking:

1. Would any of you have a sample file of prototypes, etc and be willing to share  how you use TBX in basic academic note-taking?

2. Does anyone have a general workflow from Endnote to TBX to Scrivener — is it possible to import bibliographical detail from Endnote?

3. The following is what I've gathered that might work for me — Is there anything that I'm missing, that should be done now to avoid having to go back and correct later? In other words, how can I improve this?

I am taking two different kinds of notes: --

a) interactive notes based on reading (this is basic bib info, abstract, and my responses)
b ) citeable notes — notes I take from my interactive notes that I can insert directly into an outline or manuscript       & would include name/year/page # &  a short statement or direct quote

There would only be one interactive note per source, but there might be several citable notes per source. The title of the citable note would be a key phrase +
Author and year)

I want to be able to sort the citeable notes into key categories (for example — theory, methodology, current problems, key people) --
I also want to be able to use these key categories to show up within the outline on TBX.

*So far, I have one prototype for  Source Notes — including a key attributes for bibliography info, whether it is crucial, used, and  citeable;
This is so I can carry over the bibliographic information from the initial interactive source note to the citeable note.
Would it be better to create a second prototype for Citeable Notes?  Then I could use an agent, as Mark suggests, to look for a citable note with a particular text or key word.

Do you keep all of your notes at one level and organize them later, or organize as you go along? On a shorter project, this is a non-issue;
However, I have potentially hundreds of sources.

**I see that I can use adornments to separate citable notes into categories, but the organization doesn't show up in the outline view. The only way that I've found around this
Is to use container notes for to hold citable notes. Is there a better way to organize citable notes within the outline view?

Thank you for your help.


Title: Re: Academic Note-taking
Post by Derek Van Ittersum on Sep 26th, 2011, 5:00pm

I don't have time for a longer response, but here's my general workflow:

all reading notes for all projects go into DevonThink. I find DevonThink's hierarchical nature useful for organizing reading notes alphabetically, and it also lets me tag things by project to create smart folders. Plus, there's some useful fuzzy searching for discovering relevant notes that I didn't tag the first time around.

When I start a writing project, I create a new TBX map and start brainstorming--writing notes of my own, cut+pasting text from my reading notes from DevonThink, etc.  Sometimes this is as far as I go in TBX, other times I create agents for searching themes, adornments that assign tags or other metadata to notes, etc. Sometimes I'll create outlines in TBX, other times not.

From here, I'll move to Scrivener. This is where I start drafting text and adding quotes with citation information (thus I can't say whether endnote will play with TBX).

As has been mentioned before on this forum, many folks don't see TBX as a good "everything box" where all your notes would go, but instead as a project box.

Title: Re: Academic Note-taking
Post by Barbara on Sep 26th, 2011, 5:19pm

Hi Derek,

Thanks for your quick reply! Since I am new to TBX, it may be that I don't quite
understand what it's best used for. I would like an  "everything box" for this particular
project. You say DT is better for this. I was hoping for a database +  mapping and outline functions all to be in one program. It may be a tall request. :-) Apologies -- I know that my questions to some extent have been posted elsewhere by others.


Title: Re: Academic Note-taking
Post by Lucas D on Sep 26th, 2011, 5:30pm

Hello Barbara,

Thanks for your post. Just a quick response now as I've got to run.

I'm currently doing research for a dissertation in social anthropology, and so far I've found Tinderbox highly useful, although I wouldn't say that I've arrived at a refined system. One of the mantras here seems to be that one needn't design the entire system ahead of time, but rather one can just begin working and adapt the system as one goes along. Indeed, in my case that has proved to be true: I've invented and abandoned a number of different organizational elements within my main Tinderbox file, and my data is none the worse for wear. As my understanding of the program develops, my ability to organize my data improves, thus making the data more useful.

The beauty of Tinderbox lies for me in the power of user-defined attributes and the ability to search by and modify metadata using agents. So, for instance, to assign categories to your citable notes, you could create a user attribute 'Categories' (probably a 'set'-type attribute), and you could make this information visible in Outline View by showing the attribute in a column and/or using an agent to give some visual distinction to those notes (change of color, badge, etc).

I'll have to stop there for now, but I'd be interested to hear how your system develops.

--- Just saw your reply to Derek. Yes, for me Tinderbox is an ideal everything box. Just bear in mind that in my case that means "everything textual". It has useful functions for linking non-text files and including images, but of course its core functions are textual (as well as visual mapping of relationships between notes).

Title: Re: Academic Note-taking
Post by Mark Anderson on Sep 26th, 2011, 6:27pm

I concur Lucas' last point. TB's best points relate to textual analysis. TB can use pictures in some contexts** and it can link to files/folders. But it doesn't try, in terms of main design intent, to perform the 'everything bucket' (tracking all files/formats) perform of tools like DEVONThink, Yojimbo, Curio. Whilst it seems logical at outset to look for a tool that does one's entire task, as one gets into the detail of the task, it's often useful to use several tools that do a limited part of the task extremely well than to push a single tool to do everything (less well).

** I believe that aspect is slated for major overhaul ere long (presumably the next major version).

Title: Re: Academic Note-taking
Post by Mark Bernstein on Sep 26th, 2011, 7:06pm

Don't be shy of using big containers in your map view to hold collections of your (citeable) notes.  

* Use adornments (or simply clusters of notes) when you're unsure of your categories and their boundaries, or when you want to be free to try out experimental organizations

* Use containers when you're fairly confident that a category will be useful

You can reorganize things fairly easily, even if they;re inside a container. But containers are more emphatic than adornments and so they do tend to discourage experimental renovations.

Title: Re: Academic Note-taking
Post by Barbara on Sep 26th, 2011, 8:18pm

Thanks to Lucas, Mark Anderson and Mark Bernstein, for your replies!

It's good to know that you find TBX very helpful in your dissertation work. It does seem to be a program one grows into; I just want to be sure that I can use it in at least the most basic way for note-taking and organization, before throwing my hat over the fence, so to speak. It also helps to know that you don't find making changes in your system to be difficult. Certainly, another fear was spending more time on getting my notes right than on my project.  Thanks also for your suggestions about the categories. I did try this out, but all of the categories are showing up for all of my notes. I will keep working on this. I also found the column feature you mentioned for the outline. Progress!

Mark A.,  
Ok-- I see about the use of the term 'everything box.'  I guess by everything, I meant a place for all of my textual notes, as well as a way to map and categorize (and cross-categorize). I don't mind using Endnote for searches and citations, and Papers for categorizing and reading my pdfs, and Scrivener for writing manuscripts, and ultimately a word processor for full drafts.

There was just that one gap where I want to keep all my textual notes and ideas in one place and move them around until I had them in the order that makes sense. I have always been a "notecard" person, and my master's thesis involved many boxes of these. I was hoping that TBX would be an appropriate and perhaps more sophisticated electronic tool for being able to visually move my notes around without "losing sight" of them. As a Windows user I can download "Writer's Blocks," but TBX seems to be better suited for visualizing relationships between notes. I have also used MindJet, but it doesn't seem robust enough for extensive note-taking. If this were just a short paper, I would have simply cut and pasted my notes into a document. I have tried posting notes into Scrivener, because it has the note-card view. This would seem to work only if I posted many notes into one section/ category, as opposed to single notes.  TBX seems more flexible in this regard. I am not familiar with DT, but it seems to be only a database (although a very useful one). Would it be appropriate to see TBX as an everything box for textual notes with mapping and outlining features, or rather a hyperlinked index card system with a desktop floor for spreading those cards about, and a desktop bulletin board to see them in a particular hierarchy?

Mark B,
Thanks for the additional tips on the differences between organizing containers vs. adornments. I will go back and work on this a little further. I'm feeling more confident about how I might use the program!

Title: Re: Academic Note-taking
Post by Mark Anderson on Sep 27th, 2011, 3:43am

Would it be appropriate to see TBX as an everything box for textual notes with mapping and outlining features, or rather a hyperlinked index card system with a desktop floor for spreading those cards about, and a desktop bulletin board to see them in a particular hierarchy?

A key thing to grasp is that a map does not show the entire outline but rather just the siblings of a common parent container. When a map is opened on a selected note, the map view is of its parent container - i.e. the selected note and its siblings. Outline/Map view differences are discussed in more detail in this wiki article.

So, whilst your TBX can be a textual everything bucket, if you want to use a single map as a primary review area, you'll need all notes of interest to be in the same container (or to have aliases within said container).

Title: Re: Academic Note-taking
Post by Ben Worthington on Sep 27th, 2011, 5:13am

I attach a link to a copy of my research template, a version of which I use for my (sadly neglected) history degree, and a version of which I use in my day job too: http://cl.ly/3o0t3h2u3s3C1I3t3n46

It is heavily based upon this system: http://calnewport.com/blog/2007/10/01/monday-master-class-how-to-build-a-paper-research-database/

It has 4 note types: printed sources, quotes, lectures and interviews.  The way I have used it is to list out all the sources on a given topic (starting by copying-in the course reading list, and adding others as I go) and then work my way through them one by one, building a list of quotes to use when it comes to writing up that dreaded essay or thesis. The quotes are linked back to the Source using a link type called 'quote'.

I have found when taking notes say on a journal entry or a book chapter, I prefer to capture them in a single container rather than starting the whole process in a map view or outline view with lots of little notes.  This might not be best practice, but I don't want to think about structure at all when I'm taking notes, I just want to get the words down - you can explode the note later if you want to.  

I do take lots of notes when I read, but I agree with the linked article - the key stuff is the quotes from primary sources, and this system is really designed to capture them methodically and reliably.

The huge advantage of Tinderbox over other systems is that once the information is there, it can be analysed in so many different ways.  I use agents to search for themes.  You can also open the various note containers in map view and play around with grouping things into themes. Try smart adornments for this.  As I am interested in history, I make good use of timeline view.  One of the best ways to identify themes I have found is to use Common Words in the View menu.  Click on a word and you run a search.  In the attached example, the quotes bucket only has two quotes but no doubt yours will run to thousands.  Initially, I would start by using seperators to mark off divisions of notes in the outline, but once past hundreds of notes this would get difficult - at which point, agents would be very helpful to captures notes by theme.  

Tinderbox is great for tracking what I've read, linking quotes to notes etc.  But I use lots of other programmes too and then link to them in Tinderbox (I think it really helps not to be too rigid when doing this stuff - you can agonise over which programmes are best for certain 'workflows', but I think its best just to get on and read and write, and then sort the notes out later in Tinderbox).

Edit: On a related note, ages ago someone here posted a link to a chapter of The Social Imagination, by C Wright Mills, in which he explained his method of note taking.  I thought it was quite interesting and did a little summary of it (far too simplistic for the OP to find of use): http://cl.ly/3q0I0L0p1e0o223n2J0B

There are two really simple points, with which I agree: 1) in order to understand something, you must give form to it and 2) avoid any rigid set of procedures, method or technique.  


Title: Re: Academic Note-taking
Post by Stéphane R on Sep 27th, 2011, 6:47am

@Ben, thanks for that. Do you happen to have that MindMap as text or TBX file?

Title: Re: Academic Note-taking
Post by Ben Worthington on Sep 27th, 2011, 6:52am

It's actually a Mind Node file.  If you have Mind Node I can post that file, but here's an opml version which you can open with TBX: http://cl.ly/2e0s47360q2m2O3E0h3p

Title: Re: Academic Note-taking
Post by Barbara on Sep 27th, 2011, 4:41pm

Thanks Mark, for the comment and wiki-link about maps and outlines and to Ben for the sample files and information about note-taking and workflow -- I will get a look at these and get back to you. Barb

Title: Re: Academic Note-taking
Post by Derek Van Ittersum on Sep 27th, 2011, 4:50pm

Good stuff here. Ben's file is great!

I guess I'd characterize my use of TBX as a more targeted than trying to wade through a huge pile of all my notes. I like to work in maps, and as Mark A points out, maps are limited to viewing notes on one level (primarily). Putting all my reading notes for a project on one level would be more than I could handle. I suppose I could use the automaticity of agents and smart adornments, but I prefer to find the relevant information manually--and DevonThink makes it easy for me to structure notes to find stuff manually. Plus, I like keeping all my pdf notes in there too for searching.

When I move to TBX (for a writing project) I want to work with a subset of notes I know are important and relevant, and visualize them on the map.

But, as others have pointed out, there's no reason I couldn't keep all my notes in one container, and keep my targeted map analysis in another and transfer back and forth. So I think both your metaphors, Barbara, will work. At the same time, I find any metaphor applied to this program ultimately simplifies to a great degree--it's really a thing unto itself.

Of course, what's awesome about TBX is the flexibility. For non-writing projects (like my time-tracking dashboard, or my syllabus-creating machine), I make use of many more of TBX's features--agents, display plots, etc.

Title: Re: Academic Note-taking
Post by Jean Goodwin on Sep 28th, 2011, 4:52pm

Hello, all.  I've been away from the forum--researching!  Not to mention teaching and so on.

Personally, I keep article notes near the article pdfs and article citations, which in my case means Endnote.  At the other end, I write in Word--clumsy, but what everyone wants.  So like Derek, I use Tinderbox mostly for the very broad in between:  map view just to get ideas out there and to begin to make connections, slowly transforming into a writable outline in, duh, outline view.  There is no other tool with even a portion of the power for this key but overlooked stage, where a large portion of the thinking really gets done (in my case, at least).

Barbara, two pieces of advice:  First, everybody researches/brainstorms/thinks differently.  If you had a way that worked for you like for your MA, start small by implementing some part of it on Tinderbox.  Inventing the perfect workflow on Tinderbox is an extremely pleasurable way to procrastinate, but in my experience produces imperfect results.  I'm wiser in what I actually do than in what I think I should do!

Second:  Keep in mind that in Tinderbox, the same note can be in two places at once.  Try making an agent that collects all your notes (or all of a certain kind), and then freeze it.  This will give you a set of aliases that you can spread out on your e-floor, while the organization you've given your notes elsewhere in the document remains unchanged.

Good luck!  The beginning of any big project is a lot of fun.

Title: Re: Academic Note-taking
Post by Lew Friedland on Oct 24th, 2011, 11:44am

Great thread. Derek, would you mind posting your "syllabus machine?" Thanks.

Title: Re: Academic Note-taking
Post by Derek Van Ittersum on Oct 24th, 2011, 12:50pm

You can get the syllabus machine as part of the eastgate tutorial package: http://www.eastgate.com/Tinderbox/Tutorial_CD.html

or from my site, referenced in this thread: http://www.eastgate.com/Tinderbox/forum//YaBB.pl?num=1281439077/13#13

Title: Re: Academic Note-taking
Post by Ben Worthington on Oct 25th, 2011, 1:43pm

An interesting article and linked website which may of use in a dissertation: http://www.stevenberlinjohnson.com/2011/10/introducing-findings.html

(he says having not explored the service at all - sounds interesting in theory though).

Title: Re: Academic Note-taking
Post by Elizabeth on Mar 8th, 2013, 2:54pm

Hello, Barbara!

I was excited to see someone else talking about tools to manage academic citeable notes.  I find 'citeable notes' to be a really useful way to think about my academic reading -- like I'm 'processing' it into reusable chunks for future writing.  It's great to have a little repository of categorized points, arguments, supports, and criticisms from other scholars that I can quickly interpolate into my own writing.  Extends my memory, for sure.  Even organizing these notes is a kind of good scholarly exercise.

Currently I'm building up a system of citeable notes in Scrivener.  This works reasonably well so far (not been doing it long!).  I can copy the same notes to different folders and even kind of experiment with rearranging copies of notes in different ways for different projects.

It is of course pretty rigid and hierarchical, though.  I could get excited about Tinderbox as a tool for growing categories of notes up more 'organically,' and establishing more visual-spatial 'nurseries' to test out different arrangements and clusters for different projects.  

I would be SO interested to hear what kind of work flow you settled on -- I could very much benefit by hearing about your experience.  I know there's a danger to hopping from tool to tool, but again, I only started seriously investing in my Scrivener system recently, so weighing other arrangements is not yet totally counterproductive.  :)

Hope you are still around!  Would love to hear from you.


Title: Re: Academic Note-taking
Post by Mark Bernstein on Mar 9th, 2013, 10:52am

Incidentally, Tinderbox and Scrivener work pretty well together!

Tinderbox reads Scrivener files, and it's also got nice export to Scrivener.  So, it's not too bad to move thinks back and forth.

Title: Re: Academic Note-taking
Post by Elizabeth on Mar 11th, 2013, 12:50pm

Wow, I am very, very excited to hear that Scrivener and Tinderbox play nicely together.  I can begin to imagine some nice little workflows using both.  

Thanks for the tip!

Tinderbox User-to-User Forum (for formal tech support please email: info@eastgate.com) » Powered by YaBB 2.2.1!
YaBB © 2000-2008. All Rights Reserved.