Zettelkasten tools

Christian Tietze has started a page collecting the various software tools available for the implementation of the Zettelkasten method of note-taking, storage and retrieval. He is inviting contributions for suggestions and reviews. Access it here: Zettelkasten Note Archive Software.

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Using colour in outlining

I was glad to see that the latest version (3.6.3b) of Noteliner now supports “unlimited colors for lists, note highlighting and sections of text.” For me colour has always been an important factor in outlining. There seem to be two main approaches.

Noteliner exemplifies the approach whereby you are given complete manual control over changing the colour of the foreground (the font) or the background (highlighting text). This approach comes in handy when you want to mark up an existing outline in different colours to emphasise particular meanings or functions. The downside is that it is a manual process, so in the case of a long outline it would be rather fiddly to be changing every item to a different colour.

This is where the alternative approach excels: outliners that provide an automatic colouring-in option using some kind of a template. Natara Bonsai 5 (Desktop Edition) — my favourite single/dual/triple etc.-pane outliner — does this very well. If you choose Outline > Text Color from the main menu, you are presented with four options.

Natara_Bonsai_edit_colorsYou can colour in your outline automatically according to each outline item’s category, priority or due date, assuming that you have added these values to the outline items.

My favourite feature is the fourth option, “By Level,”  which means that each outline item will be coloured in according to its place within the hierarchy (available up to 16 levels). You can even select a custom colour for the completed items, in case you opt to have a check box in the outline.

Natara_Bonsai_color_by_attributeBelow is an example of such a coloured-in outline. I like this feature because it makes it so much easier to analyse a long, complex outline and comprehend the relationships between concepts at different levels of the hierarchy.

Natara BonsaiAlso, under View > New Outline Defaults you can set up a colour scheme for any new outline, whether created from scratch or imported or pasted in from elsewhere. The colouring-in options are saved thereafter for each new outline.

The downside of this approach is that (at least in Bonsai) there isn’t a way to do ad hoc highlighting or colouring-in of font (as there is in Noteliner). It would be nice if one could still mark up an automatically coloured-in outline with additional highlighting.

Other outliners I’m aware of that can do some colouring-in are StoryView/Outline 4D, Inspiration, BrainStorm, and UV Outliner.

Update (26/07/2013):

There is also Redhaven Outline, which has an interesting implementation of colours (see their Youtube video on that).

Workflows and toolchains

Apparently there is a word for the system that I’ve been constructing out of various software and hardware: it’s called a “toolchain.” Check out the use of toolchains in ethnography here and here. I’m glad to see that there is another researcher for whom ConnectedText works as a replacement for a mainstream QDA software (in this case Atlas.ti).

Academic writing process and associated tools

The main stages of my academic writing process:

  1. Note-taking (empirical data collection or taking reading notes);
  2. Analysis and evaluation, resulting in
    • an abstracted list of observations;
    • a selection of evidence (quotes and notes);
  3. Organising these findings by: [2 and 3 can be done concurrently]
    • Ordering the list into a hierarchical outline;
    • Attaching selected evidence to list items;
  4. Developing a separate outline for a draft (journal article or thesis or book chapter):
    • creating a hierarchical list of items (titles);
    • attaching a selection of evidence (quotes and notes) to the items as inline notes;
  5. Writing the draft;
  6. Adding a reverse outline (headings and subheadings) to the draft [5 and 6 are a more or less simultaneous, recursive process] .

academic writing process

Tools needed:

  1. Note-taking (empirical data collection or taking reading notes);
    1. TOOLS:
      • CT (ConnectedText) – Clipboard Catcher (or clipboard extender)
      • Nebulous Notes on iPad/iPod Touch > Dropbox > CT
      • Dragon NaturallySpeaking (on PC) > CT
      • GoodReader, PDF Expert on iPad > email > CT
  1. Analysis and evaluation, resulting in
    • an abstracted list of observations;
    • a selection of evidence (quotes and notes);
    1. TOOLS:
  1. Organising these findings by: [2 and 3 can be done concurrently]
    • Ordering the list into a hierarchical outline;
    • Attaching selected evidence to outline items;
    1. TOOLS:
      • CT outline (occasionally exported to and imported back from Natara Bonsai)
      • CT outline + linked CT topics
  1. Developing a separate outline for a draft (journal article or thesis or book chapter):
    • creating a hierarchical list of items (titles);
    • attaching a selection of evidence (quotes and notes) to the items as inline notes;
    1. TOOLS:
      • CT Project Outline with links to topics
  1. Writing the draft;
    1. TOOLS:
      • Outline 4D
      • Freeplane
  1. Adding a reverse outline (headings and subheadings) to the draft.
    1. TOOLS:

Update (24/01/2013)

The above chart could have been more representative by having an arrow between ConnectedText in Step 4 and Freeplane in Step 5, as the CT project outline would be exported as a .mm file and imported into Freeplane. This is an important relationship as the links to the selected CT topics will be preserved and remain clickable, thus turning CT+Freeplane into a virtual dual-pane outliner/notes organiser.

Also, Steps 5 and 6 should have been alongside each other or at least there should have been arrows pointing back from 6 to 5, as the reverse outlining process is part of the drafting process. After writing 3 or 4 paragraphs I immediately add headings and sub-headings and slot them into Outline 4D’s single-pane hierarchical outline.

Update 2 (24/01/2013)

Here is an amended chart, taking into consideration the above corrections:

academic writing process 2Update 3 (24/01/2013)

Upon further reflection this is still not an entirely accurate picture of the entire process and set-up. An additional element emerges in Stages 5 and 6: the management of writing fragments that have to be removed from the draft in Outline 4D during interim editing and need to be kept apart. I may reuse some of these later, if and when the need arises.

Initially I just used a text document in NoteTab for this. But as the number of fragments grew, I needed a more sophisticated solution with the ability to split text into paragraphs and rearrange them in a hierarchical outline. For now I’ve been using Scrivener for Windows for this, which works well as a two-pane organiser of notes and also has the handy “split selection with title” command for breaking up a text into segments. However, I find Scrivener a bit of an overkill (and too slow on my Windows 7 system) for this. I’d prefer to use a lightweight, small footprint two-pane outliner that allows for the easy rearrangement of fragments.

Developing a final outline

The problem with developing a final outline for a PhD dissertation chapter is that it is difficult to know when the outline is really final. It will be final of course when you are confident enough that it is of the requisite quality. The difficulty is how to identify the boundary between the conceptual development stage and the stage of writing-up for presentational purposes.

For academic writing it is the former that is the main headache, i.e. coming up with the content, rather than putting it into its final shape. It happens all too often that you think you are in the second stage, only to discover that you have more conceptual development and clarification to do, and you are thrown back into stage 1.

For now I can’t seem to find a better answer than to push on with aiming to reach a final outline, even if it turns out to be an interim stage of conceptual development. Then I just start developing a new “final” outline, hoping that it will really be the final one. As part of this process I am constantly switching between software tools, in search for specific features more suitable for the particular tasks in the subsequent stages of development.

This reflexive and recursive process of dealing with multiple outlines in multiple software tools eventually reveals an arrangement of outlines in an arrangement of software tools, and a shape-shifting process flow that adjusts itself continuously. It is like an experimentally assembled moonshine distillery for the purpose of abstraction to be achieved by routeing ideas (textual content) from one vessel to another, until they acquire sufficient clarity to be bottled and labelled and sold to a discerning public.

Here is a slightly revised graphic (following on my previous post) showing the current distillery and the process flow. Its shape has become slightly clearer to me.

writing-up process flow

On  the left we start with the notes database in ConnectedText. It is the base, the alpha and the omega. It contains the fruits of my research work. However, I now need to extract the spirit and the flavours with my distillery apparatus. Initially I extracted and organised the main conclusions in Natara Bonsai outlines. Bonsai is the fastest tool I have for organising lists into meaningful hierarchies and then drawing ‘final’ conclusions from these conclusions.

Parallel to this I have been developing a chapter outline in Outline 4D. I have also used O4D to summarise some ConnectedText meta topics which were already extractions of important findings (as opposed to the summaries of specific articles that have been analysed in Bonsai). As O4D allows for inline notes in its outlines, I have also pasted in selected quotes (from CT, which came from the original readings) to support particular outline items (my observations).

I also have a 7000-word draft in MS Word that I wrote at an earlier stage partly as an effort to break out of the circular outlining process and force myself to finish this stage (the target is a 10,000-word chapter). However, the draft writing process just turned out to be another stage of the distillery, as I have found some gaps in my conceptual structure. It felt like Word was a laboratory where I tried to assemble the parts but the trial failed and I needed to get back to the drawing board.

VUE was the drawing board, and concept mapping was the process of drawing out the issues for my conceptual apparatus and reorganise my argument. VUE was a kind of an experimental space, a sandbox. It is placed at the top of the diagram because it is an overview of everything that is going on. First I created a reverse outline of my Word draft, to get a better understanding of my argument so far. Then I also developed an outline (well, more of a concept map) for the next stage of writing.

I should mention that I also have an overall outline for the entire thesis kept in a Scrivener project, which contains some relevant material for this current literature review chapter as well. I will need to review it as I embark on constructing my “final” outline.

I have settled on a Freeplane mind map as a way of constructing my “final” outline, which would hopefully lead me through the final – presentational stage – of writing up. In the past I didn’t quite see the point of formal mind maps, as I preferred the freedom of concept maps. But now I see that a mind map – combined with Freeplane’s functionalities – is an excellent way to develop a final outline.

First, a mind map forces you to define a final hierarchical order between sections, ideas and paragraphs, which the final draft needs to have. Secondly, a Freeplane mind map is very economical with screen space, allowing you to cram a lot of information in and be able to navigate it and visualise it easily. Thirdly, it allows you to switch between a mind map and an outline view. Fourthly, it allows you to add notes to items, which can be chosen to be displayed inline, effectively operating as a single-pane outliner with inline notes (of which only a handful exist in the world).

Fifthly, it allows you to export into RTF file format in such a way that the inline notes get displayed below their items, and the items are assigned headings according to their hierarchical level. So for example in Word or LibreOffice, items can be viewed as section headings in the Navigator window, a set-up that can be used as a dual-pane outliner. Also, the headings can be used to create a table of contents.

Finally, (building on the fourth and fifth point), you could construct a complete sentence outline in Freeplane by using items as topic sentences and notes as the evidence to support the topic sentences (e.g. quotes or other details). Even a simple “copy and paste” into Word creates a bullet-pointed hierarchy, which then can be transformed into a draft (although with this export method you don’t get the headings formatting preserved – but that may be preferable in some situations).

I am planning to do the final writing in Outline 4D though (which will require importing the RTF file with the headings and notes), in recognition of the possibility that this “final” Freeplane outline may not turn out to be entirely final, and rather than create yet another reverse outline or concept map to keep track of the underlying and implicit conceptual structure, I could just use O4D’s outlining functionalities to keep track of the evolving implicit outline of the draft. This could also be done in Word, simply by modifying the headings that get displayed in the Navigator (as a dual-pane outliner set-up). However, I find O4D’s single-pane view more conducive for this simultaneous writing and real-time (reverse) outlining, as O4D has many helpful alternative visualisations of the text and the outline.

Do I worry that I get carried away with playing around with software tools instead of doing the writing? You bet. Although there is definitely a ludic aspect to this, in the end the distillation process is real and necessary. I would need to carry out the abstraction process somehow in any case. I am hoping that by constructing a sophisticated distillery I will be able to extract and construct a higher quality final product.

Could I be wrong about that? Yes, that is a distinct possibility. However, academic research is by definition an experimental process and experiments (and experimenters) can fail (and they often do), perhaps even more frequently than they succeed (which is why so many PhD students never complete their theses). All I can do is carry on and hope that my experimental process and set-up produce a satisfactory result.

ConnectedText window across two monitors

After having seen Brian Lennon’s setup of a ConnectedText window stretched across two monitors, of course I couldn’t rest until coming up with my own ideal two-monitor configuration for my current workflow. I would suggest that any CT window configuration is workflow-specific, i.e. different projects require different arrangements of panes to maintain optimal workflow. (CT allows you to save your desktop configurations, so you can have as many variations as you like and switch between them freely.) See my two examples below, one with the browser pane in the second monitor, the other with the Navigator pane. I’m using CT’s help file, “Welcome to ConnectedText,” as my project example.

The rationale behind my arrangement is the following. My current task requires me to work with topics (rather than the reading displayed in the browser), therefore in Monitor 1 I prefer to focus on information that pertains to the topic at hand (such as its “Table of Contents” or its links in the “Summary” pane). The “Topic list” is there for easy browsing and so that I can drag and drop topics into the body of a topic when I need to create a link between two topics (such as adding a reference to a citation). The “History” pane serves as a quick way to alternate between topics that I’m currently working on.

Monitor 2 contains panes that I would use less frequently, so that I can still switch off this monitor when I need to block them from view, such as when I need to focus on writing in the main topic edit pane in Monitor 1. The “Category” pane lists all categories within the currently opened project (database file). The “Search results” pane shows all topics sorted by relevance that contain the search term I’ve recently searched for. To my great delight CT has recognised my default PDF-XChange Viewer plug-in, which means that I can do searches and add annotations (highlighting, notes) to my PDF files directly in XChange Viewer, without having to leave CT.

The only downside of the two-monitors view is that should you need to use an external application for anything else, you can’t work in both the CT window and the other program at the same time. So either CT needs to be minimised or the CT window needs to be dragged to a smaller size, to allow for screen space for the other application. [Update 14-Dec-12: Just found a solution to this. Install Direct Folders (it’s free and it was already on my Favourite Tools list) and by right-clicking on the “Close” button of the non-CT window that you want to stay on top, it will stay on top of the CT window. Brilliant!] This is where alternative saved CT desktop views may come in handy. [Click here and here for full-size images.]

ConnectedText across two monitors, example 1

ConnectedText across two monitors, example 2

If anyone else is willing to share their CT window configuration, just send me an email with your screenshot at docandus [at] gmail.com and I’ll be happy to post it on this blog.

Docking panes in ConnectedText

ConnectedText (CT) is a highly modular application, with a large number of panes that can give different views of your data more or less simultaneously. Viewing a lot of panes at the same time requires screen real estate, therefore CT can particularly benefit from having a second monitor. Users with two monitors are presented with a decision to make: one could undock some of the panes and move them over to the other monitor, or one could keep them all docked but stretch the CT window across both monitors.

I belong to the first camp and I only use my second monitor for undocked floating CT panes (especially the Navigator pane, occasionally the Outliner pane). My main reason for this is that I only turn on the second monitor when I really have to, as I usually find it too distracting when I need to concentrate on working in the main monitor. However, recently I came across Brian Lennon‘s screenshot of his CT setup, who prefers to work with the CT window stretched out across both monitors.

I find Brian’s setup very interesting. There are clearly some benefits to this approach as well. You can have a more complete and diverse view of your project. You can have a more fluid workflow by staying within the CT environment, rather than using e.g. an external PDF viewer and web browser, as I do, which requires me to switch back and forth. (In fact only now I’ve understood why CT needs an internal browser and file viewer: so that you can create this sort of total CT environment.)

Below is a screenshot of Brian’s CT window (remember, it’s stretched across two monitors). I have added some labels and arrows to show all the different panes that are visible and the relationships between them. As you can see, Brian even had a bit of space left over in the right-hand side monitor, so he could have stretched the CT window out even further and made more of the panes visible. His CT project is also an interesting example of a reading notes database. (If you do have two monitors, you could try to stretch out the image across both of them to see the screenshot in its actual size and full glory.)

ConnectedText panesMany thanks to Brian Lennon for giving me permission to use his image.

P.S. Novices may find the docking process in CT rather tricky at first. Watch the second tutorial video to see how to carry out the docking of panes in ConnectedText.