Taking reading notes with ConnectedText

Recently I have developed a reading note-taking process with ConnectedText that follows the Zettelkasten method more closely and is an alternative to the note-taking process with Freeplane that I have described earlier. The main difference is that the earlier method with Freeplane produced one large mind map that contained all the reading notes in a single document and which tried to capture the inherent outline (logical hierarchy) of a book’s argument, while this new method produces many small index cards with quotes and notes, which nonetheless can be assembled into an overall outline at the end, to reproduce the overarching flow of the original text’s argument. The main advantage of this latter process is that it results in bite-size chunks of texts that can be connected and reassembled in many other ways, thus providing more versatility and ease of use during the analysis and synthesis stage, and throughout the life the Zettelkasten.

Here is my process flow (when reading a book in PDF format):

  1. I read the PDF document.
  2. I copy and paste interesting passages into NoteTab (plain text editor) to fix the line breaks with CTRL+J and use CT’s markup to preserve formatting (mainly italics and superscript for footnotes), if required.
  3. I paste in the quote into a new “date topic” in CT. Date topics are CT documents with some special properties. E.g. they are prefixed automatically with the date and time of the creation of the topic and allow the topics to be listed in chronological order in the “Topic list” pane. Before starting to take notes for a section of the book (e.g. a chapter), I create a dedicated template (a plain text document) for that section. CT remembers the last template used, which means that whenever I create a new topic, I don’t need to worry about selecting the template again. The template contains all the major fields of a reading note you’d expect, such headings for “Quote,” “My comment,” “Bibliographic reference,” link to page in the PDF file, and “Categories.” The reference is already marked up with CT’s “attribute” tags, which allows for automatically gathering topics with the same attributes. In the “Categories” I would include any labels (tags) that will pertain to all the notes within that particular chapter (including the chapter’s title and the author’s name). I also set up a phrase with the “author date” format in PhraseExpander, so that when I create a new topic, I won’t need to retype that bit again. Here is the sub-process for creating a new date topic in CT:
    1. click on the “new topic” button in CT.
    2. click on the “add current date/time” icon in the “new topic” dialog box.
    3. start typing author’s name and select phrase from PhraseExpander’s pop-up, e.g. “Smith 2013”
    4. type a descriptive title for the quote. The final topic title will look something like this:
      1. 29/04/2014 10:34 Smith 2013 definition of scientific method
    5. click “OK” to create new CT date topic.
  4. paste in the quote from NoteTab.
  5. Add any comments, such as interpretations or ideas triggered by the quote.
  6. Use yellow and pink colour to highlight any crucial sentences in the quote (optional).
  7. Add the page number for the PDF page link (to be able to go back to the source page with one click).
  8. Add labels (tags) in the Categories section to characterise and categorise the quote.
  9. Save.
  10. After having finished reading a chapter, I drag and drop all the newly created date topics into a CT outline file (.cto) I  created for the whole book, and organise them into a hierarchical structure, thus recreating the underlying logical structure for the chapter’s argument (and gradually for the whole book). This is the process and mechanism that replaces the single Freeplane mind map with the previously described method. Should I still wish to see this outline as a mind map, I can export it into Freeplane, where each outline item would be a node, and each node would have a link that leads to the quote in CT, thus acting as a virtual dual-pane mind map/outliner.


My minimalist writing environment

…with research question permanently displayed

As I’m writing up my PhD dissertation, I am continuously striving to streamline my writing process and simplify my writing environment. For this reason I have been drawn to minimalist writing applications that reduce unnecessary distractions, such as too much chrome and colourful menu buttons in applications. I use different software for different writing situations. Currently I am writing up a chapter for which I have detailed notes organised in an elaborate Freeplane mind map, which I keep in my right hand monitor.

My central monitor is where I do the actual writing. Currently, this consists of a WriteMonkey window that takes up most of the left and centre of the monitor area, while on the right I have a Notepad2-mod window open to take some ad hoc notes and organise them into a quick outline prior to writing. To do the actual writing, I use Dragon NaturallySpeaking to dictate directly into WriteMonkey, while looking at my Freeplane mind map, which I check off gradually, as described in this post.

Notepad2-mod is a recent discovery for me. It is a replacement for Windows’ own Notepad. I have learnt about it at the Donation Coder forum, where you can find instructions on how to turn it into a very simple plain-text-based outliner. I like to use it in conjunction with WriteMonkey, as it is easy to copy and paste unformatted text from one to the other, and I also find it distraction-free enough. I also use Notepad2-mod as a scratch pad area, to work out ideas quickly, before dictating them into WriteMonkey.

There’s one more screen element that has become an important part of my setup. As I was writing my chapters, I continually wished that I was able to view my main research question at the top of my screen, so that I would be reminded of it at all times, in order not to lose my main focus. However, I had a hard time finding a solution that would display a single line permanently at the top of my screen, without there being any chrome around it, and without it being obscured by maximised windows.

Eventually it was another of Mouser’s brilliant little solutions that allowed me to do this. It is a very simple little application called DesktopCoral, which lets you reserve an area of your screen and prevent other software from covering it. Besides other uses, you can also select a .jpg image file to be displayed within it. So all I had to do was to take a screenshot (using Mouser’s excellent Screenshot Captor) of my research question displayed in a single line in WriteMonkey, and insert it into DesktopCoral’s docking bar, which I docked to the top of my screen. It takes up just a tiny sliver of it. As you can see (exactly because you cannot actually see it!) from the screenshot below, the DesktopCoral bar blends into my screen environment seamlessly.

WriteMonkey, Notepad2-mod, DesktopCoral, Winsplit RevolutionTo achieve this effect, I also needed to enlist Winsplit Revolution, which I used to position the WriteMonkey window into the centre-left area while in full-screen mode (otherwise WriteMonkey would cover up the DesktopCoral bar, as full-screen mode is different from maximised-window mode). (By the way, I’m not bothered by my Windows taskbar at the bottom of the screen. It allows me to quickly switch between applications with the mouse, and I don’t find it too distracting.)

If I did not need the Notepad2-mod window, then I could just centre WriteMonkey in full-screen mode (again, with Winsplit, in order not to obscure the DesktopCoral bar), and the research question area at the top would simply look like it belongs to WriteMonkey itself, except that it is permanently there, and it does not disappear when I scroll up or down, or indeed do anything else: it remains visible even when I close WriteMonkey and switch to other tasks.

At the moment nothing is more important to me than remaining mindful of my research question, therefore I do not mind at all that it is always in my face. I could imagine that other people might find this solution useful for pinning important reminders—or even inspirational quotes—to the top of their desktops to permanently remind them what is important.

The most amazing thing is that, with the exception of Dragon, all of the above tools are free– though their developers do welcome donations, and they deserve them, too. I just love these tools to bits—or should I say, to bytes?


If this is just not minimalist enough for you, you could always 1) turn off the numbering in Notepad2-mod, if it’s too distracting, or 2) instead of Notepad2-mod just use another instance of WriteMonkey and position it on the right with Winsplit Revolution, and 3) make the Windows taskbar autohide. With 2) and 3) it would be truly just a single-coloured background with a single-coloured font, and nothing else to distract you. Here is what the screen would look like then (the file name, word count, and time info in blue at the bottom is optional, as is Winsplit’s little floating tool in the bottom right corner):

WriteMonkey with DesktopCoral and Winsplit RevolutionP.P.S.

WriteMonkey’s developer tells me that it is also possible to display the research question with WM’s own Corkboards plugin. And it turns out you may not even need full-screen view + Winsplit to get rid of WM’s Windows chrome: you can just CTRL+right-click with the mouse on the right side of WM’s window, and the chrome disappears. Here is his screenshot of the Corkboards feature:

WriteMonkey with Corkboard plugin

Taking reading notes with Freeplane

For some time now I’ve been using Freeplane as my reading-note capturing application. I would be reading a book at my desk, in front of my computer monitor(s), and use Dragon NaturallySpeaking to dictate my notes and quotes into DragonPad first, and then paste them into Freeplane. In the case of electronic materials, mainly journal articles in PDFs, I would convert the PDF into a Word file with ABBYY FineReader (so that I preserve word-wrapping and formatting while copying), and then would paste the quotes into Freeplane.

What are the advantages of this method? Firstly, it allows me to reverse-outline the book’s argument by organising the quotes and notes into a hierarchical mind map. Such a reverse outline helps with reconstructing and understanding the main train of thought of the reading, as the hierarchy records logical relationships between ideas. Here the mind map format has an advantage over a traditional vertical outline, as the individual nodes are easier to see and comprehend when distributed across a wide monitor in landscape form.

Secondly, each node can have a title and a note, and the latter can be seen inline (as opposed to being separated into another pane, as in most dual-pane outliners). Also, Freeplane can preserve rich text formatting (unlike let’s say Natara Bonsai). You can use icons and different styles to mark important notes. It is easy to restructure the outline by dragging and dropping nodes and branches around.

Thirdly, it is easy to convert a Freeplane mind map (which uses Freemind’s .mm file format) to other file formats. I use iThoughtsHD on iPad as my Swiss-Army Knife converter of mind map formats. I usually convert it into OPML, in order to import it into Bonsai, if further organising and analysis is needed, or simply to convert it into RTF, so that it can be imported into my main database, ConnectedText, which is the final destination of all my notes. I also link to all the different formats of a file (.mm, .opml, .otl, .rtf) from the final CT document, so I can easily find them later.

But Freeplane is useful not only for capturing and organising my reading notes into a hierarchical outline. It also comes in handy when it’s time to write up the notes for a chapter or article. I start a new Freeplane file as my outline for the new piece of writing, and I can simply copy and paste selected nodes and entire branches of quotes and notes from other Freeplane files, thus gathering relevant information for one author from let’s say five other mind maps with notes for five books by that author. (It is useful though to have two monitors for this, to take full advantage of the landscape orientation of mind maps.) Then as I write the final piece, I use a big red X icon to mark off the nodes and branches that have already been discussed.

Freeplane reading notes

I hear people complain about Freeplane not being pretty or visual enough. To me that is an advantage. I find pretty colour schemes distracting. All I want is black font and a white background. I do like the automatic colouring-in of the lines representing the branches, as that guides the eye and helps comprehension. But otherwise I want to be the one who decides when to apply additional colour or an icon to introduce new visual information. And I only do that to highlight important nodes, so I can quickly pick them out from a complex mind map. I thank the developers for keeping the main interface simple.

By the way, don’t be confused by the screenshots on the Freeplane website. Obviously, the developers are trying to show off all the different features. However, pretty much all the colour noise can be switched off, and you can use it as a minimalist, almost black-and-white (or whatever colour-combination you like) note-taker and organiser.


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.

Academic writing workflow with ConnectedText, Freeplane, and Outline 4D

A large part of the academic writing process has to do with taking notes, collecting quotes, analysing and evaluating them, coming up with your own interpretation, then developing an outline, and finally writing up the material into a draft. I’ve experimented with various set-ups to tackle this process in the past that involved a lot of different pieces of software (see here and here). However, recently I’ve come up with a simplified workflow that ‘only’ requires three pieces of software: ConnectedText, Freeplane, and Outline 4D (aka StoryView).

  1. I import quotes and notes into ConnectedText (CT) as I’ve described elsewhere, using my latest reading notes template.
  2. As I am reviewing the document, I identify key quotes and notes that I would like to consider as material for the draft. When I come across an important or interesting quote or note, I select the text and type CTRL+ALT+/ to activate Manfred Kuehn‘s “copy to new topic with link” AutoHotkey script (see below), which copies the selected text, creates a new CT topic with it, and also inserts a link under the original text to this new topic.
  3. Simultaneously to this process I create an outline for the intended draft using CT’s own Outline tool. Whenever I create a new topic with a quote or note using the process described in point 2, I add a corresponding item to the outline and drag and drop this new topic on it, which creates a hyperlink between the outline item and the selected quote or note. Clicking on the outline item opens the corresponding quote.
  4. I export the CT outline as a Freemind (.mm) file and import it into Freeplane (a mind map application). The CT outline has been thus transformed into a mind map. Nodes with links remain clickable, which means that clicking on a particular Freeplane node with a link opens up the corresponding quote or note in CT. I can add further notes using Freeplane’s own Notes functionality and develop and restructure the outline, if I wish.
  5. When I’m finished with outlining and am ready to begin to write the draft, I tile Freeplane and CT vertically in my second (22in) monitor, so I can look at both the mind map (i.e. my outline) and the corresponding quotes and notes in CT. Effectively Freeplane and CT have been integrated to form a funky “dual-pane” outliner, where the first pane is a mind map, and the second pane is the viewer for the note/quote attached to individual mind map items.
  6. In my main monitor, I fire up Outline 4D (aka StoryView) and start writing my draft, while also using O4D’s outlining functionalities for almost real-time reverse outlining, i.e. as soon as I write a larger chunk of text, I add headings and sub-headings to it to crystalise the final implicit logical structure (outline) of the emerging draft. All the while I’m following and ticking off the branches of the mind map and copying across selected quotes and notes from the associated CT topics.


This workflow could of course be further simplified, as you could simply use CT’s Outline pane and its view pane as the dual-pane outliner in steps 4 and 5, altogether leaving out Freeplane. However, the benefit of using Freeplane is that it gives an airier spacial view of the outline and it also has its own inline note capability, which CT’s Outliner doesn’t have.

As for step 6, you could use any old word processor or editor to complete the writing. However, I find that the draft usually develops its own implicit logical structure which won’t be identical to the one in the mind map. To put it differently, there is still abstraction and conceptual development taking place during the writing process and not everything in the mind map will make it into the draft. New ideas may emerge from the draft as well. Hence it’s necessary to engage in reverse outlining to keep track of the emerging logical structure.

I did try to use MS Word 2010 with its navigation pane for this (by using headings), however I found that Outline 4D as a single-pane outliner with inline note capability was better suited to the task of real-time reverse outlining, thanks to its multiple options to collapse different sections or view only headings or only text or a custom-mix of both.

Here is Manfred’s AHK script. If you haven’t used AHK before: 1) download, install and run AutoHotkey_L on your PC; 2) create a new text document in Notepad (or your favourite text editor – I use NoteTab); 3) copy and paste the script below; 4) save the text as e.g. “copy_to_new_topic.ahk” on your desktop; 5) run it by double-clicking its icon; 6) use it by selecting the desired text in CT, typing CTRL+ALT+/ and then naming and saving the new topic.

By the way, you could also just use CT’s own built-in “cut to new topic”  (CTRL+ALT+N) command, which does not require AutoHotkey and which also leaves a link behind in the original topic. However, I prefer to use this “copy to new topic” AHK script because I want to preserve the integrity of the original document (which e.g. could be the full text of an academic article).

; Copy to new topic         |

^!/:: ; copy to new topic

clibboard =
Send ^c
InputBox, OutputVar, Topic Title, Enter the title of the new topic:
if ErrorLevel <> 0
     MsgBox, You cancelled
     WinActivate, ConnectedText
     SendInput {Right}%A_SPACE%
     SendInput `[`[%OutputVar%`]`]
     SendInput !t
     SendInput %OutputVar%`n
     IfWinActive, Confirmation
           SendInput ^v!e

Update (24/01/2013)

Here is a visual representation that summarises my academic writing workflow with the associated tools. It should be read in light of my additional comment below (i.e. there are two different types of outlines and sets of evidence represented). I have also included the tools that I use for note-taking (step 1).

academic writing process

Analytical process flow for reading notes in ConnectedText

Currently I’m working on my literature review. Here is my analytical process flow for importing data, analysing it, and outputting information using ConnectedText (CT) and a variety of other tools. This process flow is just a snapshot, it’s not set in stone. It keeps changing as my needs change and as I gradually develop approaches that better suit the creative process of analysis, evaluation and synthesis.

  1. Importing reading notes into CT:
    1. I read and annotate academic articles in PDF form using GoodReader (if the text can be highlighted) or PDF Expert (if the PDF is a scanned image) on an iPad.
    2. Then I email the notes (highlighted text + my comments) and the annotated file to myself.
    3. On the PC I replace the original PDF file with the annotated one, re-link my EndNote reference to it, and copy and paste the highlights and the comments from the email into a new CT topic in my “Readings” project (CT database) under the ==Quotes/Comments== heading in my CT reading notes template.
    4. With printed books (i.e. not e-books) I take notes using a pen and a paper notebook, and when I’m finished, I use Dragon NaturallySpeaking to dictate the selected quotes and my comments into DragonPad, from where I copy and paste them into the CT template as described above.
  2. Analysing and evaluating reading notes in CT:
    1. I use CTRL+H to “search and replace” (also available from Search > Replace) the headings inserted by GoodReader/PDF Expert with either ===Quote: === (for highlighted text) or ====Comments: ==== (for my own comments).
    2. I review the text and extract the essence of the quoted text and comments and add it into the headings, such as ===Quote: cognitive functions are socially acquired===, followed by ====Comment: I agree with this====.
    3. I use yellow colour to highlight particularly important quotes and comments.
  3. Organising conclusions:
    1. If the CT topic is short, I can develop and record my conclusions immediately under the heading =Evaluation=. I summarise my main point in a final couple of sentences under =Verdict=, including them in the attribute [[Verdict:=My concluding sentences go here.]], so that they show up in the Infobox at the top of my CT topic.
    2. If the CT topic is long (i.e. it contains a lot of imported quotes and comments), then I need to use additional tools to organise the annotated headings.
      1. I remove the [[$NOTOC:]] markup from my template, so that the Table of Contents (TOC) becomes visible within the topic.
      2. I highlight the contents of the TOC, right-click, copy, and paste it into a blank Natara Bonsai document. In Bonsai I already have the new document template set up, so that different hierarchical levels appear in different colours, to aid the sorting of information.
      3. Using Bonsai’s outlining functionality, I reorganise the imported contents of the CT TOC into a meaningful hierarchy.
  4. Developing an outline for the draft chapter:
    1. The whole purpose of evaluating reading notes is to come up with my own interpretation, supported with evidence. The next (and parallel) stage is to develop an overall outline for the draft thesis chapter. Depending on the complexity of the material, it may require several tools still:
      1. I keep CT open to be able to view given reading note.
      2. I consolidate material (my main points supported by key quotes) in a final Outline 4D outline (which is a single-pane outliner that can have inline notes, in contrast to Bonsai.)
      3. During this whole process I use an overall VUE concept map to work out relationships between concepts and to develop an argument.
      4. I record the very final overall outline in the form of a Freeplane mind map.
  5. Writing up:
    1. to manage the final writing-up process, I use MLO to record to-dos as they develop.
    2. I do the final writing-up in an Outline 4D document. The advantage of using O4D for this is that it obviates the need for another application to do reverse outlining as the text grows, because it is easy to alter headings for multiple hierarchical levels and toggle them on and off, when you only want to see the text. I find this better than dual-pane alternatives such as Word with Navigation Pane or Scrivener.
    3. To add references, I simply type the reference such as (Smith 2008: 35), so as not to be distracted and disrupted by having to switch to EndNote every time (and it is not compatible with O4D anyway).
    4. I export O4D text to Word.
    5. I replace manual references with EndNote references, to build bibliography.

Here is a graphic just showing the latter stages of my writing-up process flow. I embed these types of process flow graphics in the home page (dashboard) of my reading notes wiki, so that they remind me every time I get stuck. Chances are that in a few days it will be replaced with a modified process flow, as I keep tinkering with it.

writing-up process flow