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.

Outline 4D for drafting and reverse outlining

In my previous post I mentioned that Outline 4D (formerly known as StoryView) has become an integral part of my academic writing workflow, as my tool of choice for writing the first draft. O4D may sound like a surprising choice for this, and its emergence as such was unexpected for me as well.

O4D is primarily known as a scriptwriting tool or an outliner targeting creative writers. It is quite old and it no longer seems to be developed. Originally I thought I would be using ConnectedText, Scrivener for Windows, MS Word 2010 or LibreOffice for writing up my PhD thesis. But through a trial and error process Outline 4D has emerged as the winner.

The main reason for this surprising development has to do with the fact that Outline 4D is a single-pane outliner with inline notes capability and with a wide range of visualisation options, which make it particularly suitable for both writing (as in developing sentences and paragraphs) and for reverse outlining (structuring the developing draft into a logical hierarchical structure). There are surprisingly few single-pane outliners with inline notes. I’ve tried them all and O4D is the most versatile in terms of visualisation and the speediest in terms of writing and reverse outlining operations.

Why not use a dual-pane outliner and writing tool such as Scrivener or a word processor such as MS Word or LibreOffice with navigation pane enabled? The main reason is that in a dual-pane tool you can’t just collapse and expand an arbitrary selection of sections and hierarchical levels to make only a particular part of the outline structure visible and still be able to work on a section of your choice for which that particular view is relevant.

Also, it’s just more helpful to be able to view the “headings” (“titles” in O4D) within the same pane, rather than have to look for them in a second pane. I will provide a screenshot below to illustrate how this is done in Outline 4D. Before I get to that one though, let me just walk you through the main options for visualising your developing draft in O4D.

First, let’s take a look at the plainest view. You have a classical single-pane outliner with inline notes here. O4D allows you to customise the font and the background of each hierarchical level of the text. Each outline item or text snippet (called “event” in O4D, reflecting its scriptwriting origins) consists of a title and the inline note (called “content”). Both are optional, i.e. you don’t need to have a title if you don’t need one, and you don’t need to add content to the title if you don’t want to.

Outline 4D - plain viewThis text can be viewed (in  the main “Outline View,” as opposed to the “Timeline View,” which I’m not going to discuss here) in four different ways, which I find extremely helpful. The first one can be seen in the screenshot above, which shows both “Titles and Content (Ctrl+Shift+8).” This is the most complete view, i.e. all the textual content is visible.

However, if you’d like to view the underlying logical structure only (as marked up by the various headings and sub-headings), you can click on “Titles Only (Ctrl+Shift+9),” and you get the following skeletal view, which hides all the inline notes (content):

Outline 4D: titles only

I like to add a heading or sub-heading to every single paragraph that I write, so that the above two views provide me with an overview of my entire logical argument and content. With a large document (10,000 words is a typical length for a PhD thesis chapter), this may at one point become overwhelming and you may just want to view the text itself, without all the headings and sub-headings. This can be easily achieved by hitting the “Content Only (Ctrl+Shift+0)” button. All you see here is the content of your paragraphs:

Outline 4D: content onlyIf this was not enough flexibility for viewing your content in different ways, there is still the “Custom Visibility (Ctrl+Shift+7)” option. It allows you to individually customise every single item (title + content, which for me equals a paragraph and its topic) in your document, so you can hide for example meta commentary that is not strictly part of your text.

The beauty of O4D is that these views are not just there for visualising the text differently on your screen but you can also print or export your text as an RTF file in the selected view. Even the word count tool allows you to exclude event titles or only include selected “events” (outline items). Here is an example of a custom view. I hid the contents for level 1 titles and I hid the titles for level 3 and 4 content.

Outline 4D: custom visibilityAnd there is more. There is also something called the Level Selector, which allows you to select text residing at a particular hierarchical level in the outline to be displayed on its own. Here I deselected all levels except Level 4:

Outline 4D: Level SelectorAnd this is what “Level 4 text only” looks like:

Outline 4D: Level 4 onlyI haven’t used this feature yet for my current project but I could see it becoming useful once large texts become available and let’s say I’d only like to see the Level 1 text, which would be all the introductions to various sections, thus giving a quick overview of the overall project, allowing me to check for logical consistency, ease of comprehension and transition between sections.

Until now I have kept colour out of this discussion, as I didn’t want it to be a distraction while discussing the above features. But when it comes to outlining, I’ve always found the ability to colour in an outline on the basis of hierarchical level very useful, as it just makes the navigation of the outline and comprehension of its logical structure so much easier. (This is one reason why I love Natara Bonsai so much. Sadly Bonsai doesn’t have inline notes.)

When it comes to adding colour, one is spoilt for choice in Outline 4D. First, O4D allows you to customise your font colour on the basis of the hierarchical level, so you can have different colours for both the title and the content for each level. This works automatically, every time you add a new section. Here is an example with different font colours for item contents:

Outline 4D: text colour by levelPersonally I don’t use this feature in O4D, as I find it too busy for viewing inline notes (although I use it a lot in Bonsai for a regular outline without inline notes). Instead, I prefer to colour in the background of the outline items. There are several options for that. Similarly to the font colour, you can customise background colour per hierarchical level (but there are other options as well).

A discreet and quick way to turn on a partial background view is by clicking on the “Toggle Structure Column” button, which brings up the Structure Column that shows the hierarchical relationships between the outline items and shows a bit of their background colour:

Outline 4D: structure columnIt is also possible to colour in the entire background of the outline items (these obviously change automatically when you indent or outdent an item):

Outline 4D: coloured backgroundIt depends on the stage of the writing and the particular writing or editing task whether I opt for a distraction-free all-white background or I turn on a partial or full background-coloured view.

Here is a screenshot I promised at the beginning of this post to illustrate why I find O4D better for reverse outlining than dual-pane outline setups like Scrivener, WhizFolders or MS Word 2010 with navigation pane. Here I collapsed Part I and Part III completely, so I can focus on Part II. Even within Part II, I can selectively collapse or expand particular sections, depending on whether I need to see them during the writing process.

Outline 4D: collapsed eventsHere I’m working on the section entitled “Ut enim.” You can see that the body of the active section has a white background, which makes it easier to see where you are and also to indicate that work is being done here. I have written three paragraphs already, so the next step would be to do the “reverse outlining,” which would involve splitting off these paragraphs into their independent sections, giving them a title that summarises them, and indenting or outdenting them according to how they fit into the overall train of thought logically.

Finally, it is also possible to mark up the inline text with a limited selection of rich text formatting. There is yellow highlighting only, bold, italics, underlining, and you can also change the font colour further. It is possible to designate URLs and email addresses as such, but they would only become functional after the text has been exported as RTF.

Outline 4D: rich text formattingI don’t tend to bother much with formatting my text because here I want to concentrate on writing, not on word processing. Outline 4D is not compatible with citation software either but that doesn’t bother me, as I find using EndNote referencing during writing distracting anyway. Instead, I just type my references manually such as (Smith 2010: 345), and then I replace them with EndNote references once I’ve exported the completed draft into Word.

Another useful characteristic of O4D is its multiple document interface (MDI). This means that you can open and display multiple O4D documents within a single window. This becomes useful when you want to compare multiple documents (e.g. different versions of a draft) and edit them simultaneously. Here is a view of eight O4D documents tiled vertically across two monitors:

Outline 4D: eight windows tiled

The downside of MDI is that you can only run one instance of O4D, which makes it a bit awkward (but not impossible) to view a set of O4D documents in one monitor and write another O4D document in another monitor. I get around this restriction by doing the writing in StoryView, which is an earlier (and 99% identical) version of O4D. If you decide to buy O4D, it’s worth asking the developer or the retailer whether they can also give you a licence for StoryView.

I hope I have managed to demonstrate why I think Outline 4D is an excellent writing environment for drafting and reverse outlining. As I mentioned it in my previous post, this stage for me comes after the note-taking and outlining stage, for which I prefer to use ConnectedText and Freeplane.

The next step would be to export the Outline 4D document as an RTF file, convert it into a .docx file in Word, add my EndNote references, convert the O4D headings into Word headings in order to produce a table of contents, and add any further rich text formatting necessary (which would mostly consist of adding italics for emphasis). Then it’s off to the printer.

If you decide to give Outline 4D a try on a Windows 7 machine, make sure to run it in Windows XP mode and as an administrator (right-click on icon, choose “Properties” and click on “Compatibility” tab). Even then I needed to disable “User Account Control” (UAC), to stop the annoying Windows pop-up.

I did come across one bug: it crashes sometimes if you change some options in the “Outline 4D Options” window while in “Timeline View.” So make sure to save your work before changing those options. Having said that, I haven’t lost any work in O4D so far. But I do save my work often (there is even an automatic reminder you can set to save after a given period) and export it into RTF daily, just to be on the safe side. It’s an old piece of software after all.

It’s an oldie, but a goodie!


Addendum (14/01/2013)

I’ve just realised that there is yet another relevant view of the outline that I forgot to add. If you select all items and click the “Summarize (Ctrl+[)” button, Outline 4D provides you with a summary view of your outline, consisting of all the titles and the first line of each content section. There is also an “Unsummarize (Ctrl+])” button to revert to the full outline. This summary view is an interim step between the “Titles Only (Ctrl+Shift+9)” view and the “Titles and Content (Ctrl+Shift+8)” view. It can be useful for skimming your document and getting an overview of the general flow and coherence of the text.

Outline 4D: SummarizeOf course there is still the “Timeline View,” but that is such a complex feature that it would take several blog posts to do justice to it. It’s like having yet another completely different piece of software, although it is intrinsically linked to the “Outline View” in some very ingenious ways. Hats off to the original developers, wherever they may be!

Addendum 2 (17/01/2013)

There is yet one more colouring-in option for Outline 4D. You can also choose “Draw Event Frames,” which is more subtle than “Draw colored event backgrounds,” as it only draws the borders of the “events” in the background colour that was selected for each hierarchical level:

Outline 4D: draw event framesP.S. Although above I linked to the developers’ (Write Brothers) website, where you can download a 5-day trial version, if you are interested in purchasing this software, it is worth shopping around. E.g. currently the download version is $89.95 at, while at the Writers Store it is $79.00. But occasionally you can get it even cheaper from Amazon (the boxed version) or from small retailers outside the US, or if you catch a promotion at (it was $65.00 back in November 2012).

Addendum 3 (30/01/2013)

I have discovered yet another cool feature in Outline 4D (not sure what took me so long). If you find that your outline is getting too big and you’re finding it difficult to get a sense of the overall document, or if you need to look at two (or three or more) different sections of the outline that are far away from each other and can’t be viewed simultaneously, you can always open two or more versions of the same outline and tile them vertically. This way you can get two (or more) live views of the exact same document, meaning that changes are updated to all open windows. This is how you do it: go to Window > New Outline Window and then choose “Tile Vertically.” Here is an example:

Outline 4D dual viewAddendum 4 (31/01/2013)

Although I said I wouldn’t mention Outline 4D’s Timeline View in this review, the previous visualisation gave me the idea that if you do the same trick with the Timeline View (i.e. go to Window > New Timeline Window > Tile Vertically), and then choose “View > Fit to view” for the index card version of the outline item you want to edit, you can emulate – and to some extent even improve upon – BrainStorm‘s famous “aerial view” or the much missed “document view” of GrandView. In the following screenshot you can see an example where an outline item is being edited as a standalone piece of text in the left window, while you can have any of the aforementioned 11 visualisations in the right (Outline view) window:

Outline 4D timeline with outline

P.S. In fact this feature can turn O4D from a single-pane outliner into a dual- or even multi-pane outliner. You could have a top-level outline open in the left pane, a more detailed outline in the next pane to the right, and then the single-note (document) view in a third pane (which would make it into a three-pane outliner).

P.P.S. Here is a screenshot of Outline 4D as a three-pane outliner. The left pane is “Titles only” view; the middle pane is “Summary” view with first line of content showing, and the right pane is in “Timeline view” with “Fit to view (Ctrl+3)” on, only showing one item in focus.

Outline 4D three pane outliner

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

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.

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

Recursive outlining and writing

I am in the middle of writing my dissertation, and I’m constantly experimenting with my writing process flow and set-up. I have two monitors, a 19 and a 22-inch one. The overall writing process appears to be a recursive process of  alternating between outlining and writing (though the two are not always clearly separable).

My actual writing started once I got to a point that I had so many outlines in different outliners that the only way out of that morass was to start writing them up. Let’s call that condition obsessive-compulsive outlining behaviour (OCOB), and the cure “writing.” The reason for the many outlines is that I use outliners as part of a distillation process, for extracting and abstracting information by translating ideas from one outliner into another. This is a fun and productive process until it gets out of hand and you end up with more outlines than you can keep track of. At that point I decided to start writing, so that the written piece be the place where all the information from the various outlines can be consolidated into a final train of thought.

To my surprise I have selected Word 2010 as my main writing tool. I considered Scrivener and DragonPad, but I found that Word trumped them by being compatible with the most software that I wanted to use during the writing process. For one, I could dictate directly into Word and all the Dragon NaturallySpeaking functions would work the same as in DragonPad, making DragonPad redundant. Scrivener on the other hand couldn’t handle direct Dragon dictation. But I also already had a detailed outline in Scrivener (using it as a two-pane outliner), so it seemed sensible to keep that open in my second monitor, while doing the writing in another software in my main monitor.

For times when I wouldn’t be using Dragon, I would want to use WordExpander to speed up the typing, and it turned out that it would display the pop-up menu of word choices by the cursor in Word but not in Scrivener. Finally, Word has an EndNote add-in, so I could directly be inserting references as I write, rather than using a more roundabout way of referencing in Scrivener by having to paste in raw EndNote code first, and then having to convert it once the Scrivener draft had been exported into Word. While Scrivener has strengths when it comes to tracking word count and to switching from an individual section view to a total document (Scrivenings) view, word count in Word is acceptable and I can use headings to navigate the document when the Navigation Pane is enabled.

So, Word is open in my 19-in monitor that is facing me and where I do the final writing up (dictating with Dragon or typing with WordExpander). I also have a little 4-inch (10 cm) of a NoteTab Light window open on the right of the Word window, where I type quick notes I need to refer to or text fragments I want to use a bit later.

In my 22-in monitor that I have on my right-hand side at an angle, I have a number of software windows open, though not all at the same time. At most there would be two open at any one time, arranged vertically.These would include my three main outlines which I have given up on consolidating into a single overall outline. They are in Natara Bonsai (a single-pane outliner), Outline 4D (a single-pane outliner with inline notes), and Scrivener (a two-pane outliner). Scrivener holds my overall outline for the whole PhD, for all 8 chapters. Outline 4D holds a detailed outline just for my current chapter.

The advantage of Outline 4D over Scrivener (as an outliner) is that it is single-pane, so I can see the entire text with its headings and sub-headings in a single window. Although Scrivener does have the “Scrivenings” view which combines all its documents into a single view, it is more of a ‘tape’ view than an outline view. Plus in Outline 4D you can select different colours and fonts for the different hierarchical levels, which makes navigating and comprehending the outline easier.

Finally, I have an even more detailed outline of just one section of the chapter in Bonsai. Bonsai’s disadvantage over Outline 4D is that it does not have inline notes (notes can be displayed in a separate pane to the right of the outline or at the bottom, which is just not the same). On the other hand Bonsai is faster to operate than Outline 4D, can cram more information into the same amount of window space, and it also allows you to colour in hierarchical levels.

Besides the outlines, I also need to have ConnectedText (CT) open, as it contains my reading notes. This information is more detailed than the one in the outlines. If I need even more detail about the particular source (usually an academic article), then I look at the corresponding PDF with the original article in PDF XChange Viewer (it’s called up by one click on the PDF link in CT). Finally, I also have Directory Opus open, should I need to look for a file that way; EndNote, so I can insert references directly into Word as I’m writing; and Waterfox, so I can look up things on the Internet, when necessary.

This describes the set-up of my outline-to-writing process. It’s a matter of gathering and weaving the information from the various application windows together into the written text in Word. However, the reason I called this “recursive outlining and writing” is because after I had written a reasonably big junk of text, I need to go back and outline some more. The reason for this is that the actual written text has its implicit outline of its own, which does not fully correspond to any of the original outlines. First, it already started out as an amalgam of the other three outlines, so it naturally can’t be identical with any of them perfectly. However, the work of outlining and conceptual development continues during the writing process itself. The writing itself is the workshop where some of the final ideas get eventually hammered out. The text has some new content.

In order to fully grasp the implicit structure of the argument that I have developed in the course of the writing, I need to re-create it in another outline. (It’s difficult to discern this structure easily in the written text itself, once you have thousands of words in a complex academic-type writing). Let’s call this step “retrospective” or “reverse outlining.” The perfect tool for this I found in VUE. I did try Noteliner first, but I found that using a visual concept-map worked better than yet another text-based outline.

I maximised the VUE window to the entire 22-in monitor, and starting at the top, flowing from left to right, and then downwards, I started to map out the core argument of each paragraph in the form of a concept map. When the screen filled up, I just continued scrolling down (there seems to be unlimited space). I also used colour to mark out important moments such as theses, propositions or key findings. Each major section of the chapter is represented by nodes in different colour. Arrows are used to represent logical relationships.

This is the overall shape of the concept map for the chapter that I’m currently working on, in a 25% zoomed-out view (text becomes visible at a 50% zoom):

This reverse visual outline helped me find gaps in my argument, as well as redundant sections. It also worked as an analytical tool, as it helped me discover new relationships and come up with new findings and interpretations. It also helps with developing a sense for what to write about next. This recursive process of outlining-writing-outlining (with the help of VUE as the virtual whiteboard where I sort all my conceptual issues out) is likely to become a permanent part of my writing practice. I am even considering printing these VUE maps out and pinning them on the wall. This would enable me to survey the entire line of argument from chapter 1 to chapter 8 of my dissertation, that represents a text potentially the size of 80,000-100,000 words.

Modelling process workflow for thesis writing

Recently I’ve been finding that whenever I’m stuck in my odyssey towards writing up my dissertation, modelling my process flow in a concept-mapping software (such as VUE) usually helps. In this (hopefully) final stage of my PhD project there are so many resources scattered around in various software and folders on my computer that I need a formal “concept map” (if that’s the right term) to pull them all together and work out the relationships and interactions between them.

Here is for example my last concept map that I’ve knocked up when I was unsure how to proceed with writing up the first four chapters of my dissertation. There is nothing particularly scientific about this map and it probably doesn’t follow any of the conventions of process workflow modelling. But who cares: it did the trick and allowed me to plan out the next stages of what I need to do.

Actually at least 2 or 3 days of deliberation are captured in this chart. First, I needed to decide whether I was going to use ConnectedText or something else for doing the actual writing. Through trial and error I established that it’s better to use another software because however much I love working in CT, it does have some limitations. One of them is that you can only have one instance of CT running and only one edit/view window open. Since I’ve decided to use CT as my database for my reading notes, I need to use another software, so I can be writing in one software in one monitor, while referring to the CT notes in the other. Also, there isn’t an easy way to track the word count of your document while writing in CT.

I had considered WhizFolders briefly as an alternative, but I find its interface too busy to be able to concentrate on the actual writing. So I settled on Scrivener for Windows, which works well both as a two-pane outliner and as a writing tool with decent word-count tracking.

As the sequence of the process flow is not apparent from the chart, let me describe it briefly. I start with importing my master outline with inline notes from Outline 4D (via Word). The reason I created my outline in Outline 4D is because it is a single-pane outliner that allows you to have inline notes, which you can also view in an index card view on a corkboard. Then I use Scrivener to break up the imported document into a 2-pane outline using Scrivener’s handy “Split with Selection as Title” command. As I start writing the actual text (I’m working on the first 4 chapters of my thesis, which need to be contextualised within their respective literatures, namely the Introduction, the Literature Review, the Conceptual Framework, and the Methodology), I begin to review my existing reading notes.

Over the years I have read all kinds of things that are no longer relevant. Therefore I need to deploy some kind of a filtering process to select the most important notes, as well as any new reading that still needs to be done. To consolidate my final reading list (a list of bibliographic references), I use a Natara Bonsai outline. First I import into Bonsai an existing outline document that contains some of my selected references that I have kept on my iPod/iPad in CarbonFin Outliner. Then I go through my old conference papers and other writings to extract references that are still relevant and which are kept in Word files and an old Scrivener project.

Simultaneously to this process I have also designed a ConnectedText project for keeping my final reading notes and quotes, using a similar model to the one I have developed for my empirical analysis. As my old reading notes and quotes are kept in a WhizFolders database, I will need to review those and transfer them one-by-one to the CT database (I deliberately don’t want to import them en mass, as I need to separate the wheat from the chaff). I will also use the CT project for recording any new reading I still need to do. I am designing this CT database not simply just for this writing project. Very likely it will become my main database for all my future readings for years to come. This is just an opportune moment to get started with it, as I no longer want to use WhizFolders for this.

Getting back to the chart, there are basically two important elements to it: 1) the big blue Scrivener rectangle which represents my writing, and 2) the big green rectangle below it which represents the CT reading notes database. If we look at the arrows pointing to the latter, we see mostly the data that needs to be transferred (by carefully sifting through) from my old files, as well as new reading notes that will be created in iPad.

As for the arrows coming in or out of the Scrivener project, those have to do mostly with referring to external sources. In the end I won’t need Excel for planning the word count because Scrivener has good enough tools for that. I will also use Dragon NaturallySpeaking for dictating, whenever I feel the need. Sometimes it’s easier to write without it, other times it speeds things up. As for EndNote, it is simply the central database for my references, which are linked to the PDFs that may need to be read for the first time or reviewed.

But my main point here is that it was the creating of this concept map that was crucial for getting me started with the whole writing stage. Without it I would have probably sat in front of a blank page with a writer’s block for days. Now I feel fairly confident that I know what I need to do next.