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.

 

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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.

Nuance software 50% off in the UK this weekend

Dragon NaturallySpeaking 12 is an indispensable tool for me and this weekend (begins midnight Thursday, ends midnight Monday) Nuance has a 50% off sale for the home edition, and also for some other software, at its UK online store. I’m not sure if these offers are also available to non-UK shoppers but it might be worth a try. Here are the prices:

Dragon NaturallySpeaking 12 Home – £79.99 £39.99

PDF Converter Professional 8 – £99.99 £49.99

PaperPort 14 – £49.99 £24.99

OmniPage 18 – £79.99 £39.99

I already have DNS 12, but I’m looking for an OCR application to convert entire (including scanned) PDF articles to text (that would be OmniPage then), so I can import them into ConnectedText in one go and then delete the unnecessary bits, rather than continuing with my current piecemeal method of converting bits of text with the otherwise excellent ABBYY Screenshot Reader.

Update:

After a bit more research I’ve decided to pay the extra couple of pounds and go for ABBYY FineReader 11 Pro. For one, it has generally better reviews than OmniPage 18, but also I’ve been so impressed with their Screenshot Reader – which I got for free and have been using for years – that I’m happy to reward them for that.

Update no. 2:

Wow, OCR applications have moved on since the last time I used them a few years ago! So far I’m very pleased with ABBYY FineReader. It only took a couple of seconds to convert a 17-page PDF article to Word, complete with not only all the footnotes and headings but also all of the images.

The main purpose of the scanning is to end up with a text version to be imported into ConnectedText. The scan wasn’t entirely perfect in the sense that the first page with the abstract ended up appended to the end of the Word document, but it was easy to fix that with a cut and paste job. There were a couple of italicised words in the original that weren’t kept in italics in the scan and some block quotes didn’t end up looking the way they were supposed to, however the OCR-ing, which matters to me the most, was very close to 100% accuracy.

Update no. 3:

Correction: in fact the ABBYY FineReader scan was perfect: the problem I mentioned regarding lost italicisation and indentation of block quotes had nothing to do with ABBYY. Those features got lost in the conversion process from .docx to .htm and the CT import process. Apologies to the ABBYY folks…

Dragon NaturallySpeaking 12 and ConnectedText

I have been a Dragon user (I’m talking about the speech recognition software) since version 9, although I have only started using it on a regular basis since version 11, as previously it was just far too temperamental. Version 11, and especially 11.5, on the other hand reached near perfection compared to what it had been before, with its 99% plus accuracy (as long as you used Dragon’s own DragonPad to dictate). Unfortunately it didn’t play nicely with ConnectedText, producing errors that made Dragon effectively unusable with CT.

A month or so ago Dragon 12 arrived on the block, pre-marketed to existing users initially. Up until today I held off, thinking, “I’m not going to risk having to upgrade my hardware, should it turn out to be a monster of an upgrade” (like version 11 was), not to mention the amount of money it costs to upgrade from what numerically seems like a tiny step from 11.5 to 12. But this morning a discounted offer landed in my mailbox and it made me think: “What if…? What if this upgrade might just make Dragon compatible with CT? I could always downgrade and ask for my money back…”

Information on CT’s compatibility with DNS12 was nowhere to be found, so I took the plunge and bought the upgrade this morning. As I started installing it, there were a few hitches which almost made me regret my decision. First, InstallShield wasn’t able to close down one of the applications that it needed closed down: “Acresso software manager.” I tried to go into “msconfig” and shut it down, it still wouldn’t do so. In the end I tried to click “Help” on the “InstallShield” window to find a solution, which it somehow interpreted as “next” and carried on and installed the software anyway. After the installation I discovered that the problem apparently was caused by InstallShield itself, as the name of its company – and therefore of the software – changed from Acresso” to FLEXnet because of trademark infringement. So it was a weird loop caused by InstallShield not recognising itself, it seems.

The second hitch was a cryptic message at one point in the installation process, which said something along the lines of “Dragon has installed C++, do you want to remove C++?” What?? Why are you asking me that for?? It would have been one thing to say one was an older version than the other and no longer needed, but there was no additional information whatsoever. I wonder how they expect average Joe Bloggs to know what that was all about. In the end I decided to keep C++. If Dragon had bothered to install it, I assume it knew what it was doing? Anyway, so far there haven’t been any adverse consequences of that decision.

The third hitch presented itself during the upgrade tutorial. After a few screens Dragon just stopped recognising my input, suggesting that what I said was not recognisable or that my mic was not up to the task. I have a Plantronics headset that I bought specifically for Dragon a few years ago, and while this model is obsolete, it worked just fine with v. 11.5. “Here we go,” I thought, “I can start shopping for a new headset. So that’s why they gave me a Logitech 30% discount voucher at the checkout…” But, once I finished the tutorial and launched Dragon proper, my Plantronics mic worked perfectly again.

All’s well that ends well… After the somewhat rocky installation Dragon ended up working like a dream. The touted 20% improvement in accuracy (which is already around 99%) was noticeable to me because there were only 1 or 2 corrections to be made where I would have had 5 or 6 mis-recognitions before. This is near perfection.

However, the litmus test and indeed the whole rationale of the purchase was to see whether Dragon 12 would work with CT. I was pleasantly surprised. It’s not the perfect solution yet, but progress has been made. The perfect solution would be if I could just dictate straight into CT and it would work like it does in DragonPad. We’re not there yet. However, dictating into CT now triggers Dragon’s Dictation Box, which then pastes the contents directly into CT. See the two screenshots below for the Dictation Box and the results pasted in. This is an improvement, as it saves having to dictate into DragonPad and then do CTRL+A, CTRL+C, and CTRL+V, plus having to click in and out of windows to activate them, in order to copy and paste content (which I didn’t bother to do anyway). With the Dictation Box, it’s now down to one or two clicks. Just wake up Dragon (I assigned it to F1), and start talking, then click “transfer” and that’s it. I might start using Dragon with CT more frequently after all.

Verdict: I’m happy with this purchase (minus the initial aggravation).

Dragon’s Dictation Box:

And the results transferred into CT: