Kami or Squid for annotating PDFs with stylus on a Chromebook? Mini Review

Recently I got myself a Samsung Chromebook Pro (which comes with a Wacom EMR stylus), and I was looking for apps to annotate PDFs with a stylus. In the end Kami (formerly Notable PDF) and Squid (formerly Papyrus) emerged as top contenders. It’s not entirely a fair comparison, as one is a Chrome extension, the other an Android app, and I used two different PDF files to annotate, but here are my main observations.

Where Kami is better:

  • If you have the Kami Chrome extension enabled as your default PDF reader, you can start annotating as soon as you download a PDF file, as it opens automatically in Kami, with all the annotation tools ready. With Squid it’s a few more steps, as you need to save the PDF first somewhere where Squid can import from (local download folder, Google Drive, Box, or Dropbox), then launch Squid, hit the new note button, choose “Import PDF”, and then navigate to the PDF file to import it.
  • In Kami you can scroll through the entire PDF file during annotating. In Squid, you can only see one page at a time, and you can move forward or back by only one page at a time.
  • As long as you are online, Kami syncs every change instantly to Google Drive, so you have a backup copy, should anything happen to the local device, and can have multiple copies open and synced live on multiple devices (and possibly multiple users, if you’re sharing your PDF file with others). In Squid, there is no sync. Instead, there is a “Cloud backup” option, which only works with Box and Dropbox, and there is only an option to back up every 6 hours or manually. There is also an “Export PDFs” option, which can similarly be set to “every 6 hours” or be triggered manually. In my experience, the Squid backup was not very reliable. Sometimes it failed to upload the backups (blaming it on “network errors,” “I/O errors” and so on), sometimes it only uploaded some of the files, and Box for some mysterious reason failed to sync the files with its Windows client on my laptop. For Chromebook users there are obvious benefits with Kami being so seamlessly integrated into the Chrome browser and Google Drive, and not having to pay for Box or Dropbox. But the instant sync notification in Kami can be a bit distracting during reading and annotating.
  • In Kami you can choose not to use your fingers at all and use the stylus for scrolling and all other actions, if you don’t want to be touching the screen.
  • Kami maintains zoom level as you scroll through the document, while in Squid you need to reset the zoom level each time you navigate to the next page or back.
  • Using Kami to annotate PDFs leaves Squid free for taking additional handwritten notes, and it is easy to switch between Kami and Squid via the shelf. If you’re annotating a PDF in Squid, it is more awkward to switch to another Squid note, as you need to exit each in order to be able to navigate to the other.
  • Kami’s tools (which are in a vertical bar on the left of the screen) are a bit more easily accessible (especially for a left-handed person), and it’s easier to switch between e.g. the pen tool and the highlighter, than in Squid, where the tools are in the top right corner (which right-handed people might still find easier).
  • In Kami it’s possible to scroll the page with a single finger, while in Squid you need to use two, otherwise you end up erasing your annotations. Unfortunately, this can still happen if your two fingers are not entirely in sync, and you accidentally erase stuff in Squid while trying to scroll up or down the page.

Where Kami could improve:

  • While Kami does work offline, the “undo” button is obscured by the offline notification tooltip, so “undo” cannot be accessed in offline mode.
  • When switching between tools, the tooltip labels for the tools (e.g. “Drawing”) persist, intruding into the margin that could be used for annotations, so you need to scroll up or down to be able to annotate on that spot. I don’t see any value in these tooltips persisting (and any need for them at all).
  • Normally when you start annotating a newly opened PDF in Kami, there is a popup asking you if you want to save it to Google Drive for syncing. This is a nice feature when you’re online, but if you happen to get it when you’re offline, the popup persists and is impossible to close, obscuring a part of the PDF, which is pointless and annoying. Even when the internet connection was re-established, I could only get rid of it by refreshing the whole page and reloading the PDF. It looks like a bug.

Where Squid is better:

  • There is no distracting sync notification (but there is no sync either).
  • The exported PDF is properly flattened, meaning that when you open it in another PDF viewer on another operating system, the annotations are fixed, and you can freely copy and paste text from the PDF, without interfering with the annotations, or the annotations interfering with the copying. Kami’s exported PDF on the other hand does not properly flatten the annotations, meaning that they remain floating objects, so if you e.g. want to copy some text from the PDF, you can accidentally start dragging the annotations out of place. Personally I can put up with this (and just use the clean version of the PDF file for any copying), but it could be a problem if someone else might need to read your annotations, and they might unwittingly drag them out of place. Also, Squid’s PDF export was PDF/A-1b standard compliant. But I don’t know if that had something to do with the underlying PDF file and not Squid.
  • Squid (at least on my Samsung CBP) had pressure sensitivity, which meant that annotations could be done in thinner handwriting than in Kami. In general Squid allows for more granularity in stroke thickness etc.
  • While I used different files to annotate for this review, so this information is not directly comparable, it seemed that Squid’s annotations required less overhead in terms of increase to the file size. After annotation, the PDF in Squid increased from 376KB to 791KB in size, while in Kami it increased from 364KB to 6.31MB. For this to be a fair comparison I should have made the exact same annotations to two copies of the same file, but on the whole it suggests that Squid is more economical with its use of data.

Verdict

For now I will probably stick with Kami, as I like the live Google Drive sync, I like the fact that I can scroll through the entire document, and that I don’t risk deleting annotations if I use my finger to scroll up or down. I also like the option of being able to use Kami and Squid together, annotating in the former, and taking additional handwritten notes in the latter. These benefits for me outweigh the negative points about the floating annotations and the big increase in file size.

Update (27 May 2018):

I have also posted this review on the Chrome OS Reddit site, and there was a bit of a discussion.

Notable PDF is getting there

I’m not sure if I mentioned it here before, but last year I got myself a Chromebook (a 1st gen. HP Chromebook 14), to replace my aging and increasingly decrepit (or should I say decrapit) iPad 1 as my main portable note-taking and web-surfing machine. I quickly became a Chromebook convert, especially after I discovered how easy and convenient it is to use Chrome Remote Desktop to access my Windows 7 PC, thus always having my office with me.

The only area where my Chromebook and Chrome OS were lacking and where my iPad 1 (with the GoodReader app, for instance) was still superior was PDF annotation. It was certainly possible to read a PDF on a Chromebook but there was no satisfactory solution to annotate a book-sized PDF, both online and offline, and then be able to export the annotated PDF file or the annotations themselves. Not until Notable PDF appeared on the scene that is. I have been using Notable since its beta days on and off, but until recently I kept running into problems that made me return to annotating on the PC or on my old iPad.

However, in recent weeks I checked back again and I was very pleasantly surprised that Notable have ironed out some of the obstacles that kept me from adopting it permanently. Finally I was able to download my annotated PDF file and open it in PDF XChange Editor on the PC, and I saw all my highlights and annotations in place. It is still not perfect, as the highlights in XChange Editor show up as some kind of colour overlay rather than XChange’s own native highlights, but hey, I can live with that. What is more important is that I am now able to read and manipulate my Notable annotations in XChange Editor.

Moreover, Notable has some tricks up its sleave that give it a distinct advantage over some other PDF annotating options. Notable PDF is a Chrome browser extension, which makes it cross-platform on desktops, as long as you have Chrome installed on your other machines.* It appears to save the annotations in the cloud, which means that it doesn’t matter where you keep your file, and how many copies of your file you have, it will sync the annotations to that file (and its copies) across all the browsers. You can even have two different copies of the same PDF file open in different machines in Chrome, and the annotations will sync live and automatically, in front of your eyes. This feature of course would be very useful for collaborations, as you can see instantly what others are commenting on that file.

To me, this feature means more flexibility. For example, the copy of  the PDF file I’m reading is saved on the hard drive of the Chromebook. When I’m offline, the annotations are saved offline, and then synced when I’m back online. However, I also have a copy of the same file on my Google Drive account in the cloud, and if I’m on another machine, let’s say a PC at work and I do not have my Chromebook with me with the original file, I can just open the copy from Google Drive, and Notable recognises it as a copy of the annotated file and it populates it with the annotations saved on their server. I find this rather clever and very useful.

In any case, I just wanted to say that I’m happy now to include Notable PDF among my favourite apps and recommend it to others, especially Chromebook users. While it’s not entirely perfect for my needs (I wish the yellow highlights could be converted to native highlights in PDF XChange Editor, so they can be extracted from there), it is probably the best option for PDF reading and annotating on Chromebook today. Also, I have been following them for the past year, and development has been on-going, so I am hopeful that Notable will continue to be improving.

Update:

* Having just looked at their website more closely, it turns out now they also have a web app, so in fact you can use their service on any browser, not just Chrome.

Most recent process flow for academic writing

Just for the record, I thought I’d repost my comment here that I’ve just left on Christian Tietze’s blog concerning on how I go about outlining and writing on the back of Zettelkasten notes these days.

My latest process flow on Windows 7 for academic writing, using 3 monitors, so some of this software could be viewed simultaneously:

1) read the literature (usually PDF articles or books);

2) take reading notes (mainly quotes + interpretation) in ConnectedText as Zettelkasten;

3) use VUE to develop a concept map to make sense of the material, while reviewing the CT notes in floating windows (i.e. multiple notes can be viewed simultaneously);

4) develop an outline for the paper in a Freeplane mind map, building on the VUE concept map and adding hyperlinks to selected quotes and notes in ConnectedText, so they can be easily called up when writing about a given point;

5) write in plain text using Markdown in WriteMonkey (distraction-free writing software), while checking off nodes in the Freeplane outline as they get written up, and paste in raw EndNote code for academic references, where necessary;

6) paste draft into Outline 4D (single-pane outliner with inline notes) and reverse outline it, i.e. add a heading to each paragraph to see the overall logical structure and content of the paper, and edit it accordingly to improve coherence, eliminate redundancy etc.

7) Import into MS Word, do final editing, add final headings, table of contents, and convert raw EndNote code into formatted references and bibliography.

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.

 

Zettelkasten: one database or several databases?

In recent months I have decided to implement the Zettelkasten approach to taking reading notes a bit more rigorously than I did in the past, by which I mean that I started taking individual bite-size (index-card type) notes, rather than keeping all notes pertaining to a book or article within a single document. I created a separate database in ConnectedText (my Zettelkasten software) for this, which I named “Quotes.” I also created another database called “Notes” for my own ideas, which I intended to keep separate from “Quotes.” My main reasoning was that I wanted to keep “Quotes” ‘pure’ as a reading notes database, rather than contaminate it by a type of notes that were of a different provenance.

This dualism didn’t matter much until just recently, as I was almost exclusively taking reading notes, which allowed me to record my own associated comments, without the need to start populating the “Notes” database. You could say that I did not have any “original” ideas of my own to record. However, just today I had an idea, which, although inspired by my reading of a book, I thought was an original thought worthy of recording on its own. And then it dawned on me that I do not need to put that note into a separate database. I can just consider it a special type of a “reading note,” the author of which is me. Rather than recording it separately, I can just add my own name as an author in the Categories field, so that I can filter those, if needed. Otherwise there are all kinds of benefits to keeping it together with my other reading notes. For example, they can be searched together or grouped together thematically. And there is no need to be switching between databases.

I realise this may not sound like a very profound realisation that should merit its own blog post, but for some reason I found it a relief that I could reduce the number of databases for my notes. I still have my old “Readings” database, which is based on the principle of collecting all notes per publication in a single CT document. But since I’ve started using the index card approach, I had not felt the need to create another “Readings” entry. I suspect that one day I may break those up into index cards as well and merge them with the “Quotes” database (which I should really rename to “Quotes and Thoughts”).

How do you deal with quotes and your own thoughts? Do you keep them in the same database or in separate databases? Do you keep quotes and your comments about them in the same note or in separate ones? And why?

Christian Tietze on the Zettelkasten way

Here is an interesting post by Christian Tietze that spells out the main software requirements for the implementation of a Zettelkasten type notes database. This is pretty much how I manage my reading notes these days in ConnectedText. I am really looking forward to reading the software reviews that Christian aims to undertake.

Kindle is not for me

Surely I must count as some sort of a dinosaur, as it was only today that I’d purchased – and then promptly returned – my very first Kindle e-book. I managed to avoid Kindle up until now by being able to find paper books or online e-books at my university library for the titles I needed. But today I urgently needed a book that wasn’t available at my library and I couldn’t find it in any other electronic format.

I did see the book before in some kind of a PDF format for a reasonable price at Google Play, and I naively assumed that it would be waiting for me there in my moment of need. It turns out that e-books can sell out too (how exactly, I don’t quite understand), as the PDF was gone from Google Play and is nowhere to be found on the net.

The Kindle version of the book I was looking for was slightly cheaper than the paperback, and if I bought it I could have it instantly, so I took the plunge and purchased it. I downloaded a copy to my “Kindle for PC” app, and another copy to the Kindle app on my iPad. But as soon as I started reading, I began to run into several disappointing surprises.

First, there was no real pagination for this academic e-book, which meant that I wouldn’t be able to reference quotes directly. I was amazed that after all these years of kicking around, the Kindle people still haven’t solved this problem.

I also found it inconvenient that when I carried out any sort of operation with the e-book such as a simple search, Kindle would re-flow the text and it would end up looking different every time. The highlighted text with my note that I expected to find at the top of the page ended up at the bottom of the page and so on. Annoying. I need to have a sense of where stuff is in the book that I’ve already read and made a note of. Shifting its position around just makes it more difficult to comprehend an already challenging academic text.

Then I discovered that there was no direct and easy way to export my highlights and annotations from either the PC or the iOS app. The only way I could get any quotes or notes out was if I enabled an external clipboard capture software and copied each quote and note individually. I was ready to put up with that until after an hour of copying and pasting Kindle had kindly informed me that I had reached the copying limit set by the publisher. What? I’ve paid for this book, I should be able to copy out anything I like from it for my personal use, just like I can do with a paper book. I was starting to get angry.

The “icing on the cake” was when I had enough of reading on  the PC and I decided to carry on in my armchair using the iPad. When I loaded the Kindle iOS app, I fully expected to see my highlights and annotations that I had created on the PC app and which had been synced with the Amazon cloud. But after several attempts at reloading and refreshing, my notes simply didn’t show up on my iPad.

Perhaps some of the above problems had to do with me being a Kindle novice and missing some of the features that may have solved them instantly. But I just had an overwhelming feeling of being underserved and constrained by both Kindle apps and the entire platform. Both apps are very feature-poor compared to such excellent PDF readers like GoodReader or PDF Expert. I could think of two possible reasons for this. 1) Amazon can’t be bothered about the academic market that needs page numbers and annotation sync and export, or 2) it is some sort of an underhanded effort to force you to buy an actual Kindle device, where I presume at least some of the above issues have already been resolved.

Whatever the case, I’ve returned my first Kindle e-book and I will avoid buying another one, if I can help it. And I certainly won’t be buying a Kindle device any time soon. I’d rather read a good old PDF file on my iPad any day!

P.S. (12-Apr-2013):

Another shortcoming of the desktop PC Kindle app is its inadequate search function. I did a search for a single word in my e-book, and Kindle returned the suspiciously round figure of 100 results. I went through all the 100 results and then repeated the search. Not only did I get a different figure the second time (99 results), but they included results not contained in the previous search. When I manually flipped through the rest of the book, I found several occurrences of the search term that were simply not found by the Kindle app in either of the first two searches.

Together with everything else I mentioned, this makes the Kindle PC app – in conjunction with the iOS app – unsuitable for academic reading (at least in comparison with the tools available in PDF readers such the aforementioned iOS apps and PDF-XChange Viewer on the PC).

P.P.S. (12-Apr-2013):

Out of curiosity, today I had installed the PC app for NOOK Study and downloaded the same e-book (in whatever format NOOK uses) that I tested with the Kindle app. NOOK Study is directly targeting the academic audience, so I expected it to be more sophisticated. And it was, to some minor extent. For one, it allows you to export your annotations in .doc and .txt format, which would work for me. But I still found it far inferior to the PDF readers I use. I wasn’t able to test the search function because, as NOOK informed me, they were still building the search index for this book, and the search function would be available at some point in the future, depending on the size of my library. It all sounded a bit too tentative to me.

However, the problem of the page numbers has not been resolved. NOOK did provide the page numbers, but they were not the same as those of the paperback, which they claimed to have used for the e-book version. Basically they had started numbering the pages from the electronic table of contents that they had inserted in front of the cover of the scanned book, and then they kept on counting all the pages for which there weren’t even page numbers in the paperback. For this reason all the page numbers had shifted. This wouldn’t be a problem if the text of the book had not been reflowed, as I could have just recalculated the pages myself. But unfortunately NOOK re-flows the pages, meaning that the pages become meaningless and useless for the purposes of academic referencing. Too bad. PDFs it will be…

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.

StoryView

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
     return
}
else
{
     WinActivate, ConnectedText
     SendInput {Right}%A_SPACE%
     SendInput `[`[%OutputVar%`]`]
     SendInput !t
     SendInput %OutputVar%`n
     IfWinActive, Confirmation
           return
     else
           SendInput ^v!e
     return
}
return

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