The spare CPN licence is up for grabs again…

In a previous post, I tried to pass on a spare licence for Circus Ponies Notebooks. The person who received it never claimed the license key, so I’m re-advertising it. If you’d like to have the licence, just leave a comment below. Here are the criteria:

  • First come, first serve
  • You have to be an undergrad or postgraduate student. 
  • You will be using CPN for academic work (as opposed to wanting to sell it on for a few bucks…).

You can read more about using CPN for academic work here

Posted in note taking, outlining | Tagged | 4 Comments

Academic workflows revisited

It’s been a year since I wrote this post on academic workflows. The way I work has changed a bit since then – some apps have gone out, some have been added, and the relationship between some of them have changed, primarily affecting my literature review work flow. Here’s a little post on my current set up. 

The data analysis process 

This is pretty identical to what I wrote in my previous post. I still think Inqscribe is great for transcription, Curio (which I’ve written about here) is great for overall management of the writing process, and iAnnotate is great for those first rounds of analysis of my overall data corpus. In addition to Curio, I often turn to NovaMind, which is a mind mapping app with an extensive feature set. 


The writing process

I also handle the writing process pretty much the same way as I outlined a year ago.

I use mind mapping and outlining tools for brainstorming and organising my ideas (which I’ve written about here and here). I use Scrivener for my writing (which I’ve written about here), and import literature notes, data and pdfs as needed. Scrivener is a fantastic tool for writing academic papers, and I can’t see myself giving up on it anytime soon. When their long awaited iPad app arrives, it will be even more useful.

Towards the end of the writing process, I switch to Word. I use Endnote for citations, inserting unformatted citations in Scrivener and then converting them when the text is in Word. 


The literature review process 

Here’s where most of the changes have happened. I no longer use Sente. I still think it’s a very decent app, but eventually I decided to go with Bookends (which I’ve written more about here). There were two main reasons for this. The first is the ability to do a spotlight search of imported attachments and subsequently create a smart group based on the search results. I find this very useful for review purposes, and it’s a feature that Sente doesn’t have. The second reason is the extremely responsive support – the developers get back to you very quickly, and they stay with you until the problem is solved. 

So, what I typically do with my literature is as follows:

Importing literatureI subscribe to email notifications from all the journals in my academic field. From the email, I open the table of contents in Safari, and from there I import the pdfs I want into Bookends using the print feature. I then use keywords (Bookends’ name for tags) to assign each article to the relevant thematic smart group(s). I use Hazel to automatically add a copy of the downloaded pdf to a dropbox folder. This is because I want to keep a ‘clean’ copy in addition to the pdfs that I annotate. 

Reading and marking up journal articlesI then turn to my iPad. I prefer reading and marking up literature on my iPad, rather than on my Air. I can hold it in the same way as a book, and use a stylus to highlight, underline and write notes. The attachments folder in Bookends is synced to Dropbox, which in turn is synced to GoodReader and iAnnotate (which I’ve written about here) on my iPad. I use GoodReader and iAnnotate to mark up journal articles. When I’m done, I extract the annotations from the pdf file, and send them to myself in an email. My email client Postbox comes with good Evernote integration, which allows me to easily convert the email to a note in Evernote. You can also simply cut and paste the text, or use Skim as described by Joseph Flanagan in the comments below. 

Note taking. I have two main hubs for literature notes: Evernote (which I’ve written about here) and Circus Ponies Notebooks (which I’ve written about here).

In Evernote, I put all ‘single source notes’ – those are notes from a particular journal article, book chapter or book. Each source has a separate note, which includes the formatted reference, the abstract, annotations made on my iPad, and my own reflections about the text and its relevance for my work. These notes are gathered in a separate notebook called ‘review’, and organised according to tags that reflect the smart groups I have created in Bookends. Some of the reasons why I use Evernote as a hub for my single source notes, is that it works cross platform – the sync between my Air, iPad, android phone and Windows machine at the office is instant. I also like the ease with which I can organise and share my notes, and that I can create link between notes. Once the notes have been written up, I return to Bookends and use labels to mark the relevant reference with “in EN”, to make it visible that this reference has a set of notes and annotations in Evernote. 

I use CPN for reviews that are organised according to theme, rather than author/single text. I find it superior to Evernote for this purpose, due to the outlining feature of the notes pages. Outlining makes it easy to create different hierarchical levels for different kinds of information (theme, author, findings, and so on). It’s also convenient for navigating long documents, because you can expand and collapse information as needed. I also create links between different cells and pages, so I can easily refer back to things I’ve already written and connect related content. 

I export notes from both of these apps into Scrivener when I need them during writing. 


…so – that’s more or less my current set up. If you have suggestions for good academic work flows, please leave a comment below.


Related posts on this blog: 

Academic workflows: When to use what, and how

Criteria and questions for establishing your academic workflow

Posted in brainstorming, data analysis, iPad, literature review, mind mapping, outlining, pdf annotation, reference management, transcription, workflows, writing | Tagged , , , , , , , | 6 Comments

I have a spare CPN licence…

I recently got a mac bundle which included a licence for Circus Ponies Notebooks. I already have CPN (got the bundle because I wanted a couple of the other apps), so if anyone would like the licence, just leave a comment below. First come, first serve. I’m giving it away to someone who’d like to use it for their own undergraduate or graduate work (i.e. not someone who wants to make an extra buck by selling it on). 

See my previous post for links to blog posts about how to use CPN for academic work.  


Posted in Uncategorized | Tagged | 7 Comments

Sale: Productive Macs bundle

Just a quick post to let you know that Productive Macs currently has a bundle sale which includes Circus Ponies Notebook, which I’ve written about in several posts found here. Along with CPN, you get a variety of productivity tools, such as Keyboard Maestro, Default Folder X and Vitamin R, which I’m currently exploring as an alternative to Pomodoro

The bundle, which includes seven apps, is available for another 13 days from this page


Related posts on this blog:

There are several posts on Circus Ponies Notebook here:

Posted in appsales | Tagged , | 2 Comments

Digitalising your academic literature: tablets versus e-ink

Tired of those piles of paper that are growing on your desk? More and more researchers are letting go of paper and going digital with their academic articles and literature notes. For me, one of the best things about getting an iPad was getting rid of the tall stacks of journal articles in my office. The advantages of digitalising my research library have included:

  • It’s now extremely easy to find what I want, when I want it. Instead of working my way through thematically organised piles (which gradually became less and less organised…), I now do a quick search on author, title or keyword to find the file I need.

  • I always have all my literature with me. I no longer find myself in situations where that article with notes that I needed to take a quick look at is lying in the office, while I’m working at home. 

  • Digitalisation makes it easier to organise my literature. It’s easy to set up folders and subfolders for particular themes and sub themes. At the same time, I can quickly organise my literature by author, publication date, key word, or journal name. Use of tagging also solves an issue that is important to how I work: I can assign a given article to more than one thematic group. 


Over at, there are regularly questions from academics about the best device for reading pdf files. Many request e-ink devices (such as Kindle Paperwhite) rather than tablets, as e-ink devices are generally considered easier on the eyes when you are reading for a longer period of time. The debate on e-ink versus LCD screens (which is what you find on tablets) has been going for a while, and if you google the topic you will find many articles debating whether the eye strain factor of LCD screens is ‘real’ or not. In practice, however, it is largely an issue of personal preference and what you feel comfortable working with. 

When it comes to dealing with academic literature, and journal articles in pdf format in particular, my own clear preference is for tablets rather than e-ink, and here is why:

  • On a decent tablet, scrolling and page rendering is very fast. This is extremely important to me, as I frequently go back and forth in a document to check a reference or to reread the data analysis in light of the concluding discussion, or I may quickly skim an article as part of an initial stage of a literature review. Doing this on an e-ink device would slow me down compared to working with paper – and I want my tools to make me more efficient, not to slow my performance. 

  • The annotation capacities on tablets are far superior – for example, with a good pdf annotation app such as iAnnotate (which I have written about here) or GoodReader, it is easy to distinguish by colour how some text relates to method, some to theory, and some to review findings, hand writing is much more accurate, you can insert blank pages for additional comments, and it’s very easy to export your annotations. 

  • On a tablet, you can easily transfer an annotated pdf to the notebook of your choice, such as Evernote or Circus Ponies Notebooks (which I have written about here and here). It therefore makes it very easy to consolidate the annotated pdf and your literature notes, if you keep the latter in a separate location from your pdf library. 

  • Tablets come with advanced solutions for pdf management that are designed for research, such as Sente, Papers, Bookends or Mendeley. In my opinion, having a strong workflow for managing literature is key when you do research, especially when you are dealing with a few thousand pdfs or more.

  • Finally, I tried e-ink and it was a pain. Now, just to clarify, I love e-ink for recreational reading and use it extensively for epub and other e-book formats – but I don’t believe current e-ink devices were designed for pdf reading (with a couple of exceptions such as the Kindle DX), and they certainly weren’t designed to support serious research activity. For this reason, using e-ink devices to read pdfs will often entail cropping and reflowing and other adjustments, and even then it might not come out very well. When I work with literature, I want to be able to just open the document and get on with my work, rather than be distracted by the tool itself. 

So, that’s my take on e-ink versus tablets. Personally, I use Bookends, iAnnotate and GoodReader on my iPad – they meet all my needs for organising, reading and marking up pdf files, and exporting highlights and annotations. I can read comfortably on my iPad for long periods of time, as long as I adjust the screen to a low setting of brightness, and find it much better for reading than a laptop/desktop. However, as with many other things this comes down to preference, so if you have good experiences using e-ink, please let us know in the comments section. 


Related posts on this blog:

iAnnotate: a Swiss army knife for marking up articles, paper drafts and data

Managing your research literature: Sente versus Bookends

Academic note taking: Circus Ponies Notebooks versus Evernote


Posted in iPad, literature review, note taking, pdf annotation, productivity, workflows | Tagged | 6 Comments

Outlining your research: Organising literature notes, data, and writing in progress

Over the past year, I’ve increasingly started using outlining tools as part of my work flow. Outlining is great, and I use it for pretty much everything. In this post, I’ll write a bit about how I work with outlines, and some of the apps I like working with.

Here are some of the things that I create outlines for:

  • Organising ideas: This is usually after a first brainstorming session using mind maps. Sometimes I convert mind maps to outlines after the ideas become more structured, other times I start from scratch with a new outline, because building the outline from the ground up helps me sort the ideas more critically.
  • Sorting data: As I’ve written about before in my post on mind mapping, I find mind mapping and outlining very useful in the data sorting process. I use these tools both in the initial, inductive phase of data analysis, but also after I’ve zoomed in on particular parts of the data material that I want to analyse in more detail with the help of particular concepts. Outlines help me frame that process of systematically reviewing and analysing that data.
  • Paper dispositions: This is probably one of the most obvious usage areas for outlines. Thinking through what your paper should look like before you start writing is always extremely useful, and outlining tools are great for that.
  • (Re-)-organising sections or paragraphs for papers in progress: During the writing process, I always rework different sections and paragraphs in my papers multiple times, with a view to refining and clarifying my argument.
  • Taking literature notes for a particular piece of academic work: As I’ve written before in my posts about Circus Ponies Notebooks (e.g. here), outline pages are very useful for note taking.
  • Taking literature notes for thematic or conceptual ‘clusters’. For example, I have outlining documents comparing different theoretical approaches, or different perspectives on the same theory or concept.
  • Preparing teaching and outlining lesson plans.
  • Taking meeting minutes and research administration.

So, what makes outlining different from a rich text document? In my view, it’s the following:

  • the ease with which you can create and visually display hierarchical relationships
  • the ease with which you can cluster information as you take notes
  • the ease with which you can move chunks of text around, as well as sort them
  • the opportunities for combining and linking (although this will depend on the app you use) different kinds of media and attachments to specific pieces of text, or creating links between different cells 

Apps for outlining

Circus Ponies Notebooks

One obvious and strong alternative for outlining is Circus Ponies Notebooks, which I’ve written several posts on previously. This post in particular deals with outline pages.

CPN is a very powerful outlining tool, and over at the blog Organising Creativity you’ll find lots of additional information on how to maximise the use of outlines in CPN for academic work.

OmniOutliner Pro

I’ll declare some bias up front: I love this app. It’s solid, feature rich, and provides a range of options in terms of formatting and adding various links and files. 

OO comes in both a mac and iPad version, but I only recently got the iOS app so I’m more familiar with the former.

On the mac, you can write up your outlines in OO’s own file format, which allows for a range of rich text formatting options, the creation of multiple columns, numbering and attaching a range of files as attachments. Here a screen shot for example, where I’ve also included some of the different inspector windows that will give you a flavour of the formatting options:


Screen Shot 2013 04 07 at 13 49 56

However, if you want something plain text that converts more readily to other outlining or mind mapping apps, you can also save your outlines in opml format. OO also comes with a range of exporting options, including plain text, RTF, Word, html and Keynote. 

Some of the features I like in this app include: 

  • a lot of rich text formatting options
  • the ability to attach files such as pdfs and images to your outlines
  • the possibility to create and customise templates, which I find extremely useful for literature review purposes 
  • the option of multi column outlines (the only app features in this post that can do so)
  • the rich export options 
  • the ability to isolate and focus in on selected parts of the outline when you’re working with long documents

The iPad version is not quite as visually pleasing as the mac app, but it’s user user friendly and solid, with the most important function keys available at the additional menu bar above the keyboard. That menu also offers a short cut for taking voice recordings. Here’s a screen shot of the ‘welcome outline’ from OO iPad:

IMG 0010 


My main gripe with OO is the current lack of seamless sync between mac and iPad. In short, it’s a royal pain in the ***, and it’s made me give up on using OO for my main literature overviews that I update on a continuous basis. Basically, there’s no DropBox support, no iCloud, and no simple way of emailing files back and forth (they transfer as zip files). The developers have an own sync service you can use, but I find it too inconvenient for everyday use. My use pattern is one where my iPad is always with my and my Air isn’t, so easy and preferably seamless transfer of files from mac to iPad is key. If this isn’t important for you, these sync issues might not matter that much. For more information on syncing with OO, consult this post on the developers’ web site. 

OO comes in both a standard and a pro version, and the differences between the two are outlined on this page



I came across Tree a bit by accident when browsing the net, and was taken by the way in which it can act as a cross between a mind map and an outliner. The main difference between Tree and other outliners is its capacity to branch out the outlines in a horizontal tree view (hence the name), as illustrated in this screen shot:

Screen Shot 2013 04 07 at 13 57 16

It also features a ‘conventional’ outlining view, and you can switch between the two views with a single click.  Other features include

  • rich text formatting
  • labelling of cells
  • notes section
  • export to plain text, RTF, Word and OPML (although my experience is export to RTF/Word is a bit more messy, formatting wise, than with OO)

The strengths of Tree is that it’s very intuitive and easy to use, as well as aesthetic. It’s also very reasonably priced compared to OmniOutliner, so if you don’t need all the features that OO offers, Tree is a very good option. Personally, I think it’s a beautiful little app and I like working with it when I’m dealing with simpler material that is likely to stay inside the proprietary Tree format. When I’m dealing with large literature overviews that are likely to be regularly exported to RTF formats and that have elaborate formatting templates, I use Circus Ponies Notebooks or OmniOutliner. 

The key weakness of Tree is that it doesn’t talk to iPad. There is no iPad version, and you also can’t save (only export) Tree outlines in ompl format. 


Curio is much more than an outliner – but if you want outlining plus, or outlining as integrated in broader project management, it’s a very powerful app. I’ve written more about Curio here and here

Cloud Outliner

Cloud Outliner is a simple outlining tool for mac and iPad with seamless iCloud sync. There are no fancy features or options for rich text formatting or adding attachments, and no folders for organising your outlines on your iPad – but if you simply want plain text outlines with optional check boxes seamlessly synced between your mac and iPad, it’s a very nice alternative. You can export your outlines in OPML format. Cloud Outliner also has Evernote integration, so you export your outlines to Evernote. 

Here are a couple of screen shots of the mac version (first image) and the iPad version (second image). 


Screen Shot 2013 04 09 at 13 36 41




IMG 0011 2




Some comparative reflections: 

  • If you want both rich text formatting and seamless sync between mac and iPad, Circus Ponies Notebooks is the way to go 

  • If you’re someone whose work lives in the cloud and you’re happy to go with just the basics, Cloud Outliner with Evernote integration is a good option

  • If you don’t have an iPad and purely need something for mac, OmniOutliner is probably the most impressive app out of them all – although CPN would come a very close second IMO. Their user interfaces are very different – for example, with OO you would be working with a standard file structure in Finder, whereas CPN offers a more integrated approach to your notes and the ‘look’ of a physical notebook. While OO provides some additional features in terms of multiple columns, templates and the ability to perform calculations, CPN allows for creating links between different cells, pages, and notebooks, and has a powerful multidex that makes it easier to relate your notes to each other. 

  • If you don’t have an iPad and don’t feel the need to pay the extra money for all the OO advanced features, Tree is a very nice alternative and offers good value for money. 



Related post on this blog:

Circus Ponies Notebooks part III: Organising review notes with notes pages
Organising your writing projects with Curio
Mind mapping your research: Organising your ideas with iThoughtsHD and Curio


Posted in data analysis, literature review, note taking, outlining | Tagged , , , ,

Criteria and questions for establishing your academic work flow

I’ve spent a fair amount of time (and probably too much money) trying to set up the academic workflow I want over the past year, and looking back I’ve now tried to consolidate the key criteria that are important when you’re designing your work flow. What questions should you ask when setting up your academic work flow on a mac? Here’s a short list of things I find useful to consider (‘it’ here being the app you’re looking at): 

Does it have an iPad version? If yes, does it talk to the mac version, and how?

With some rare exceptions, an iPad counterpart is a key criteria for me when I’m looking at apps for mac. My iPad is always with me, my mac isn’t. The second key question here is how they talk to each other, and whether that connection requires effort on your part (see next point). 


Does it sync? If yes, to what and how? Will the sync require any effort on your part?

Some apps are easier to sync than others. For example, while some sync seamlessly across iPad and mac, others require this to be a manual operation (e.g. Sente versus Bookends). 

Cross platform sync is also an issue for those using both Windows and OS X, and applies to e.g. Scrivener, Papers and EndNote. 


Does it communicate with other apps? 

Some apps, like Evernote, Scrivener, PostBox and Curio, have actively addressed integration with other apps – which can make your work flow that much smoother. Explore what the different apps offer, and how that might help your own workflow. 


Do you need to work across platforms (e.g. OS X and windows, iOS and android)

If you, like me, work in a windows environment but use mac privately, this is important to look into. For example, Word, Scrivener, Papers and EndNote work across OS X and Windows, while Pages, Sente and Bookends don’t. 


What do the reviews say?

There’s a large number of reviews available on almost every mac and iPad app out there. Do some proper googling and make sure the posts you read are recent (I usually only go 12 months back in time) before you shop. Ask for advice on forums such as MacRumours and ask your connections/followers on social media what their experiences are. 


Will it be on sale soon?

A lot of apps are frequently on sale. I’ve saved a fair bit of money looking out for the apps I’d like on AppShopper, a site that has consolidated lists of apps on sale for both mac and iPad. Bookmark this site if you haven’t already – they also have RSS feeds.  


Any other questions and issues you think are important to consider? Please leave your comment below! 

Related post on this blog:

Academic work flows: When to use what, and how 

Posted in mac & windows, productivity, workflows | 6 Comments