Macademise is at the end of the road.

It’s been great experience working on this blog, but the journey is now coming to an end.

As some of you will have noticed, it’s been a long time since the last update – life has been busy, new commitments are taking up my time, and I’m finding it increasingly challenging to find the time and space for this blog. Rather than leaving it abandoned, I’m posting this last message to say a big THANK YOU to everyone who has stopped by here. It’s been a great experience posting here and interacting with you in the comments section, and I hope some of my readers have also come away with something small after visiting.

All very best,

Macademise.

Getting rid of #distractions: the Freedom app

Everone who spends a whole work day in front of a computer knows how irresistable internet distractions can be. My own greatest sins are twitter, photography blogging, and browsing various news providers and interesting blogs. A lot of people use the pomodoro technique to stay focussed, which I’ve written about here. I use that from time to time, but sometimes I need something a bit more interventionist, and then I turn to the Freedom app.

The principle behind the Freedom app is very simple: it shuts down your internet for however long you ask it to. So why not just disable your wifi from the menu bar? Because it’s so easy to turn it back on. With the Freedom app, there’s no changing your mind – the only way to get back online is to reboot your computer, which raises the bar considerably for just ‘having a quick look at that twitter stream’.

So, here’s how it works. You start the app, and it asks you how long you want to stay offline. You can disable your internet connection for up to eight hours.

…and that’s it. Distractions eliminated (unless, of course, you have an iPad lying on your desk…).

Personally, I find myself turning to this app more often as I write. There’s a psychological benefit where turning it on somehow clears out clutter from my mind – not just in terms of  unproductive procrastination, but also with regard to emails I know are waiting for my response, or work related tasks I need to do online. Once the Freedom app is on, they simply have to wait.

If you need to be online to write up your research, but you’re prone to being distracted by social media, the developers also have a companion app, Anti-Social, which allows you to block only selected sites, such as facebook and twitter.

Happy writing!

General maintenance and organisation: apps that make your life a bit easier

This post does not speak directly to academic tasks such as writing papers or reviewing literature. Instead, I’m going to briefly describe some apps that does useful ‘background work’, which in turn helps me spend less time on being organised and more time on doing my actual work. I’m not offering a full review of these apps, but rather pointing to some options designed to help you organise your files and work flows.

Tags

As I’ve said before, I’m a great fan of tagging as a means of organisation. Tags is a nice and user friendly app that easily allows you to tag different file types across your mac, including emails stored in the native mail app and safari web pages.

One thing I like about working with tags is that you can assign more than one tag to a file, and you can subsequently use smart groups in Finder if you want additional folder organisation to supplement the use of tags. It’s a much more dynamic way of organising your stuff than static folders.

If you would like some free alternatives to Tags, Tagger is worth checking out, and can be used in conjunction with TagLists.

Default Folder X

Another app that helps with file management is Default Folder X. First, this app adds an additional part to you Finder window when you save files, where you can add open meta tags, labels and spotlight comments as you are saving the file. Second, this app allows you to associate particular folders with particular apps, so that when you want to open a file within, for example, Pages, Scrivener or Circus Ponies Notebooks, Finder will automatically be directed to the folder of your choice.

Leap

Leap is a little powerhouse for those who want to rely on tags rather than folders as a main principle for file management. It’s a swiss army knife for searching, retrieving and tagging your files. It might be overkill for a lot of people – but if you’re looking for a maxed out Finder option which will never put you in a situation of ‘not finding that file’, it’s worth having a look at this app.

Hazel

Hazel is a little app that works in the background with general housekeeping. You can ask Hazel to automate a lot of tasks that are then just executed without you having to think about them. Some of the things that Hazel does for me include:

• regularly clearing out my downloads folder
• regularly clearing out the camera uploads folder in dropbox
• batch renaming files uploaded to the camera uploads folder in dropbox
• erasing files once a day from a folder where I stick stuff that I’m just temporarily editing or saving
• automatically opening new journal articles that I download in Bookends. I first save them in a separate folder in Dropbox, because I like to keep a separate set of my PDFs without any annotations. These files are all gathered in a dropbox folder and organised by tags. When I tag the files with ‘bookends’, Hazel automatically opens the PDF in Bookends (thanks to Aleh Cherp at blog.macademic.org for this tip!)
  

These are just some examples – Hazel can do a whole range of things, and also complements the native Automator very well.

TextExpander

TextExpander does exactly what the name suggests, it expands text. For many years, I’ve had a system of abbreviations when I take notes. For example, instead of writing ‘knowledge’, I write ‘kno’, and instead of writing ‘educational theory’, I write ‘edul th’. Especially when you are writing by hand, this saves a lot of time and effort. TextExpander expands these snippets for you as you type. This means that when I’m writing literature notes or academic papers, I can type much faster because TextExpander has all my snippets stored in them.

TextExpander is also very useful for filling out forms or dealing with emails or other forms of correspondence where you typically repeat particular sentences or paragraphs. For example, I have snippets for all my email addresses, my phone number, my postal address and frequently used abbreviations.

Alfred

Alfred opens and finds stuff for you. It opens applications, finds files, and searches the web for you, activated a little keyboard shortcut. I primarily use Alfred, rather than the Finder, to open apps and files, because it’s very quick and easy.

Do you have other recommendations for apps that help you keep productive and organised? Please leave a comment below.

 

Academic reference management: Some useful features in Bookends

Bookends, which I’ve written about previously here, has been my reference manager of choice for a while. In this post, I’ll highlight some useful features in Bookends that help me organise and manage my literature.

Keywords and smart groups

I’m a great fan of tagging in terms of organising my work, and I have a set of tags that follow me across applications on my mac. In Bookends, tags are called ‘keywords’, and I use keywords to organise all my literature. Whenever I import an article, I assign it relevant keywords based on the theme and the methodological and theoretical orientation of the article. I also make a note if it is part of a special issue, or if the empirical research relates to a particular country. An advantage with using keywords (and smart folders) instead of traditional folders is that you can assign an article to more than one category, which is key for how I work.

I then use these tags to organise my literature into smart groups. For example, I may create a smart group for all entries with the keyword ‘ethnography’. If I later add an article to Bookends and assign it the keyword ‘ethnography’, it will be automatically added to the ‘ethnography’ smart group. Smart groups are very flexible. While I mainly organise them by keyword, you can create smart groups based on a whole range of search combinations, including author, title, journal and text in the note cards.

 

Tag cloud

The key words you enter into Bookends are in turn organised into a tag cloud. In this screen shot, you’ll see the tag cloud for my whole reference library at the bottom.

You can tell Bookends to limit the number of tags shown to the top 50, 100, 200, 500, 1000, or alternatively, it can display all of them. I primarily use the tag cloud to view keywords, but you can also tell it to display authors and editors, or the most common words from abstracts or your notes.

In addition to offering a quick way to navigate your literature, the tag cloud can also be used to narrow down the number of articles in a search. For example, I might want to identify all articles with the tags ‘anthropology’ and ‘educational theory’. Using the command button as I click, I can select both of these tags, and the references containing both of these keywords will be displayed:

You can also ‘drill down’ the tag cloud itself. For example, I may start by selecting the tag ‘anthropology’, so that all references with that keyword will be displayed. Then, from the contextual menu in the reference set, you can select “Create Tag Cloud From This Reference Set” from the bottom of the list.

The tag cloud will then change to reflect only the references that contain the keyword ‘anthropology’:

…and from there you can narrow down further, based on whatever criteria you are working with. If you like tagging (which I really do), Bookends is a great tool to work with.

Hyperlinks

Each reference in Bookends has a hyperlink. You find the hyperlink by selecting a given reference and bringing up the contextual menu:

You can then use these links to connect the reference in Bookends to your literature notes kept elsewhere. For example, I keep a lot of my literature reviews in Circus Ponies Notebooks (which I’ve written about here and here). When I refer to a particular article in my reviews, I can just insert the hyperlink from Bookends. Then, if I’m reading through my notes in CPN and want to have a look at the original PDF in Bookends, I simply click on the link and it directs me straight to the relevant entry. This is what it looks like in CPN:

 

Integration with Devonthink

As I’ve written about here, Devonthink is a powerful data base that many academics use to organise literature notes. In Devonthink, there is a Bookends template for directly linking to entries in Bookends. You first need to select the relevant reference in Bookends. Then, switch to Devonthink, and find the Bookends template:

This opens a template which will automatically import the meta data for the selected PDF. It also inserts one of the hyperlinks described above, so that you can easily navigate to the original PDF in Bookends from your literature notes in Devonthink. The template looks like this, and from there you can add your own notes, import annotations, and so on:

 

Using labels

Bookends has labels that you can customise with the text and colour of your preference, and use to organise your literature. The label that I use the most is ‘in Evernote’. This indicates that this is a PDF that I have read and taken notes from, and that these notes are stored in Evernote. When you deal with a large number of PDFs, I find that it’s easy to loose track of what I have read, and what I haven’t. In this way, the entries I already have notes for are easily identifiable by a green label in my overview. Other labels include ‘to read’ for articles I should prioritise, ‘incomplete’ for entries that need editing or fixing, or labels that refer to particular writing projects.

Full text spotlight search

This was one of the main reasons why I switched from Sente to Bookends. Bookends offers a full text spotlight search of your entire library. Some of the things I use this for is to make smart groups of all texts that refer to a particular author, or which contain a particular concept. The spotlight search is available from the search field in the top right hand corner.

Tagging and searching note cards

Bookends is the only reference manager I know of with the capacity to tag individual notecards. The notes pane in Bookends, where you can insert any notes to an entry as you see fit, is divided into multiple notecards. These notecards can be tagged individually by inserting a % sign before the tag. For example, you could assign a tag to all notes that deal with a particular methodology, or a concept, and so on. These are in turn searchable. Bookends also gives you the general option to search notecards only.

So, these are some of the features in Bookends that I think are really helpful for organising literature. If you have other tips for how to use Bookends, please leave a comment below.

Related posts on this blog:

Managing your research literature: Sente versus Bookends

Reference Management: Exploring Sente

There’s another good blog post written by Ben Taylor on using Bookends in conjunction with PDF Expert here.

25% off on writing and productivity apps

This is just a quick post to let you know that you can currently get 25% off on a lot of good quality apps for writing and organising information. Click on this link for more information about discounts on:

• Scrivener
• DevonThink Pro
• Scapple
• Tinderbox
• Nisus Writer Pro

PDF annotation on iPad: why GoodReader has replaced iAnnotate and PDF Expert

I use my iPad as my main tool to annotate research literature, as well as sorting data and commenting on draft papers or student work. I have previously sung the praise of iAnnotate in this post, as I consider it one of the best apps for marking up PDFs on an iPad. I have also previously used PDF Expert quite a lot, and decided a couple of days ago to test out their new app, PDF Expert 5.

However, both of these apps have now left me with a problem which is a complete deal breaker: they lump words together when I export annotations.

Exporting annotations is an integral part of my work flow. Every time I have marked up a PDF on my iPad, I extract the annotations (this is a feature in all good quality PDF apps for iPad), and email them to myself as plain text. I then create a separate file in Devonthink (copied to Evernote), where I add my own summary and comments to the annotations.

However, back in March I started noticing that iAnnotate seemed to lump a whole lot of words together, which were not lumped together in the original text. For example, in a recent article I worked on, a sentence which looked like this in the actual PDF:

Instead, if we accept the general point that in cultural terms, teachers, like other workers, are creatures of their occupational situation, then we might do better to address ourselves to how the material circumstances of the occupation might be modified so as to elicit a different kind of cultural response

looked like this in the annotations I emailed to myself:

Instead, if we accept the generalpointthat in cultural terms, teachers, like other workers, are creatures of their occupational situation, then we mightdo betterto addressourselves to how the materialcircumstancesof the occupation mightbe modifiedso as to elicit a different kindof culturalresponse 

And that’s a total pain in the butt to edit manually.

I had an exchange with the developers at iAnnotate about this, and was very sad to hear that they couldn’t do anything about it in the short term. They suggested that I attempt to go through an additional step of rescanning the document in Preview or Adobe Acrobat on my mac, but since I already had GoodReader which didn’t give me this problem, I just switched apps rather than adding an additional step to my workflow. I compared a range of PDFs from different academic publishers, both old and new, and the result was consistently the same: iAnnotate would lump words together, while GoodReader didn’t. So, GoodReader it was.

When I tried PDF Expert 5 a couple of days ago, I ran into the same problem. I immediately contacted the developer, and they had the same response as Branchfire (the developer of iAnnotate): they don’t know how to fix this in the short term.

So, I’m back to GoodReader. And that’s not a bad thing. GoodReader is a high quality app, and at 5 dollars in the app store it’s arguably better value than some of its competitors. I miss the continuous scrolling and the set mark/return to mark feature of iAnnotate, but apart from that it has all the features I need. The sync with Dropbox (I sync my Bookends library to GoodReader) works well, and an advantage of GoodReader compared to iAnnotate is that it has a proper zoom function for hand writing, which makes it much easier to leave comments by hand, which I often prefer to typing on the iPad keyboard. They do, however, have a smaller feature set than iAnnotate – but GoodReader will take you a long way.

Some of the features include:

• highlight, underline, squiggly underline, strikeout, free text, free hand writing, ‘bubble’ notes
• two way sync with Dropbox
• bookmarks for navigation
• horizontal and vertical (but not continuous) scrolling
• search within document
• cropping
• easy access to ‘undo’ button (something I also missed in iAnnotate at times)
• tabs for displaying different PDFs at the same time

Here are a couple of screenshots. In the first, you see the user interface when marking up a PDF, and the menu for exporting annotations.

If you select “E-Mail Summary” in the menu, your annotations are extracted and placed in an email. Here’s a snapshot of what the annotations look like as they are being exported:

I’m sad to leave iAnnotate, and I hope they sort out this issue at some point. I was also excited about the new ‘review mode’ in PDF Expert 5. But for now, GoodReader is doing the job, and it’s doing it pretty well.

Update on 07.01.14: The developers at PDF Expert has now told me that the issue with jumbled text will be fixed in a future update, but there’s no specific date yet. The developers at iAnnotate has told me that “they cannot provide an immediate solution”. Finally, GoodReader just came out with an update yesterday. 

Related posts on this blog:

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

Organising your research (and the rest of your life) with Devonthink

I’ve been meaning to write a post on Devonthink for a while, and while I initially wanted to explore some more of its features first, two things prompted me to write this up now: First, a conversation I had with Cassady over at Macrumors about the relationship between Devonthink and Bookends (I’ve written about BE here), and, second, because I noticed that a visitor had been directed to my blog through the search term “can Devonthink replace Sente” (I’ve written about Sente here and here). It seems people are increasingly considering DT as an alternative to more custom made reference managers for academic literature. Therefore, I thought I’d do a brief introduction to Devonthink, and say a bit about how it differs from reference managers like Sente and Bookends.   

First, the basics: Devonthink is a document manager, and a quite powerful one at that. It comes in four different versions, and you can compare their features here. Personally, I’ve gradually worked my way up from Devonthink Personal to Devonthink Pro Office. It was the conversion to searchable pdfs (OCR) that prompted my latest upgrade, and when I went from Devonthink Personal to Devonthink Pro, the main pull was the ability to create more than one data base. 

Here’s a screen shot from my DevonThink Pro Office:

 

A frequently cited downside with Devonthink is the user interface – it’s very old fashioned. However, I’m willing to forgive the developers for the lack of aesthetics because the app is otherwise awesome in so many ways. 

 

So, what is Devonthink good at?

It’s really good at capturing all kinds of stuff. Depending on which version you have, you can throw almost anything at DT. It takes a range of file formats (see the link above to see the specifics for each version). It has a good web clipper that works well in Safari. It has a sorter window, where you can drop things you want to add to your data base. This sorter can be mobilised from just about any app, and can be used even if DT is closed. I have configured my sorter window to include the folders I’m mostly likely to stick stuff in:

 

It uses powerful artificial intelligence to analyse and organise your documents. I haven’t used this much myself – but the features Keywords and ‘See Also and Classify’ are designed to make recommendations about what content goes together. To many users, this is what really makes DT stand out for document management. Personally, I have a very well established system of tags and smart groups that follow me across apps, so I don’t make much use of this capacity. 

There are a range of options for organising your files, including different databases (for DT Pro and up), static groups, smart groups, labels and tags. You can also link different files to each other. If you want a particular file to exist in more than one folder, you can either duplicate or replicate it. Duplicates are simply copies. Replicates allow you to have the same document in different places, but when you edit one of the versions, the edits will be visible in all of the clones. Which I find a bit magical. 

You can both import and index files. This means that you don’t have to import all the documents you want to work with into DT. For example, I have decided to index (rather than import) the attachments in my Bookends library. That way, I can link the pdf to different notes, images or other files in DT, but I maintain the advantages of using BE for importing reference information, and for syncing to my iPad. More generally, there is a long standing debate on importing versus indexing over at the Devontech forum. Ultimately, what works best for you will depend how your overall work flow is put together. Indexing also makes it possible to partially integrate file types that are not supported by DT (in my case, that’s usually files made in mind mapping or outlining apps). 

 

For my purposes, the main issue I have with DT (apart from the look of the UI), is that their iPad version isn’t great at the moment and the sync is a bit of a pain in the butt. While I have their iPad app, Devonthink To Go, I never use it. However, the good news is that they are rebuilding the iPad app from scratch, with much improved sync features. Once that’s in place, I think DT will have a more central place in my work flow. 

 

What can you use DT for?

So, does DT add value to academic research? This is where we get to the question of DT versus reference managers such as Bookends and Sente. 

There are two things DT doesn’t do that Sente, Bookends and EndNote do: importing reference information for your journal articles, and providing cite while you write capacity. Because DT To Go also isn’t very well developed yet, I personally don’t find DT to be an alternative to BE for managing my pdfs. I do, however have the Bookends attachments folder indexed in my DT data base for academic files, and for a good while I used to either import or type up all my literature notes in DT, and link them to the relevant pdf. DT also has templates for Sente and Bookends, which automatically imports meta data, abstracts and tags from either reference manager, and I find this a very useful feature. That template also includes a link which brings you straight to the relevant reference in BE or Sente.

However, until DT To Go has got the iPad app sorted, I’ve decided to keep all my literature notes in Evernote (and, to some extent, in Circus Ponies Notebooks – see my previous post on academic work flows). The sync with both of these apps is seamless, and Evernote in particular speaks to all my devices. Even when I sit and work on my Air, I tend to read notes using my iPad – it functions like my virtual notebook. So, painless sync is quite high up on my list of criteria. 

On the other hand, if you don’t have an iPad (or don’t care whether your literature notes are synced to your iPad), DT is probably much more interesting as a place to store academic notes. It’s also very convenient if your research includes data such as images, screen shots and web clippings – BE and Sente weren’t really created with lots of different files types in mind. I’ve heard of many historians in particular who find DT a very useful tool for organising data. 

When the new iPad version of Devonthink To Go is launched, I’ll probably use it more for academic work. At the moment, it’s primarily a more conventional data base for me. I keep all my personal files in one data base, various web clippings and other things related to my academic work in another (but not academic literature), and lots of web clippings for a future book project in a third database. However, on a general level, I warmly recommend the app – so if you think DT has a place in your academic workflow, don’t hesitate to try it out. All apps by Devontechnologies have trial version, as well as educational discounts. 

 

Related posts on this blog:

Reference Management: Exploring Sente

Managing your research literature: Sente versus Bookends

 

 

 

 

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. 

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 literature. I 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 articles. I 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

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.