Academic workflows…

For the past couple of weeks I’ve been working on my end of year report for the first year of my PhD, I’ve also been conducting individual interviews as part of the first stage in the data gathering for my thesis – all very exciting. It has ended up with me feeling quite overwhelmed at times and made me think about my workflow and where I need to be improving on this – I’m not sure if these are useful thoughts, or simple procrastination. I thought it might be useful to write a, perhaps somewhat tedious, post about my current workflow and return to it in the future to see what has changed and think about any room for improvement.

There are some excellent websites and blogs out there that I dip into occasionally for example – Macademise and Mac academic workflows.

I thought I would structure the blog according to the main day-to-day tasks that I’m currently working on both in academic work and clinical practice.

  1. Literature searching and management
  2. Task management and organisation
  3. Writing

Literature searching and management

This is an area that I recently changed slightly and am still settling into, so it will be interesting to see how things change in the future. Previously I would receive an e-mail table of contents from various journals that I’m interested in on an almost daily basis, but this meant that my e-mail inbox was getting snarled up, particularly over weekends or when unable to access journals immediately. So I thought I would try something new…

Reeder is a nice, clear, app for iOS and Mac OS X that accesses whatever RSS reader you choose, in my case Feedly. This then organises all of your feeds into one place and you can arrange into folders etc in a manner that suits you. So far I’m finding this to be a much cleaner way of keeping up with articles that the table of contents update e-mail. I also put blogs etc that I follow into Reeder and can access any references they cite.

As well as tables of contents and journal RSS feeds I also use a website called PubCrawler – this is a simple search engine that will automatically run PubMed searches for you at a frequency you choose (monthly in my case) it then e-mails you to say the search is complete and generates a list of hits that are new since the last search was run. All very clever.

Once I’ve identified any new references I might be interested in I then import them directly into my library management software – Papers 3. Papers 3 is, obviously, an update to Papers 2, which is when I started using the software. The new update arrived last year and has been somewhat slammed by many professional reviewers. I’m finding however that the stability is increasing rapidly and that the sync features between my iPad and MacBook are now quite stable. The library is shared between devices using dropbox and the whole process is a little clunky and slow at times – but the sharing of annotations and library between devices is for me very useful as my iPad is where I do most of my journal reading now. Somewhat frustratingly the “Open in Papers” link for PDFs on my iPad is not working in the current update and I hope this will be sorted soon. I’ve also run three systematic reviews through Papers 3 so far and it has handled these fine with no crashing or loss of data.

Articles imported into Papers get put into a “To Read” folder (which is depressingly full at the moment). After reading through the article I then file it into different folders and tag with keywords and phrases I took from the article. The search facility within Papers is quite good making finding articles relatively easy when you only vaguely remember reading something about whatever at some point in the not too distant past.

Task management and organisation

The hub for me in this is Evernote. Evernote is free to use, although I have upgraded to a premium membership because I think the service they provide is quite brilliant. Basically Evernote lets you, unsurprisingly, create notes which are then tagged and filed in notebooks which are searchable at a later date. PDF files within notebooks also get searched and you can annotate PDFs using the companion app Skitch. Notes can be tagged with reminder dates and the whole thing then syncs between devices. So – if you e-mail me and tell me you have a piece of work for me to do I immediately forward this e-mail into Evernote (which comes with your own unique e-mail address for this purpose). Within Evernote I will then begin to make a task list of what needs to be done for the project you’ve sent me. I then link to other resources within Evernote or on the internet as need be so that everything is organised within one place. If we want to share out work I can share the notebook I’m working in with you so that you can edit notes there as well. Finally I then set a reminder for the note that will cause an alarm on my phone at the time I’ve set, generally at 8 in the morning on the day I want to address the task.

The problem I’m currently having with Evernote is that the reminder system itself is fairly simple – remind me on this date at this time. There are better task-management systems out there, but the ones that I think would really improve on Evernote are quite costly and don’t integrate as well as Evernote with other apps etc I use. So… there would have to be quite a considerable, clear, benefit to make me want to switch away from Evernote at this point, and, as the updates keep coming, Evernote gets more and more features…


Most of the writing I’m doing at the moment is either clinical reports, for example case summaries, or writing drafts for possible journal article submissions. I use the same process for both essentially.

I start in Evernote, looking at the project and the subdivision of tasks I’ve laid out. I then open an app called Scrivener – which is, quite simply, brilliant. It has features that I have no idea how to work with but does what I need it to do very well. Scrivener files are called projects – each project starts with two master folders – the draft and research. I start with research by dragging all the files and links into the research folder that I think I will need access to to write the piece. I will then switch to Papers and flag all the articles that I think are relevant to the current writing I’m doing. I then switch to an app called Scapple – which essentially reproduces a piece of paper on your screen. I use Scapple to write down ideas I have about the project I’m working on in a, sort of, mind map approach. I then import this into Scrivener and copy as a PDF to Evernote.

Back in Scrivener I then start documents within the draft folder with headings relating to the writing – for example Introduction, Methods, Results, Discussion. I will then start writing to fill these documents – generally I do this in a linear fashion as it helps me to structure the argument, but not always. Sometimes for example with a clinical document it is easiest to write a summary of the most recent clinical interview first and then tie in history and conclusions before writing a summary introduction with key points. Anyway – the point is that however I want to approach the writing I can. Also Scrivener lets you split your workspace view however you want – so I can keep the ideas I wrote down in Scapple within view whilst writing if I want to for example. Scrivener also has the advantage of being more reputably stable than other, infamous thesis dumping, apps such as Word.

Once you’re done writing in Scrivener you compile what you have written and export it either for printing or review by others. for example as a Word file. I think Scrivener is very good at managing feedback / drafts as, for example, I can put a file that my supervisor annotates into the research folder and then view side-by-side with the current draft to make any necessary changes. One of my supervisors likes to print out drafts and annotate by hand so I scan these pages to PDF and import that into Scrivener to view side-by-side as well. For referencing the cite-as-you-write features of Pages work within Scrivener.

Once I’m happy with the drafting within Scrivener I then import the document into Pages for Mac. Now unfortunately during the last Pages update Apple removed many of the third part App access features from Pages which means that Papers can no longer format document – but I’ve kept the previous version as a backup so this is easily worked around. I then format the document using Pages and begin to arrange any titles, tables of contents etc as needed within Pages – which I find works better than Word and is free with Mac OS X updates…

Pages also allows simpler documents, like blog posts, to be handled on iPad and iPhone and to sync between devices – this is quite handy and the new Mac OS update coming soon looks like it will be adding some more features to this process.


That was a very long winded post – if anyone has managed to read this without falling asleep and had any thoughts on my current workflow / advice from their own workflow I’d be really interested to hear…


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