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About me

Desktop app of the week: Papers 2

Papers 2 icon

I spent five years at university studying medicine, yet somehow remained completely unaware of the existence of referencing software. I don’t know how this came about, but I manually referenced every single assignment I did during my medical degree – and so did Wendy. How the existence of EndNote in particular passed us both by, I’m not entirely sure.

By the time I embarked on my Masters in 2010, I was aware of EndNote, but we were far from friends. The couple of times I’d tried to use it, I’d had nightmarish corruption errors, and had always quickly reverted to referencing by hand. With the prospect of a whole load of Masters assignments and a dissertation looming, I thought that there must be a better way. And I discovered Mendeley.

Mendeley is an excellent free reference manager. It stores your reference library in the cloud, so that you can (should you so choose) even access it via an iPhone app. I never really found a use for that feature, but Mendeley did see me through a number of Masters assignments. But Mendeley, like Endnote, has an occasional irritating moments of stubbornness, where it will claim that a document connection has become corrupted, or some such nonsense, and will require a bit of sorting out. Generally, copying and pasting the entire text into a new document did the trick, but the frequency with which this happened make me nervous.

Then, I discovered Papers 2. It’s completely brilliant. I actually don’t really understand how it works, but it doesn’t rely on flaky plugins, or any requirement to use specific word-processing software. It just works, has fully cite-while-you-write functionality with a global shortcut, and is a joy to use. It isn’t free, but does have a free trial, and offers a generous academic discount for students. It has an iOS app too, but I’ve never used it, as I still don’t understand why I’d want that functionality. It’s available on Windows as well as Mac, though I’ve never tried that version.

Before using Papers 2, I’d thought that the whole software category of reference managers was, by definition, flaky and unreliable. Yet I don’t think I’ve ever seen Papers 2 crash, and it has certainly never messed up the references in an actual written document.

Papers 2 is a total, total joy to use, both for organising papers, and for citing them. It’s an app I cannot recommend highly enough for anybody who does even vaguely academic writing. It’s completely brilliant.

This 1,657th post was filed under: Favourite desktop apps, Technology, , , , , , .

Photo-a-day 79: Journal of Public Health


I know journal editors have a strong proclivity for austere covers, but it is a little dull. This journal generally sits around the house for a week or so before I get round to opening it, so uninviting is its cover. I’ve made this photo monochrome since I gave up trying to accurately capture the bright orange cover colour.

I think a medical journal with a cover styled like Monocle would be fab: it would be a lovely combination of austerity, uniformity, but also inviting imagery… Though I guess the additional colours in the printing process might push costs up.

This 1,572nd post was filed under: Photo-a-day 2012, , , .

Innumeracy and risk-perception in healthcare

Which of the following numbers represents the biggest risk of getting a disease? 1 in 100, 1 in 1000, or 1 in 10?

Almost 30% of Germans and 25% of Americans answered this question incorrectly in this study of statistical numeracy.

It’s an interesting reminder that healthcare professionals shouldn’t underestimate the statistical complexity of risk concepts: I think I’d previously have thought that these descriptions were fairly clear, but clearly they are not well understood.

This 1,515th post was filed under: Diary Style Notes, Health, , , , , .

Photo-a-day 38: Lacking perspective


This has been sat on my kitchen table for a few days now… and yet I’ve only just noticed the word in the cover image. Duh.

This 1,512th post was filed under: Photo-a-day 2012, , , .

The sheer bloody idiocy of medical journals

This morning, I was sent a list of seven papers in medical journals by a colleague. The titles looked intriguing, and I wanted to read further.

I have access to various journals via a number of means: the NHS provides me with access to a given selection via Athens, comprising about 1,500 journals; I personally pay the RSM to give me access to another 1,000 or so; and my BMA membership allows me to access perhaps 100 others. Clearly, the numbers are too large for me to retain details of which portal gives me access to which journal.

So, having found a given article, I then have to cycle through the three access methods, generally in the order outlined above, to find which works. That’s three sets of logins to three different sites (neither the BMA nor the RSM allows direct login from journals’ own sites). This is maddeningly frustrating, especially when I’m trying to glance through seven articles. Accessing each article can take, perhaps, five or ten minutes, which is sheer lunacy. I often don’t have that kind of time.

Now, let me share with you the process for just a couple of the seven papers I happened to be accessing this morning.

First was the Journal of Medical Ethics. I stuck the article title into Google (1 click). The second result was on a bmj.com domain. I often read things in JME, so I knew that I could access this via the BMJ domain with my NHS password. So I clicked the link (2 clicks), and ended up on the abstract page. I hunted for the “Full Text” link, which took me (3 clicks) to a login page. I clicked the “Login via Athens” button (4 clicks), which took me to an institutional login page. I clicked the “Login via Athens” link on this page (5 clicks), entered my username and password, and got redirected (6 clicks) back to the full article.

I make that six clicks and one login to get from my email to the article, for something I know how to access. Clearly, no-one in the field has heard of the three click rule.

Second on the list was a 2011 article from the Journal of the National Cancer Institute. Again, I copied and pasted the title into Google (1 click). The top result was from Oxford Journals, taking me to the abstract page (2 clicks). I clicked the “Full Text” link (3 clicks) to be taken to a log-in page. I clicked “Login via Athens” (4 clicks), and then “Sign in via Athens” (5 clicks) on the resulting page. I entered my NHS Athens details (6 clicks), and got redirected back to the journal’s login page, with no explanation as to why. Out of confusion, I clicked “Login via Athens” again (7 clicks), then “Sign in via Athens” (8 clicks), and again got redirected to the login page with no explanation as to why.

I assumed (correctly) that the NHS doesn’t pay for access to this journal. So I accessed the RSM website (9 clicks), and clicked “Library” (10 clicks), then “E-journals collection” (11 clicks). I logged in (12 clicks), and searched for “National Cancer Institute” (13 clicks). No results.

So I accessed the BMA website (14 clicks) and logged in (15 clicks). I went to “Library Services” (16 clicks), chose “E-resources” (17 clicks), and “Login now” under e-journals (18 clicks), despite having already logged on earlier. This gave a list of journals, on which JNCI didn’t feature.

At this point, I gave up. I could’ve requested the article from the BMJ or the RSM for a couple of quid, or emailed round to see if anyone else had access (e.g. via a university). But for an article I’m browsing for interest and to casually increase my own knowledge, it’s not worth the hassle or cost.

So now, I’m left more ignorant than I need be because of incompetence (the system is crazy), stinginess (my employer isn’t paying for access), and a touch of defeatism.

I struggle to see how conducting research and then hiding it from people is ethical – isn’t that precisely what skeptics constantly berate Big Pharma for doing? Granted, there’s are important ethical and practical differences between non-publication and sticking an article behind a crazily high pay-wall, but I’m sure there’s an extent to which people on the ground are less informed than would ideally be the case because of this broken system.

Why can’t somebody (perhaps the UK Access Management Federation) compile a composite list of journals I have from various sources, and provide some kind of auto-login toolbar or cookie that gets me straight from the abstract page to the full-text page without the faff, or morosely reports my lack of paid access if none of my providers subscribe?

And why can’t journals like PLoS and BMJ Open have more sensible publication fees for individual authors who, for want of a better metaphor, don’t want to hide their light under a bushel? Funded research should factor in the cost of publication in such journals into it’s funding; un-funded research should be admitted for a nominal fee (or, preferably, nothing).

Anyway, it strikes me that the whole system is pretty crazy – something I’ve thought frankly since I started reading medical journals almost a decade ago. And I needed a cathartic rant. Thanks for reading it.

This 1,498th post was filed under: Health, Technology, , , , , .

What’s a 30% chance of rain? And why does it matter to doctors?

The news reader announces a 30% chance of rain tomorrow. Thirty per cent of what? Most people in Berlin think that it will rain tomorrow 30% of the time. Others believe that it will rain tomorrow in 30% of the region. In New York the majority believe that it will rain on 30% of the days for which the prediction was made.

This is the (edited) opening of BMJ 2012;344:e245, a fascinating paper about single event probabilities by Gigerenza and Galesic. It’s only short, quite fun, and may convince you to change your practice. Well worth a read.

This 1,488th post was filed under: Diary Style Notes, Health, Quotes, , , .

Photo-a-day 5: Book room


My concentration on revision is slipping as I get increasingly bored of it. I’ve just spent at least 30 seconds trying to puzzle out why you’d need to provide a “book room” for a focus group. I’m not usually so slow. It’s from this book, if you’re wondering.

This 1,468th post was filed under: Photo-a-day 2012, , , .

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