Bibliography software (mac)

I like playing with software. Sad but true. One of the most important bits of software for me is that which manages my pdf collection and bibliographies when writing manuscripts. Over the years I’ve tried Mendeley, EndNote, Bookends, Sente, and others.

I used EndNote throughout my PhD, and the first years as a post-doc. This was a while ago, in the late 1990s. The problem was back then, that using any advanced features like ‘cite while you write’ was basically an invitation to the combination of Word and EndNote to ‘crash whilst you work’, resulting in unsaved lost changes, confused bibliographies, and a generally unacceptable requirement for bad language. Surely, I thought, there must be something better.

So I started playing with alternatives. Bookends and Sente were my initial favourites. I have quite a large reference library, mostly with attached PDF files, which now is greater than 10,000 references. It’s a great resource, but really exposes the weaknesses in programs. The killer is the speed at which the library can be searched, without spinning wheels of death and the sound of endless drumming of fingers on the desk. It’s great to have the articles available to read and examine, but if you can’t find them when you want them, or searching for them to insert into a document takes a few seconds and you loose your train of thought, it’s more of a nuisance. You end up going back to PubMed, even when the reference is already in your database. The winner here? Always Bookends. I’m not quite sure how it maintains its indices, but it searches fast and well.

Then, fateful day, a colleague persuaded me to try Papers. This is a very pretty piece of software. I remember the upgrade to Papers2, with its lovely cite anywhere feature, so I could use it with Google Docs, Word, or any other word processor without specifying something in preferences. Very clever. Papers2 looked gorgeous as well. The early versions of Papers2 were buggy and slow, but gradually, on a very fast mac, it turned into a useful program. I was keen to try Papers3, and upgraded early. Once again, the software seemed to be being released at too early a stage. With a large library, it does all of its operations at very slow speed. Trying to search for references: slow. Finding a reference to insert in a bibliography: slow, approaching a grinding halt. Syncing to dropbox: a great idea, but seems to slow its operations down even more. Want to do something in Papers3? Probably waiting for it to sync somewhere. Looks: pretty as a picture.

It’s interesting. Running Bookends, no-one ever says ‘gosh that’s a great looking piece of software, what are you using’. Running Papers, often people comment on how nice it looks. I love tabbed browsing of local PDFs, to compare and read documents. But again these early releases of Papers3 are just slow, slow, slow. I can’t search without going off for a quick coffee, and I keep loosing the thread when working on documents.

So, I’m back to Bookends 12. Let me sell it to you:

– It can manage a huge library, with loads of PDFs, with complete aplomb. It won’t slow up or fail to find references quickly. You can browse your PDFs in the main library, or open up in any relevant application. You can have multiple libraries. Libraries open quickly and are immediately available for searching. You will never have to go off for a coffee whilst waiting for something to happen.

– It’s got a useful set of features on its inbuilt browser, and works well with ezproxys to get PDFs when you’re off campus.

– It doesn’t crash (at least, hardly ever).

– It’s got Jon. He is about the best ever tech support on email I’ve ever come across, for any program, ever, anywhere. I’m not sure he sleeps. Or he’s got a twin and they work on rotation.

– It works well with Word, and remarkably well with Mellel (a slightly quirky but rock solid word processor that’s great for long documents).

– If you want a feature, it can probably already do it. There’s a mature, well-written help manual, and when that fails, there’s Jon.

– It’s got the easiest, best, style-editing approach for output styles in bibliographies. You can create custom bibliography styles in minutes. The first few I made in Papers2 took me ages, trying to learn CSL editing. Grr.

Still Papers is slightly prettier. But for me, the speed, stability, and customisability of Bookends has won again.

What is significant?

How do you decide what is significant? I’m thinking here of how we bridge between the humanities and science or medicine.

I count significance in so many ways. We all do. In the lab or in clinical trials, I’m interested in statistical testing of results. I want to know that things haven’t occurred by chance alone. Reliable repetition of high quality experiments is the key. There’s an element of this that is about the objective describing of underlying truth, though it’s easy to misread data and get confused about truth, or fail to see hidden bias in thought or experimental design.

What’s significant to me is, of course, rather different. Data makes me happy, but not as happy as my friends, family and loved ones make me. Significant events in my life can’t be measured by p values.

My friends in the humanities undertake research using different standards of evidence. They talk about stories, and the value of individual lives. They ‘triangulate’ evidence from historical texts to make conclusions about the past and the present, though these conclusions are not really testable by experimentation. Stories tell us the truth about ourselves, often even when they’re purely fiction. John Steinbeck in Sweet Thursday said “There are people who will say this whole account is a lie, but a thing isn’t necessarily a lie even if it didn’t necessarily happen.”

So here’s the dilemma. If I want to see lives change for the better, in people with an illness, I can study and measure things about the disease. I can quantify and prove that specific pathological processes occur, and hypothesise how this might be relevant to disease. I can measure the impact of disease on survival or quality of life, and test the effects of treatments. But how do we quantify the significance of a the history or human stories of the impact of disease? Is it even valid to try? Another quote: Wittgenstein said, fairly famously, “The limits of my language means the limit of my world”. What language brings science and the humanities together?

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