This is another guest post by Sarah Kendrew (blog, Twitter) a postdoc in infrared astronomy at Leiden Observatory working on instrumentation for the European Extremely Large Telescope and the James Webb Space Telescope. She’s also contributed an article about Evernote.
Staying on top of the literature, even in a narrow field, is one of the biggest challenges we face in research today. Do you have an ever-growing pile of astro-ph papers on your desk you’ve meaning to read? Yeah, we all have that. In recent years a number of software packages and web applications have come on the market to help researchers organise their literature: Papers, Reference Manager, Jabref, and Zotero. Past AstroBetter posts have introduced Papers and discussed Papers vs. BibDesk. A recent addition that’s been getting good press lately is London-based Mendeley. Here I’d like to share my experience and thoughts about Mendeley as an astronomy tool.
At its simplest, Mendeley is a very handy piece of software to help organise and keep track of the papers you have on your hard drive. Via a desktop application you can create a literature library of papers which can sort, create collections, tag and make the papers searchable. The programme parses pdf files and automatically creates a record for each paper, straight from the pdf. This works really well for recent papers, but for those that are older than 5 years or so, you may need to edit some fields manually. On the upside, the programme is good at sensing it’s done a bad thing and will prompt you to verify the info when in doubt. One missing feature is the ability to parse postscript files, these have to be imported and edited manually too.
Mendeley can actually re-organise your mess of papers into an ordered directory structure, sorted according to whatever criterion you want – author, date, subject and so forth. Say, if you store your papers in C:/papers, you can tell Mendeley to “watch” that directory. Whenever you save a paper to that directory from e.g. ADS, Mendeley automatically pulls it into your library database. So you don’t have to manually create a record for each paper you save to your HD.
When I’m writing a paper, where having my literature in order is key, Mendeley really becomes most useful. There’s nothing worse than spending an hour trying to find a paper on my hard drive, only then to have forgotten what I wanted it for in the first place. I write my papers in LaTeX, as most of us do, and use BibTeX for easy referencing. In one of Mendeley’s latest upgrades, automatic BibTeX file creation for each individual collection was added. So my collection of papers on, say, star formation now has a BibTeX file connected to it that gets updated every time I add a paper to it. It’s fantastic! For those using MS Word (a necessary evil for us instrumentalists), there’s a nifty add-in for referencing and creating bibliographies.
We have only seen the tip of Mendeley’s iceberg and what it is all about. Mendeley tags itself as “Last.Fm for research”, a social networking site that gathers info on what scientists are reading and saying about literature. The uptake in the astronomy community isn’t really significant enough for the reading statistics to be meaningful yet, but the online presence has many advantages. Users’ libraries are connected to an online profile, and via the website they can connect to colleagues and friends, and discover what others are reading. This doesn’t mean that your contacts see your entire library – but you can share publications with them, and if you add your own publications to your profile they will be visible to your contacts. My whole library is synched to the website, including annotations – so even when I’m away from my own computer I can look up references. I can also add things to my library via the web, using a Mendeley bookmarklet or directly from Google Scholar, NASA ADS, or even astro-ph. That’s what those icons are for in the right sidebar – who knew? So I don’t need to have a desktop application running all the time to add papers to my library – next time I open it, it’ll get all the new stuff I added from my web profile.
One of my favourite features is the ability to create shared and public collections. Shared collections are for collaborations, everyone involved can contribute papers and annotate. I’ve actually not used shared collections yet myself but imagine them to be very useful if everyone in a group is willing. Public collections are, as the name suggests, entirely public. I recently created a public collection called Gravity, to accompany a blog post concerning a paper on a novel theory of gravity; in effect I created a reading list to illustrate what I was talking about, that I can add notes and comments to. Public collections have an RSS feed, so anyone can actually subscribe to a collection and stay up to date with what gets added. They’re also embeddable, so I can add them to a webpage. For those of us who teach, this could be a really awesome way of connecting with students, providing them with supplementary material in a very low-effort way.
I haven’t sampled all of Mendeley’s features but for me it’s proven to be a great tool to help me stay organised. I used to stress about sorting out my hard drive to organise my papers, which were nicely ordered during my PhD but are now a total mess. Now I let this piece of software do it all for me. The one thing it won’t do is send the information from the paper into your brain. There’s no app for that, only grad students/postdocs (delete as appropriate), so hang on to those for now.
Sarah Kendrew blogs about astronomy science and politics at SarahAskew (RSS, Twitter). She is also a postdoc in infrared astronomy at Leiden Observatory working on instrumentation for the European Extremely Large Telescope and the James Webb Space Telescope.