Twitter Weekly Updates for 2010-03-29

Mendeley: research paper / PDF management

A little while ago I wrote about Zotero and how I felt it came short of my expectations for a reference manager (my main contention was that it wasn’t very efficient at managing my offline content, for example, PDFs.  Incidentally, see this interview, which also mentions this shortcoming of Zotero).  Today I came across Mendeley, which at first glance seems to fulfil all of my PDF management requirements.  It’s still a beta release, so expect some bugs and stability issues.

First of all, Mendeley is both a desktop tool that’s cross-platform (major bonus points already) and web service, running locally and syncing documents and metadata to a remote server.  This has the advantage of being both a backup and online library that you can access from any internet-enabled computer.  The company provides 500 MB of storage space for members which, while not big enough for everyone, will suffice for most people.

Unlike some services that are jumping on the “social media” bandwagon and are useless, it’s inclusion in Mendeley adds a powerful incentive to use the tool.  With an emphasis on collaboration in research, the ability to locate and share information with like-minded people is a great idea.  It allows a user to search for other academics / researchers who are participating in similar work and enables the sharing of resources or collaborative work.  Users can make their entire library public, or only certain parts of it, and the software will attempt to match similar articles and recommend other members based on extracted metadata and the papers in their libraries.  Privacy concerns mean that this will be an opt-in service, rather than enabled by default.

I like the potential of Mendeley’s recent announcement concerning collaboration with CiteULike, which will allow users to integrate data from both services into one place, and share the results with others.  The company has also developed a bookmarklet that allows users to automatically import citation information from appropriate sites (e.g. PubMed) straight into your Mendeley library.  I also love that Mendeley will monitor folders and automatically add the relevant metadata into your library when you add new resources to a folder.  Another interesting feature are the “vanity statistics” (my term for it) that will enable the software to generate individualised stats on your research papers / publications based on who’s reading them.  It’s this attention to detail, as well as the social networking tools that set Mendeley apart from other document managers.

All in all, it seems like Mendeley is a great tool for managing PDFs, and the social networking aspect adds an interesting dimension to the process.  I’ll still use Zotero in the way that I have been (i.e. for working through and annotating academic content online, usually in blog form), but it seems likely that Mendeley will become the standard tool for managing my PDF library.

Open source alternatives to proprietary applications

I thought I’d take a moment to briefly mention a few open source alternatives to popular computer applications. The following programmes are all:
  • Open source – the source code is freely available, which usually means more stable and more secure.
  • Free – as in no cost and free from restriction.
  • Cross-platform – they run on multiple operating systems, including Linux and Windows.
  • As good as, if not better than, their proprietary counterparts.

So, here goes (by the way, this list is by no means complete):

Firefox – A very popular web browser that offers a more secure, more intuitive and faster alternative to Internet Explorer.

OpenOffice.org – An entire office suite of applications for word processing, spreadsheets, presentations, databases and drawing. It uses the OpenDocument format by default and as such, it’s use is encouraged, especially in academia and governments.

Thunderbird – An email client that is a fast, secure and stable replacement for Outlook and Outlook Express, especially if you just need something light to manage your email.

Pidgin – An single instant messaging client that allows you to use all of your IM accounts at once, including IRC, MSN, Groupwise, AIM and ICQ.

Miro – An Internet TV application to subscribe to RSS feeds of free content from a host of providers, including TED, National Geographic and the Discovery Channel.

GIMP – The Gnu Image Manipulation Program. A free alternative to Photoshop that, while lacking some high end, professional features, does more than enough for most of us.

Flock – Social web browser…if you use Facebook, Flickr, Digg, or any other social networking service, this is for you.

Ubuntu – Not a software application but an entire operating system, Ubuntu is a Linux distribution based on Debian. Click here for the Wikipedia article.

Another great application to run, although once it’s set up you’ll hardly ever notice it, is BOINC (click here for the Wikipedia article). After installing the software, register with various projects and join millions of other users who donate their computer’s idle time to solving complex medical, scientific and mathematical problems. I can suggest the World Community Grid to begin with.

And while I’m at it, here’s a link to a post that discusses some of the problems with using Microsoft Word. I personally don’t mind receiving Word documents and understand that many institutions don’t give their employees a choice, but the first step is realising that you actually have a choice.