Archive for category Social Bookmarking

Zotero library re-visioned

I have been wanting to use Zotero now for a while for my reference library but could never work out how back up my library using subversion. My life is contained within subversion, I do not know how I could have possibly survived before all my work; code, presentations, papers, images and not to mention my thesis, is all perfectly backed up and re-visioned and floating happily in the cloud available to me from any machine. Zotero installs itself inside the firefox profile which makes it difficult to revision within the C:\\my-subversion” folder. What I decided to do was to create a new firefox profile (instructions here) within my-subversion folder then install zotero creating:


I then only added the zotero folder to my subversion repository. You could always revision your firefox profile but I decided not to. Now every time I add a new item to zotero the my-subversion folder indicates there has been a change and requires a commit. Obviously every time you add a pdf file to the library you will actually have to “SVN add” the file itself. This is not a problem for me as I try to keep my library light and not store to many pdfs.

I am also going to try and use zotero as an interface to my subversion repository, describing and tagging documents and code that I write, but more specifically presentations, so no more trying to work out what is contained in “Presentation1.ppt” or what file name I gave to that talk on data standards which I have to give tomorrow!

I am tagging my hard drive via Zotero, its just one big cloud.


RSS readers

I have outlined my growing tendency at the minute to handing over applications to the “Internet cloud” in an earlier post.

I prefer using web-based applications because I tend to jump from several machines throughout the day at work and then use a different machine at home. Having applications, floating in the ether cloud, means moving around is considerably easier. I have been using bloglines for quite a while now for my RSS feeds. I did have a early look at Google reader when it first launched, but I felt then it was not quite what I wanted and definitely not as good as bloglines at the time. However a re-visiting of Google reader over the last week or so has dramatically changed my perception. Re-vamped with a new interface (similar to bloglines) has made reading posts alot easier. All the post from your subscribed feeds are actually saved, by default and don’t disappear once read, unlike in bloglines (unless you check the “keep new” box). I think the biggest feature for me is the ability to tag posts, combined with the saved posts facility, this should prove to be a very handy source of reference rather that just an “recent-post viewer”.

A new feature that has just been added to Google reader is the offline mode. Working in conjunction with Google Gears this provides the ability to read the last 2000 recent items, a feature I am looking forward to testing during the flight to ISMB in a few weeks.

If you use another RSS reader or have an opinion on Google reader then let me know.

With using gmail, and calendar, with trying out Google reader (and probably switching from bloglines), using google docs and spreadsheets more everyday, there is every danger that my cloud is going to be raining google. With the added prospect of Google presentations round the corner will it be long before I am floating off to the Google OS cloud?


Connotea: social bookmarking system for scientific literature

I have recently started using Connotea which is what they now describe as ” Free online reference management for clinicians and scientists”. I remember seeing a presentation on Connotea at the Data webs workshop I attended, (excellent day of talks and discussions), where Connotea was described as a “social bookmarking for scientists”. I wasn’t overly convinced to use it then and my initial perception was that it was for scientists, so why not use  On a more recent, closer look, I see they have re-branded (or re-advertised) and are concentrating on tagging publications and providing exports to various reference managers, particularly bibtex, my favourite. This feature has convinced me to give it a try and as I am writting my thesis at the moment and I am really putting it through its paces.

I am liking it so far and definately “Discovering” new resources based on my tags. Hopefully I will never need to ask the questions again “Where did I put that paper?” or “I knew I read a paper about ontologies but which one was it?”