My favourite Firefox add-ons

You'll forgive me, I hope, if I digress for a moment. I've been a dedicated user of Firefox since it was announced in 2004, and I rarely look back even now that IE 7 has copied some of the best bits. After some cajoling, even the most luddite of our editors have made the shift.

One of the great things about Firefox is that anyone can write their own add-ons for Firefox. If you can think of something that you wish Firefox could do, the chances are that somebody will already have come up with the solution. At the risk of losing you, here are my favourite Firefox add-ons:

Search engines - almost any site you care to mention has one, and if it doesn't you can write one yourself (see my previous post). Matt Cockerill, our publisher, has written a few: two internal ones to search our manuscript and user databases, one to search our published articles, and one for Google Scholar.

Tab Mix Plus. Enhances your tabbed browsing. So useful that Firefox 2.0 included some of its best functions, but it is still great.

Context Search. Highlight text, right-click, chose any of your search plugins from a drop-down list, and a search is launched in a new tab for that text. Simple, but inspired.

SmartSearch. Much like Context Search, except that it uses Quick Searches instead of search plugins. The beauty of this is that Quick Searches are much quicker and easier to write that search plugins - simply get the URL of a search result, and replace the search term with %s.

Greasemonkey. I learned about Greasemonkey from Mark Wilkinson's iHOPerator article. This allow users to create and install scripts to adapt any website.

Digger, Go Up and Link Widgets. Want to go to the home page of the site, but can't see where to click? Here's your answer. These three add-ons allow easy navigation back up and around the directory structure of a website, at the click of a button.

Universal Print. Forget clicking Print for every tab you've got open - just use Universal Print to print all your open tabs at once!

Sage blog reader. "It's got a lot of what you need and not much of what you don't".

Adblock Plus. No more annoying adverts.

Flashblock. With this installed, Flash animations only appear if you click on them.

Cooliris Previews. This gives you the option to hover over a link, and see a pop-up window of what lies beyond. Move the mouse away, and the preview closes.

Download Statusbar. See and manage all your downloads at the bottom of the window - the annoying download window is no more!

Blogger Web Comments. Click a little speech bubble icon in the right-hand corner of the window, and up pops what the blogosphere thinks of the page you're looking at. You can even leave it open all the time showing the most recent comment or comments.

IE Tab. Opens a session of IE in a Firefox tab.

British English Dictionary. Useful for me most of the time, but our website content and Research Highlights are supposed to be in US English, which addles my poor little brain.

Littlefox theme. You can pack more onto the screen.

CuteMenus. It just makes your menus look better.

Tools to search the literature, and PubReMiner plugin

Recently I came across PubMed PubReMiner, created by Jan Koster. I've been very struck by this tool, which I think is pretty much the best way to search PubMed.

I have previously tried a number of different tools (see my list of Tools to search the literature in the sidebar), and Google Scholar by far outstrips a standard PubMed search due to the use of the PageRank algorithm to pull the most prestigious work to the top of the results. The PageRank algorithm doesn't just look at citations, rather it weights them by how often that referring articles has itself been cited. A citation from a source that is itself heavily cited counts more than one from a source that nobody has ever cited.

I've tried out Kfinder, which takes an abstract or other text as the input, and suggests keywords based on the frequency of occurrence of improbable words. You select keywords, and it returns researchers who match that search in Medline at least twice. Kfinder is quite slow and limited to Medline, but it is intuitive, and a good start to selecting keywords if you haven't had much practice.

PubNet from the Gerstein lab looks really promising. It visualizes the network resulting from a query to Medline. The network to the left, focussed around Howard Ochman and Emmanuel Lerat, clearly shows a network of collaborating colleagues, but I only ran that search because I knew of the network already. It could be useful, but I've not found the time to devote to exploring its possibilities, and it takes a while to generate the visualization at times. If it were quicker and easier to navigate the results, I might use it.

I've only had a quick play with Authoratory, and while the concept is excellent (automatically mining information from the results of PubMed searches), the delivery is lacking. When Deborah Saltman, our Editorial Director for Medicine, tried it she found that she was missing, and the keyword search doesn't take Boolean searches yet. A definite work-in-progress.

e-Biosci is clever in that it accepts any text as input (an abstract, or even a whole manuscript, although it was quite sluggish!) and calculates the concepts contained within. You can add and remove concepts to refine your search, and weight how important they are, and then search using these concepts in Medline abstracts and some full text, including BioMed Central's. The advantage of this approach is that you never need to think about appropriate keywords or search terms; the disadvantage is that some concepts are quite diverse. A good example is that an abstract about physician uncertainty in medical decision-making returned some physics articles near the top! I find that it can return items that you probably wouldn't have found otherwise, and can be very accurate at times.

eTBLAST is one of the big hitters in the field. It runs searches against Medline automatically when given an input of text, much as e-Biosci does, and returns a list of related articles. You can then get list of experts in the field, journals to submit to, the history of publishing in this field and several more features. eTBLAST does all the thinking for you, but it does take its precious time. It can take minutes for the results to be returned, which makes me think that the option to have the results emailed is the only way it will get routinely used.

But, as I said at the top, PubMed PubReMiner is my current favourite. Why? Well, it takes standard PubMed queries, which makes it very easy to start using. It is quick and unfussy, and returns the results in easy-to-read columns: a list of the most common journals in the results, a list of the authors who appear most often, and a list of words that most commonly appear in the abstracts, as well as MeSH terms, affiliations and the publications by year. It is simple, but highly effective.

I liked it so much, that I made a Firefox search plugin for it. After vainly following a tutorial, I found that searchplugins.net has a plugins generator, which I've used to create one for PubReMiner, complete with a logo. It is set to the default of a 1000 abstract limit. You can view the source code, and search for it under PubMed or PubReMiner. You can also install it now.