BioStar users (of the world, unite)

Egon writes:

Can someone please plot the BioStar users on a Google Map?

Sounds like a challenge. Let’s go.

My first greasemonkey script

Seems almost compulsory for web2.0 enthusiasts to write a brief greasemonkey article these days!

Here’s my attempt. Nothing whatsoever to do with bioinformatics; instead, this one resizes Flickr images on Profilactic mashup pages, such as this one. My aim is just to convince you that greasemonkey development is quite easy, even for JavaScript novices like myself.

Google Reader subscribers Greasemonkey script

Via Google Operating System: a useful Greasemonkey script, Google Reader subscriber count. For any page with a feed, overlays a clickable count (click to subscribe) of GReader users subscribed to the feed.

Of course, people use services other than GReader for their feeds. Go on though, admit it – you still want to know how many subscribers you have :)

Web trends in science: javascript

When I first started out writing simple web pages circa 1995, JavaScript was frowned upon. It was a security risk, browser support was poor, people tended to switch it off, there were different versions and we were instructed that web page code should be compact, since most people had dialup connections.

Jump forward 10 years and a WWW without JavaScript is almost unthinkable, since it’s a major component of AJAX, which powers all the Web 2.0 applications that we know and love. It’s also used in Greasemonkey scripts, which have proved extremely useful to bioinformaticians and even merit academic publication.

Why am I musing on this topic? I’m sitting here with Zoho Writer in one Firefox tab and my CiteULike references in another. I’m thinking: surely with a little JavaScript, I could choose a reference from CiteULike and drop both a numbered citation and a formatted reference into Zoho Writer. I find myself visualising a Firefox addon in which I enter a CiteULike tag, get a drop-down list of references and insert into an online document with one click.

Sadly, I just don’t have the skills to take this further or much time to learn them. I have plenty of bookmarks on del.icio.us pointing to online tutorials, how-tos and teach yourself guides. If anyone has a favourite resource that they used to learn how to code JavaScript, XUL, Firefox extensions and the like, feel free to leave a comment.

Here we go again

My token effort at New Year reorganisation is a change of blog theme (Garland – familiar to anyone who’s looked at a Drupal site). Others have made rather more of an effort.

After 10 internet-free days there was a lot of “mark as read” happening in my feed reader, but things that caught my eye include:

• Open Lab 2007 winners. The extended essay is not my preferred writing style, but I enjoy reading the work of others. A timely reminder that there is some really good science writing in the blogosphere.
• Userscripts for the Life Sciences (my CiteULike link) challenges us once again with the question: do Javascript browser plugins make for rigorous academic publications? The answer seems to be yes and congratulations to Egon and the team on their efforts.
• Join Stew at F & L for a week of open bioinformatics research: Open Notebook 1, Open Notebook 2, Open Notebook 3.
• Obligatory NY resolutions link: Re-evaluating Your Online Commitments.
• Facebook users with publications in Medline: there’s a Facebook app for you and it’s not bad.

What would I like to see this year? More bioinformatics that addresses interesting biological problems, less bioinformatics that doesn’t. Much more to write about this as the year progresses.

Happy New Year folks. Let’s get into it.

The wait is finally over

At long last, Google Reader adds search. I can finally throw away that greasemonkey + co-op hack.

In other news, ATI are promising AIGLX by the end of the year. I’m not holding my breath.

Greasemonkey for scientists

Greasemonkey, if you’ve not yet discovered it, is a Firefox extension that allows small pieces of javascript to modify the look and function of a web page. It’s easy to install and sits unobtrusively down in the browser status bar, from where you can enable/disable it or add and manage scripts.

It might sound like a toy for people who love endless customisation, but there are some great scripts around that can benefit researchers. A few examples:

• Pierre’s pubmed2connotea – adds icons to a PubMed results page to bookmark references at Connotea, CiteUlike or del.icio.us
• Pedro’s postgenomic script – marks articles at Nature journal pages that are discussed at Postgenomic
• Connotea tools – a bunch of scripts to move bookmarks between Connotea and del.icio.us

Lots more scripts can be found at userscripts.org. Another of my favourites, not strictly science-related is two column Google, which displays Google search results in – can you guess? Much more convenient to view if you have 1280×1024 or wider.

The guys at NPG are big on greasemonkey, so be sure to keep an eye on HubLog and Flags and Lollipops. And here’s my short but growing list of resources.