October 27, 2008

OWL Experiences and Directions (OWLED) 2008

Great Grey Owl by Brian ScottThe Web Ontology Language (OWL) is a language for creating ontologies on the Web. It does exactly what it says on the tin. But what is an ontology? One way to think of it is as a better way of storing data and knowledge. Instead of just capturing and describing data in a databases, ontology languages like OWL provide ways to capture and describe knowledge in a knowledge base. Ontologies can allow more intelligent querying, integration and understanding of data than is possible using a plain old relational database.

Since 2003 developers and users of the Web Ontology Language, abbreviated to OWL (not WOL), have been gathering at a two-day workshop called OWLED (OWL Experiences and Directions). This year the workshop is in Karlsruhe in Germany. The full list of accepted papers is available, as with previous years, this years workshop has a distinctly biological flavour to the proceedings: (more…)

May 9, 2008

I Still Haven’t Found What I’m Googling For

Filed under: tom-foolery — Duncan Hull @ 8:03 am
Tags: , , , , , , , , , ,

Irish GoogleTwenty one years ago this month, in May 1987, Irish rockers U2 released their classic Joshua Tree single, I Still Haven’t Found What I’m Looking For. Those twenty one years have seen incredible technological change: the adoption of desktop computers, mobile phones, the birth of the Web and the widespread use of search engines like Google. So with sincere apologies to Bono, The Edge, Adam and Larry, it’s time we updated the lyrics for the 21st century. So, I give you “I Still Haven’t Found What I’m Googling For” (21st anniversary, 2008 webby edition)… (more…)

April 25, 2008

WWW2008: The Great Firewall of China

Passage [The Great Wall / Beijing] by d'n'cThe seventeenth international World Wide Web conference (WWW2008.org) is currently finishing in Beijing, China. There are some interesting papers this year. Thankfully, the Great Firewall of China doesn’t prevent these papers reaching the rest of the world. It’s One World, One Web (allegedly). Here are some brief highlights from the conference. (more…)

February 8, 2008

Video Killed The Webbio Star

Filed under: video — Duncan Hull @ 6:18 pm
Tags: , , ,

We can’t rewind we’ve gone too far.

Video Killed The Webbio Star…

September 5, 2007

WWW2007: Workflows on the Web

Don't PanicThe Hitch-hiking novelist Douglas Noel Adams (DNA) once remarked that the World Wide Web (WWW) is the only thing whose shortened form – ‘double-you double-you double-you-dot’ – takes three times longer to say than what it’s “short” for [1]. If he were still with us today, there is plenty of stuff at the 16th International World Wide Web conference (WWW2007), currently underway in Banff, that would interest him. Here are some short, abbreviated notes on a couple of interesting papers at this years conference. They are relevant to bioinformatics and worth reading, whichever type of DNA you’re most interested in.

One full paper [2] by Daniel Goodman describes a scientific workflow language called Martlet. The motivating example is taken from climateprediction.net but I suspect some of the points they make about scientific workflows are relevant to bioinformatics too. Just like the recent post by Boscoh about functional programming, the paper discusses an inspired-by-Haskell functional approach to building and running workflows. Comparisons with other workflow systems like Taverna / SCUFL are drawn. Despite what they say, Taverna already uses a functional model (not an imperative one), it just hasn’t been published yet. The paper also draws comparisons between Martlet and other functional systems, like Google’s Map-Reduce. It concludes that the (allegedly) new Martlet programming model “raises the interesting possibility of a whole set of new algorithms just waiting to be discovered once people start to think about programming in this new way”. Which is an exciting possibility.

Another position paper [3] (warning: position paper = arm waving) by Anupriya Ankolekar et al argues that the Semantic Web and Web-Two-Point-Oh are complementary, rather than competing. Their motivating examples are a bit lame (Blogging a movie? Can’t they think of something more original?) …but they make some interesting (and obvious) points. The authors think that aggregators like Yahoo! Pipes! will play an important role in the emerging Semantic Web. Currently, there don’t seem to be too many bioinformaticians using Yahoo! pipes, perhaps they just don’t share their pipes / workflows yet?

Running in parallel to all of the above is the Health Care and Life Sciences Data Integration for the Semantic Web workshop, where more detailed discussion on the bio semweb is underway. As its a workshop, there are no full or position papers, but take a look at The State of the Nation in Life Science Data integration to get a flavour of what is going on.

Wether functional, semantic, Web-enabled or just buzzword-friendly, there is plenty of action in the scientific workflow field right now. If you’re interested in the webby stuff, next years conference, WWW2008, is in Beijing, China. I wonder if they will mark the 10th anniversary of the publication of that Google paper at WWW7 back in 1998? The deadline for papers at WWW2008 will probably be sometime in November 2007, but around 90% of submitted papers will be rejected if previous years are anything to go by. If you’re thinking of doing a paper, DON’T PANIC about those intimidating statistics, because bioinformatics is bursting full of interesting and hard problems that challenge the state-of-the-art. The kind of stuff that will go down well at Dubya Dubya Dubya.

(Photo credit: Fire Monkey Fish)


  1. Douglas Adams (1999) Beyond the Brochure: Build it and we will come
  2. Daniel Goodman (2007) Introduction and Evaluation of Marlet, a Scientific Workflow Language for Abstracted Parallelisation doi:10.1145/1242572.1242705
  3. Anupriya Ankolekar, Markus Krotzsch, Thanh Tran and Denny Vrandecic (2007) The Two Cultures: Mashing up Web 2.0 and the Semantic Web doi:10.1145/1242572.1242684

Creative Commons License

This work is licensed under a
Creative Commons Attribution-Noncommercial-Share Alike 3.0 License.

December 1, 2006

NAR Web Server Issue: Walking in a Webby Wonderland

Filed under: Uncategorized — Duncan Hull @ 3:18 pm
Tags: , , , , , , ,

WonderlandHave you recently built a bioinformatics web application useful to the wider community that you’d like to tell the world about? Are you also looking to score brownie points for a rigourously peer-reviewed publication that stands a reasonable chance of being well cited? If that’s you, then you have one month from today (December 1st) to sort your code out, and get your abstract in, for the fifth annual Nucleic Acids Research (NAR) Web Server issue published by Oxford University Press (OUP) in 2007. All articles in this issue are published under an open access model.

As regular visitors to nodalpoint will already know, every year NAR publishes two special issues: one on databases (annually in January since 1993) and the other on web servers (annually in July since 2003). Authors interested in pre-submitting abstracts for the 2007 Web Server Issue should read the Instructions to Authors for Web Server papers in NAR and send an abstract to Gary Benson at Boston University before December 31st 2006. The deadline for final submission of full articles is January 31st 2007. Gary Benson has taken over this year from previous web server issue editor, Nobel laureate and Ignobel participant, Richard Roberts [1].

One advantage of publishing your application paper in NAR, instead of alternative open access journals like Source Code for Biology and Medicine (SCFBM), is a listing in the bioinformatics links directory [2] and a bigger impact factor [3] of 7.6, if you care about these things. There are of course, disadvantages of publishing with OUP in NAR, like the expensive open access publishing fees of $1185 to $2370 per article which are debateable value-for-money. If you’re living in a ‘List A’ developing country these charges are waived, which makes it tempting to set up a laboratory in Malawi to evade payment…

Anyway, does anyone out there know how OUP prices compare with the complicated Biomed Central membership fees which are presumably required for publication in SCFBM? Another leading open access publisher, the Public Library of Science (PLOS) currently charges from $2000 to $2500 for open access publication. Maybe I’m missing something, but aren’t these charges a lot of money to pay an administrator to shuffle a few bits of paper around and run a web server? Don’t let that put you off submitting your paper though, because in Science and academia you will either publish or perish. This is where the web is your friend because free online web availability substantially increases a paper’s impact.

On a lighter note, and now that the festive season is upon us, I’ll hand over to the Christmas crooner Perry Como to sign off:

♫ Sleigh bells ring, are you listening? In the lane, snow is glistening. A beautiful sight, We’re happy tonight, Walking in a webby wonderland. ♫

Creative Commons License

This work is licensed under a
Creative Commons Attribution-Noncommercial-Share Alike 3.0 License.

Customized Rubric Theme Blog at WordPress.com.


Get every new post delivered to your Inbox.

Join 1,485 other followers