Monthly Archives: May 2008

Too beta to be live

Yes, I’m referring to you, SciLink.

  • I create an account
  • On trying to add contacts from my address book, 7 alert windows pop up with the message “the page at scilink says error” – fixed
  • The page then hangs with a spinning icon
  • Some time later, the site spews errors including “Exception org.springframework.web.util.NestedServletException”
  • Not to be deterred I try to edit my profile
  • The “extensive database” finds 6 13 of my 23 publications and provides no easy way (e.g. PubMed ID) to add the rest
  • The dates of my education are saved incorrectly (1988-92 not 1989-93, 1992-96 not 1993-97) – fixed
  • Apparently I will be in my current post until the year 9998fixed
  • The final insult – no link to delete my account and escape

Can you tell that I’m annoyed? This is not the way to encourage social networking in science. Tip: don’t go live until your website works.

Update: I’ll say this for SciLink; they are very responsive and tolerant! Fixes and improvements are on the way.
Update 2: No, I’m just not impressed. Removed all scilink info and added a pointer here. And I want to delete the account.

WikiProteins

It’s not every day that a publication in an academic journal devoted to genomics receives wide attention all over the Web. I’m referring of course to:

Mons, B. et al. 2008
Calling on a million minds for community annotation in WikiProteins
Genome Biology 9:R89.

Nor is it every day that one of the “et al.” is a WWW pioneer; in this case a certain J. Wales. I’m looking forward to seeing S. Brin and L. Page in PubMed any day now.

This is important. The early adopters and web technology enthusiasts can evangelise for years about concepts such as community annotation of scientific data using wikis. However, the sad fact is that the majority of researchers in academia will pay no attention whatsoever until the work appears in what they consider a reputable source: i.e. an academic journal. This despite the fact that the readership of most such journals is miniscule compared to the web audience. Go figure.

Wiki Professional is here and of course, Deepak is all over it already.

Update: Euan takes a look at the implementation and is less than impressed.

Life on Mars

Late one evening back in July 1997, I was alone in the lab writing my Ph.D. thesis, several months behind schedule. I fired up the web browser (probably Mosaic in those days) on our single computer and discovered that a tiny rover was about to land on Mars. Live, on the web!

When people use the phrase “web design circa 1996″, this is what they mean. It was all very exciting back then. Up came the first image, in near-real-time. Wow!

I’ve been a Mars geek ever since. Yesterday morning there I was again, except this time I was watching live streaming video of the Phoenix lander. After a near-perfect landing, the science is set to begin and it could be pretty exciting. Phoenix is the first lander since the Viking program to dig into and analyse the Martian surface. If there ever was (or is?) microbial life there, Phoenix has a pretty good shot at finding the signs.

Get the news as it happens from:

Google Health Live

The much-vaunted Google Health is online.

There’s a good early review at TechCrunch. Expect further coverage from bloggers who cover personalised medicine issues; you know who they are.

Questions that occur to me are: (1) how much personal information do you need to enter for the service to be useful; (2) how much will users be willing to enter? This will be a real test of the degree to which people trust Google with personal information.

Proteomics discussion from the science streamosphere

friendfeed CAI discussWe find ourselves wondering why codon adaptation index (CAI) is used as a measure of protein expression level in this article.

One answer is that CAI does correlate well with protein expression in many proteomics studies; but surely these same studies contain raw data with protein expression level? On reflection, I bet the answer is that it’s too difficult and laborious to access this type of data. There are plenty of papers that describe large-scale analysis of protein expression using proteomics, but the data are locked up in the articles or as inappropriate supplementary files.

Note to self: look into open-source software and standard data formats for proteomic data.

Published #2 (2008)

It’s turned out to be a pretty good week. This one has been in press for ever, but finally hit the web:

Frith, M.C., Saunders, N.F.W., Kobe, B. and Bailey, T.L. (2008).
Discovering Sequence Motifs with Arbitrary Insertions and Deletions.
PLoS Computational Biology 4(4):e1000071. [Open Access] | [PubMed]

This paper describes GLAM2, a Gibbs sampler that finds and refines variable-width motifs, allowing insertion and deletion, in related but dissimilar sets of sequences. The work is Martin’s baby; my very minor contribution was to try it out on some test datasets. It’s open-access and open source, so you can all go and enjoy it then grab the software to try.

Two more (unrelated) in press to tell you about soon. See, I do have a day job outside of this blog.

A brief history of the platypus, in 5 parts

Who isn’t fascinated by the strangest of mammals, the platypus? It has fur and lactates, like a mammal. It has a bill and webbed feet, like a bird. It lays eggs and produces venom, like a reptile. It finds prey using electroreception, like sharks. The platypus is so weird that when first described, many scientists assumed that it was a hoax.

To celebrate the publication of the draft platypus genome, here’s a brief guide to this wondrous creature.
Read the rest…