Gene Wiki

I received an email from Andrew Su at GNF today, reminding me about the Wikipedia Gene Wiki project and asking if I wouldn’t mind publicising their efforts. No worries Andrew.

All kinds of bioinformatics

If you haven’t already, go and read Mike’s amusing and pertinent post, World of Bioinformatics Quest: Character generation. Which one are you?

I often think that in academic research at least, there are 3 types of bioinformatics:

1. Bioinformatics that provides insight into biological systems
   The ideal case being that you make a computational prediction which is then confirmed experimentally. Requires close collaboration between you and wet lab colleagues. By far the rarest category.
2. Bioinformatics that provides insight into biological data
   An example might be a statistical analysis of the PDB to identify factors common to protein chains that interact. Often useful and may overlap with type (1) in the best cases.
3. Bioinformatics that develops an algorithm or statistical procedure, but provides no insight into biology whatsoever
   By far the commonest category and the most prevalent in the bioinformatics literature. Normally takes the form: (a) amass some variables, (b) build a SVM, (c) run 10-fold cross-validation, (d) report sensitivity, specificity, accuracy etc. etc. Leading to the imminent death of bioinformatics as a respected research discipline. Largely responsible for the divide between bioinformaticians and bench scientists.

More open science links

• The New Science of Sharing – Business Week article
  “Companies such as Novartis and Intel are at the forefront of Science 2.0 by encouraging open systems of collaboration”.
• Standard Open(ed-up) Science
  Frank from the peanutbutter blog aims to make his Ph.D. data available using standards for proteomic data.

This trickle is becoming a tsunami, my friends.

The 23andme blog

23andme have been blogging for a while, but activity has recently picked up. Entitled “The spittoon” (tagline: more than you’ve come to expectorate…nice one), a recent post is bluntly headed “Why science can’t share” and points us to this NYT article by a cancer biostatistician on the difficulties in accessing raw biomedical data.

Update: the NYT article was free when I posted this, but now requires login. Ah, the irony…

The 23andme post is filed, quite appropriately and correctly, under “big questions”. A blog worth keeping an eye on.

A birthday, of sorts

Glancing through the archives at Nodalpoint, I note that the first entry is dated 2000-01-25. This may or may not be accurate (the first “real” post dates from August 1 2000) but as we approach the eighth anniversary of this venerable website, I thought a few words were in order. I trust that Greg will forgive my own interpretation of Nodalpoint history.

Google Health – almost here?

Via Techmeme – Google Health Login Page.

Here’s the Google Health site – a brief summary of features, but you can’t login yet.

Hyperlinks make the Web go round

News organisations are developing increasingly sophisticated websites: many of them display Web 2.0 features such as tags, feeds and numerous buttons to share articles at social networks. Sometimes though, they just forget the basics.

For instance, I’m interested to learn that the Old Faithful geyser in Yellowstone National Park is now on live webcam. But – where’s the link to the webcam?

I think the answer is here, but that came from Google, not Reuters. There are lessons here for anyone providing information via the Web. It works because we link to each other.

YMMV

Ah, geek humour. All my scripts will be shipping with this one from now on.

Via Andrew’s del.icio.us/programming+funny.

Science publication and assessment: our national debate

The Australian, our national newspaper, is usually not my preferred read but does have a good higher education section. Our new government has just thrown out an assessment exercise named the Research Quality Framework (RQF) – it will be replaced with something very similar, no doubt. Disturbingly, Thomson Scientific were given a licensing agreement by the previous government to supply the data for the RQF.

Imagine my delight to find newspaper articles discussing the shortcomings of impact factors, the rise of Google Scholar and the open-source software of Anne-Wil Harzing:

• Research Review Heats Up

“…commercial rivals such as Elsevier’s Scopus database and software built on Google Scholar have entered the market while the rise of research assessment linked to promotion and funding has made academics ask searching questions about the integrity of Thomson ISI as the key player.”

• Metrics debate is the rule

“Australia’s closer embrace of metrics comes at a time of fierce international debate about research assessment.”

Not entirely unrelated:

• Scientists ‘obliged’ to share wisdom – so says the science minister
• Science left to rue a roo genome – on the sorry state of genomics in Australia

WordPress.com storage

The nice people here at WordPress.com have upgraded our storage to 3 GB, for free. Storage of certain file types (video, audio) still requires a paid upgrade – which seems a little odd, but is not an issue for me.

If you’re thinking about starting up a blog and don’t want to host it yourself, there are plenty of options these days. I’ve had an excellent experience here at WordPress and would certainly recommend them to you.