Monthly Archives: November 2007

More video in science communication

A bit slow to notice this one: BioMed Central YouTube channel debuts:

We’re pleased to announce the launch of our new BioMed Central YouTube channel, which brings together videos of our authors and editors talking about their work, BioMed Central’s journals, and the benefits of open access publishing.

Video is an increasingly important way for researchers to communicate their results, and BioMed Central is at the forefront of developments in this area. We encourage authors and editors to upload suitable videos to YouTube and contact us so that we can add these videos to the BioMed Central channel.

The YouTube channel is here. I wonder what standard of comments to expect ;) .

Ah yes, the election

election.pngI suppose a brief comment on our recent Australian election is in order, although I prefer not to litter the blog with personal politics. The collage at left, culled from the weekend newspapers, summarises it for me.
It is quite uplifting when after a long, stale and conformist period in history the populace turns around en masse and says “enough, time for change”.

The Labor Party talked the talk during their campaign on science issues: higher education, IT infrastructure, skills shortages, maths/science degrees, technology development and action on climate change. Let’s just hope they deliver on some of those policies.

Stem cells and science blogs

We all know the Seed Group ScienceBlogs, but there are other, similar collections out there.

Correlations is the WIRED Science blog, featuring articles by several prominent science bloggers. I was interested to see Clifford from Asymptotia turning his hand to biology in a very good article on the much-reported recent breakthrough in stem cell research.

This news is also featured over at Scientific Blogging. I received an email from them recently (rather generic, it referred to my “site(s)” and I imagine my other blogging friends got the same invite), asking if I would be interested in the role of biology feature writer. I don’t really have the time or the inclination to write those longer, essay-style science journalism posts at which others are very good, but check out their site if you’re interested.

From hype to reality, just like that

If you’ve been wondering whether personalised genomics startup 23andMe were for real, the wait is over. Details of their service are now available. Simply pay USD 999, spit in a tube and mail it to them (in the US only so far) and they promise a personal web-based genome browser with information about disease susceptibility, ancestry and (if your relatives join in), genealogy. The technology used is SNP genotyping – basically DNA is amplified from your sample and hybridised to an Illumina array, generating ~ 600 000 data points. All the details are available here.

Some reactions (first 2 articles by people who have trialled the service):

So there you go – we talk about the hype, the technical difficulties, the ethical/legal issues and then someone just goes and does it. I suspect that increasingly, this is how the future will unfold. Shall we lay bets on the year of the first cloned human?

Handy Perl variables: @- and @+

Regular expression matching is one of the key features that makes Perl a widely used language in bioinformatics. For example, we can match a peptide to a longer protein sequence like this:

my $seq = "MVQRWLYSTNAKDIAVLYFMLAIFSGMAGTAMSLIIRLELAAPG";
my $pep = "MAGTAM";

while($seq =~/$pep/g) {
    print "Found a match\n";
                      }

Perl also uses a bunch of “special variables”, that are automatically assigned values when you perform certain operations. Two of these, @- and @+, contain indices representing the start and end of a regular expression match. Very handy for when you want to know the matching positions in the longer sequence. Note that you need to add one to the start position since indices start at 0, whereas sequences start at 1:

while($seq =~/$pep/g) {
    print "Found a match from ".($-[0]+1)." to ".($+[0])."\n";
                      }

See Perl regular expressions tutorial for more.

Friday light relief

One of my RSS feeds comes from Improbable Research, the source of many an Ig Nobel award. Yesterday’s item is a real treat:

Recurrent Clostridium difficile colitis: case series involving 18 patients treated with donor stool administered via a nasogastric tube.
Johannes Aas, Charles E. Gessert, and Johan S. Bakken.
Clinical Infectious Diseases, vol. 36, March 2003, pp. 585.
Improbable summary | PDF

Improbable feed

Yes, it is every bit as unpleasant as the title suggests.

LaTeX tip: make your own styles

Last year I wrote a short post with some ideas on how to generate citation styles. The idea being that whilst there are many styles of referencing in different journals, there is a finite set of elements: plain, bold or italic; all authors or et al. after 3; volume + number or just volume and so on and so on. Computationally, it should be possible to construct a set of questions based on these elements and have a style pop out the other end.

Well, since then I’ve moved to LaTeX and of course, it does precisely this for you. Just “latex makebst”, answer a long series of questions and you’ve got a custom .bst file. More details are available at the LaTeX Bibliography Styles Database.

Open Notebook Science: everyone’s (potentially) a winner

Cameron has written a very nice post on how open science has altered his work practices for the better:

I find that as I do my experiments and record them I take more care, I describe them more clearly, and I take more care to preserve and index the data properly. More generally I feel more inclined to share my ideas and preliminary results with others. And part of this is because I am aware that double standards will be obvious to anyone who is looking. Standards and discipline in maintaining them make for better science and for better people. Anyone who is honest with themselves knows that sometimes, somewhere, there is a temptation to cut corners. We all need help in maintaining discipline and being open is a very effective way of doing it.

It would be a kinder, gentler and more productive research world if more people went down the same road.

The Protein Structure Initiative: money well spent?

The latest issue of the journal Structure looks at structural genomics.

While the number of structures and impact has been substantive, the cost of the PSI-2 initiative is large. In the US alone, the NIH spends approximately $65 million each year on this effort. As a result, legitimate questions arise as to whether or not the money on PSI is well spent, especially at a time when funding for independent investigator-driven research appears scarce. To facilitate this debate, we will publish commentaries from both supporters and opponents of the structural genomics effort in the next few issues of Structure; we invite any additional comments from readers to be e-mailed to the Editors (structure@cell.com) We believe this debate is especially timely because of the ongoing need to shape PSI-3, which may or may not begin in 2010.

Read the rest…