This month's molecule is...

Space-filling and backbone model of 1HRY
There are a number of "Molecule of the Month" style mini-reviews on the web, which highlight one particular molecule (usually a protein) every month, in an accessible style. Two of my personal favourites are protein spotlight: one month, one protein written by Vivienne Baillie Gerritsen of the Swiss-Prot team and Molecule of the Month at the Protein Databank PDB edited by David Goodsell. Both these features are worth a quick read because they can help bio-literate and bio-curious users to increase and reinforce their knowledge relatively quickly.

A Sign, a Flipped Structure, and a Scientific Flameout of Epic Proportions

One of the most spectacular flameouts in science happened last year. In a short letter (barely over 300 words long) published in Science in the very last issue of 2006, Geoffrey Chang, a crystallographer, retracted 3 Science articles, a Nature article, a PNAS article and a JMB article. The sum of 5 years of work was destroyed, apparently, over a single sign error in a data-processing program. Read more...

I've put together a web site called which, rather grandly, is an attempt to bootstrap the biodiversity Semantic Web by providing resolvable URIs for biological objects, such as publications, taxonomic names, nucleotide sequences, and specimens. These URIs (or "GUIDs") can be resolved by a web browser to display HTML, but under the hood are resolved to RDF (which you can see by viewing the source of the web page you get for a URI).

A pipeline is a makefile

What is a pipeline? For me, it' s series of steps that munch DNA/protein data, combines it with other data using various small scripts and outputs the results as diagrams or HTML. Do we want to code this kind of software as a script? If you think "makefile!" now, then you're much more clever than I was. But personally, until recently, I've glued my scripts together using other scripts. And used makefiles only for compiling my programs. That was a bad idea. (it's a quite detailed post, click on "read more" for the full article)

Could blogs replace resumes / CVs?

Blogs may not replace résumés or CVs, but they could — intentionally or not — show a prospective employer a side of you that you wouldn't voluntarily reveal in an interview. At least according to a recent article in Nature Jobs, which also makes some interesting points about scientific blogging.

Advice to a young computational biologist

Just when I though Bosco was posting too much poetry, he comes out with this truly excellent post on advice for young computational biologists. Bosco has managed to distill his 10 years of experience into eleven succinct points that are relevant to not only those just starting out in computational biology, but experienced hackers as well. This post is a must read, I highly recommend his advice in point four on using configuration files. It is a simple way of adding value to scripts, by extracting out the parameters into a config file and then writing another script to iterate over different values. Python has a default module for this, with many other third party options. And of course point eight, using command line plotting software, my current favorite is Ploticus.

What about using Mugshot in bioinformatics?

Hi to everybody,
first of all, I would like to apologize if this could seem as a spam message, but it's not.

Recently I've found about this program: mugshot, which is supposed to be a way to share rss feeds and bookmarks among people, and which is from RedHat, and it's released under the Gnu-GPL license.

Wiki Reviews

Finding high quality up to date reviews on the current literature is always a little hit and miss. Jason Kelly has started a new page on the OpenWetWare wiki for WikiReviews (via Pedro and Depak). As Pedro points out, Writing a review on the progress of a field could be the most obvious use of collaborative efforts. The reviews could be continually updated and periodic versions could be frozen and submitted to a more conventional repository.

New Recommended Reading List

Update: I won't bother with a vote since there hasn't been a great deal of active editing of the wiki list. I've started to add the links to a 'links directory' on the main website. The suggestion to pull random links into the side bar works (thanks Alf) and should be up shortly.

Update 2: Done. The Recommended Reading block to the right should now show a random selection of links (10) each time the page is loaded. Currently there are 32 sites in the database.

Now that the site is reasonably stable, it is time to finish off the house cleaning (at least a little bit more of it). I'm inviting everyone to help reorganize the recommended reading list. I have a new candidate list up on the wiki here. Please go and have a look, add any blogs that I have missed or add comments to the ones that are there.

Virtual bioinformatics clusters with EC2

Compute Cluster: DSC00179 © Jordan Thevenow-Harrison  / CCCompute Cluster: DSC00179 © Jordan Thevenow-Harrison / CC I few months ago I was trying to track down information about Amazon's Elastic Compute Cloud, pay-as-you-go virtual clustering service. At the time Declan Butler had emailed me asking about the feasibility of running bioinformatics applications on EC2. My investigation of EC2 for bioinformatics applications turned up very little at the time, today however Andrew Perry has posted an analysis on the feasibility of EC2 for running mpiBLAST. If you're into bioinformatics clusters (of course) then go read it right away, if you've considered a cluster and balked at the expense then this may be a solution.

The down side is, Amazon's limited-beta for EC2 is now full. Hey Amazon, Bioinformatics is a growing market, might pay to help Andrew out with some account space ?

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