Bio::Blogs #13

Welcome aboard – it’s edition #13 of Bio::Blogs, the monthly compendium of bioinformatics and computational biology highlights from around the blogosphere. It’s a bumper edition this month with 28 posts in all from 18 blogs. Thanks to everyone who submitted posts.

As with previous editions, this one has a PDF version for your offline enjoyment. I’ve contacted almost all the bloggers to make sure that they are happy if their posts are reproduced and nobody objected. All posts in the PDF are fully attributed with hyperlinks – we don’t want anyone to think that we’re stealing their work for some sort of dubious publication. If I didn’t contact you and you do object, get in touch. Here it is then: Bio::Blogs #13 PDF (760 KB). Please save the forests by printing double-sided.

Let’s get into it.

Meetings

July brought us ISMB/ECCB 2007. For those not in the know, ISMB is probably the major international bioinformatics conference. It goes for days with literally hundreds of posters and presentations and can be somewhat overwhelming. Proceedings are published in a special issue of Bioinformatics which you can find here.

Winner of “first ISMB post” goes to Greg, who posted his impressions from some of the Special Interest Group sessions. He includes some links to data visualisation tools, including progress with genome browser software. This turned out to be quite prescient, as we’ll see later on.

Winner of “longest ISMB post” is Suicyte Notes, with impressions from ISMB 2007. A very interesting post with observations on the content, style and organisation of ISMB. He notes that there is relatively little blogging about the ISMB meeting given its size, although a few posts have appeared since. I suspect that some bloggers are still travelling, or perhaps recovering.

Jason from Bioperl contributes to the excellent Fungal Genomes blog and posted two ISMB articles over there. The first is a recap of some of the presentations with an evolution/genomics theme. The second recounts a BoF (birds of a feather) meeting about ISCB policies towards open source and open data. By all accounts a somewhat frustrating affair that lapsed into ideological debate, rather than focusing on the issue of whether software and data used in publications should be made available. Go and read the post to learn more about this important issue.

Jason and many others highlight one of the keynote talks from the BOSC meeting (part of ISMB): Carol Goble on seven deadly sins of bioinformatics. Follow that link to see a slideshow of her talk.

Publishing, open access and open science

Bioinformaticians tend to be enthusiastic proponents of open access and open science (along with chemists and physicists). Our first post in this category comes from Pedro who asks what is the $value$ of an editorial decision?. His post includes some interesting – some might say radical – ideas on the economics of OA publishing.

An OA success story is the Public Library of Science. Their journal PLoS ONE is now one year old, an occasion noted by the biophysicists at Biocurious. They have some suggestions for ways that you can help PLoS celebrate their birthday.

Depth-First is an excellent chemical informatics blog covering research, software and economics. Two posts of note from Rich Apodaca this month. The Journal Deadpool… argues that we would all benefit from more information regarding journal subscription cancellations. Rich’s second post addresses one of my favourite topics: the ultimate death of traditional scientific publishing as the sole means of promoting our research. I look forward to the day when our blogs are accepted as equal in stature to our Nature papers.

Several people have recommended the blog Perfect Storm to me. In this post, Tiago looks at his Google Reader subscriptions and concludes that the blogs are far more interesting than the journal articles. He suspects that this is because a blog is a labour of love, but wonders how financial incentives will affect blog post quality in the future.

Mike from Bioinformatics Zen has been trying to gather information from publishers on their attitudes towards OA, open science and pre-publication. Here’s what he’s found so far about preprint policies and open science. Incidentally, Mike has set up a page at the Nodalpoint wiki to discuss these issues, so do contribute there if you can.

Tutorials and how-tos

I’m always deeply impressed when bloggers take the time to document detailed computational procedures in the form of a tutorial or how-to. We have some great examples this month.

First up is Mike again with a detailed look at principal components analysis. This is a very useful multivariate statistical method which I’ve used a lot myself and he gives a great summary. I’m looking forward to future posts on discriminant and correspondence analyses :) .

Back over Perfect Storm, Tiago gives us part 3 of a series on developing life science applications for multi-core and grid systems. A must-read for developers with an interest in the topic, check out his other entries too.

Did someone say Google Gears? Google’s latest offering allows developers of web applications to provide offline functionality. You may know it only from Google Reader so far, but Pierre brings us an excellent tutorial, prototype application and code that uses Google Gears to look at protein-protein interactions.

Bosco may be Trapped in the USA, but it doesn’t stop him from doing great structural biology and blogging about it. This month he brings us quick and dirty minimization and introduces us to an algorithm termed sequential-univariate minimization.

If you read Alf’s HubLog, you’ll know that he loves a good API. In three short but informative notes this month, he looks at APIs for Scopus, Freebase and Wikipedia. Scopus, in case you don’t know of it, is a literature database requiring paid subscription and Alf isn’t too impressed with their API.

My own effort this month is parse the PDB using Bioperl, where I learned something new thanks to a comment. Just another example of the value of blogs.

Software

A great reason to subscribe to blogs is that they alert you to new resources that you may otherwise have missed. Here’s some software that I learned about this month.

Bosco looks at Coda, a Mac OSX application to improve workflows. He’s finding it especially useful for talking to the workhorse Linux cluster from the shiny OSX desktop.

A while ago at Nature Network, Euan asked about the AJAXification of genome browsers and sparked quite a debate. What a lot of us alluded to was a Google Maps-style interface to a genome. Via Pierre, I discovered X:Map from Tim Yates. My first impression is that it looks fantastic and is very much what people said they would like to see. Go and have a look for yourself.

Bertalan is a medical student with an interest in genetics and web 2.0 who blogs at ScienceRoll. He’s impressed by PediDraw, an online tool for drawing genetic pedigrees and NextBio, which he describes as “just like you’d use Pubmed, but in a more dynamic way”. Check out those tools and his other blog posts.

Computer science

We bioinformaticians like to tease computer scientists occasionally, but hopefully we’re learning a lot from each other too. We have a couple of more CS-related posts this month.

From the wonderfully-named Leah Culver’s Stupid Blog comes a computer science degree doesn’t hurt (much), in which Leah explains that her CS degree is actually useful in her working life!

In the “short and sweet” category, Tim Bray, who works for Sun Microsystems summarises what XML means. I was surprised to learn that XML is almost 10 years old and as Tim says, it’s not perfect, irreplaceable or the choice for every application but most times, it does what it says on the tin.

Joys of research

Sorry, I couldn’t think of a better title for this section – it covers research ideas, practices and those random thoughts that we all have about what it all means and where it’s all going.

Deepak asks: could peer production work for biological annotation? and wonders whether Freebase, in combination with community knowledge offers a system for collective curation and annotation of biological data. I enjoyed the statement “normally, I am not the biggest supporter of the wisdom of crowds” (witness the continued popularity of Big Brother, for example), but he has some faith in collective scientific wisdom.

Nodalpoint’s “king of puns”, Duncan Hull is off to Science Foo camp this month and he has some questions for Google’s founders. I think a lot of us would like to know whether Google are serious about biomedical informatics and the possible new services that might stem from that.

And last, but most definitely not least, is Andrew Walkingshaw. Andrew is part of the very successful and influential “open chemistry movement” and blogs on many topics at Brighten the Corners (an album by Pavement, if I recall correctly). His post from May, trouble in the message centre, touches on something with which many of us are familiar – trying to explain to non-scientists what we do and why it’s important. He suggests that we do this best when we are passionate about our work and that given the distinct lack of passion in a traditional journal article, it’s important to have other outlets.

Such as blogs, I would suggest. Happy reading.