Proteomics discussion from the science streamosphere

We 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.

Brief Hardy Heron notes

Nothing exciting - just a couple of notes on the Ubuntu upgrade experience from 7.10 to 8.04.

Now officially living in my browser

Firefox screenshot, from left to right: Vertical tabs, courtesy of Vertigo - because you can never have too many tabs Main window: the feeds roll into GReader On the right, almost all the functionality of FriendFeed (except search) in fantastic new extension MySocial 24×7 On the right? Yes, because sidebars look better on the right IMHO, made possible by MultiSidebar

Tenuous bioinformatics connection: well, you work more effectively if you’re happy with your browser setup

App Engine for research #2

ResolveRef, a RESTful way to resolve PubMed queries by journal, year, volume and page is Andrew’s port of OpenRef to App Engine. Simple, but very effective and a nice illustration of how to get to grips with the App Engine environment.

Keep those “App Engine apps for researchers” rolling in, folks.

An R Wiki

It’s been ages since I visited the R website, so I don’t know how long they’ve had a wiki. It’s built using DokuWiki, one of my personal favourites.

This is a great leap forward for R documentation, which is somewhat notorious for being (a) difficult to find and (b) difficult to understand when you find it. If you’re a power R user and have a spare moment, please contribute.

Around the open science, social web

This blog seems to become more about social networks/open science and less about bioinformatics every week. Perhaps that’s no bad thing. Here’s a few highlights from the activity stream this week.

• From Depth-First: User-Created Compound Monographs on Chempedia.net on the Web 2.0 approach to chemical encyclopedias
• Post of the week: in response to One Big Lab, Cameron on the science exchange
• In response: Deepak on micro-funding; thankfully one of us has a business mind
• Science Commons asks are you part of open science?
• And the iPlant Collaborative takes affirmative action on science collaboration (some nice-looking jobs at CSHL posted there)
• Nature Network announce plans for a European Science Blogging Conference
• Also from Nature Network, a record 100 comments for Jennifer’s post; admittedly the last few are silly ones to get her over the line
• UsefulChem points us to an article in Cell on open-source drug discovery
• From Bioinformatics, a follow-up to the “404″ study (thanks Paulo!); take-home message is that academics probably shouldn’t run webservers
• Rosie’s long, blog-less teaching stint is over; she returns with a discussion about making shared code readable
• Finally from the “things that made me laugh” department: Facebook group pop songs as graphs (thanks Graham)

Two great open science resources

The Twitter + FriendFeed combination is proving to be a very useful information stream; not just from other people but as a reminder of what I thought was worth sharing. Two links from there that I think deserve wider attention:

• One Big Lab proposes that we become, well, one big lab - and has some ideas as to how that might work.
• From the OWW wiki, an excellent article on python in computational biology. This has been presented at Pycon 2008 and is also a companion article to a paper in PLoS Computational Biology. Imagine if everyone described their methods in this detail.

Deepak has some commentary on what we’re now calling the “bio-twitterverse”.

First past the post…

…with a biologically-relevant application for Google App Engine, is Euan with pycite, a port of Connotea. Man, this makes me want to learn Python fast.

More thoughts and commentary at Deepak’s blog.