Wednesday, November 29, 2006

First Online EMBL PhD Symposium

This looks interesting ... the First Online EMBL PhD Symposium, a sort of 'online' conference for the life sciences. Everybody with a scientific background is invited to participate. Registration is free.

The programme (Career Development Session, Omics Session / Systems Biology, Scientific Communication 2.0 and Participant's Contributions) and speakers list makes it look sort of like a "Biology 2.0" conference.

Apart from the (possible) IRC sessions, hopefully the fact that everything is stored as video/audio + comments on their content managment system means the 'inconvenient' timezone in Australia won't limit my participation too much.

(via the worldwide bioinformatics cabal :), Neil via Pedro, Roland and Stew)

Wednesday, November 22, 2006

International Genetically Engineered Machine competition videos

The 2006 iGEM Jamboree (International Genetically Engineered Machine competition) happened at the start of this month. This is a synthetic biology 'competition' where teams of talented undergraduates from around the world engineer an organism for a specific purpose ... like E. coli that produce mint or banana smell, or form simple logic gates the could potentially be used to make a 'biological computer'.

They are encouraged to use BioBricks from the Registry of Standard Biological Parts, which at the moment is essentially comprised of series many well-characterized DNA constructs (promoters, repressors, selection markers, lots of fluorescence protein coding sequences, etc) with standardized restriction site that can be mixed and matched to produce new and interesting behaviours in bacteria, yeast or mammalian cells. BioBricks are sent out to teams in in 96-well format, so everyone has a good basic set of starting components.

Videos of the student presentations have finally turned up on Google Video. (Unfortunately, the videos only show the speakers, not the slides for the presentation ... which makes some parts pretty hard to follow).

I watched the presentation by the University of Arizona team. They printed bacteria onto paper using a stock-standard inkjet printer, with the ink simply removed from the cartridges and replaced with a solution of bacteria. They could then tranfer this to agar plates to grow in whatever pattern they printed. Very simple, but inkjet hardware hacking crossed with molecular biology is just plain cool. As a side discovery, they noticed some weird fractal patterns in colonies under the confocal microscope, apparently based on variation in the fluorescent protein expression level of cells in a single colony.

I wonder how much interest there would be from undergrads (and their supervising acedemics) to start an Australian iGEM team for 2007 ? Funding would also be a tricky issue, as always.

Tuesday, November 14, 2006

Protein structure sculpture

Check out these amazing protein structure sculptures by Julian Voss-Andreae. The GFP (Green Fluorescent Protein) in shiny steel is particularly striking.

He has even provided instructions on how to construct your own [pdf] ... Before the advent of molecular graphics on computers, making physical models similar to this was what crystallographers (and Linus Pauling) did to build protein models.

I've gotta find time to make one of these ... the question is, do I make something of personal significance, or a choose a structure that is actually a little more challenging ?

Friday, November 03, 2006

Sheik Taj Din al-Hilaly compares men to puddy cats ...

Okay, okay, so this news is a few days stale, but the outrage has only just hit me ....

In a sermon delivered in Arabic (but thankfully translated by The Australian for the sake of some racial-hatred-arousing journalism) Sheik Taj Din al-Hilaly has compared men to cats which have no free will and cannot help but eat uncovered meat left out on the street.

As a red-blooded Aussie male, I'm extremely offended at being compared to such a prissy weak rotting-meat-on-the-street eating animal. Maybe something more masculine like a rhinoceros or a Great White Shark may have been a more thoughtful comparison on the Sheiks part ... even a "big cat" such as a lion wouldn't be so bad.

But a feral flea bitten moggy eating uncovered meat on the street ! This guy should aim to improve on his metaphors.

Thursday, November 02, 2006

The SDS-PAGE Hall of Shame

For the uninitiated .. SDS-PAGE is a method that biochemists use to separate mixtures of proteins (and sometimes other biomolecules, like short pieces of DNA). It's a really useful technique, and most of the time it works perfectly, giving a nice little 'ladder' of bands with large proteins at the top and the smallest ones at the bottom.

Occasionally, something goes wrong ... enter the SDS-PAGE "Hall of Shame".

This is a hilarious gallery of botched SDS-PAGE gels, which doubles as a useful trouble-shooting guide.

Over the years, despite trying my best to avoid it, I've occasionally run gels which have suffered from most of these problems. This one resembles the gel I ran yesterday ... I was in a hurry and turned the voltage up too high. Normally I'd get away with it, but this time the cooling wasn't adequate enough. It doesn't pay to rush these things.

(For the non-scientists: SDS-PAGE is an acronym for for sodium dodecyl sulphate polyacrylamide gel electrophoresis ... sorry you asked ?)

Wednesday, November 01, 2006

Amarok 1.4.4 on Ubuntu Dapper

A new version of Amarok, my favorite music player for Linux, has been released.

This version boasts numerous bug fixes, and an nice interface to the Magnatune music store. Magnatune is cool since the full length tracks are under a Creative Commons license and are free to listen to. If you decide to support an artist you enjoy, you can buy downloads and choose how much you wish to pay. The artist splits the profits 50:50 with Magnatune, and you get uncrippled MP3/FLAC/Ogg files, which can be re-downloaded at any time if you loose them somehow. Since Magnatune operates like an enlightened version of a traditional record label, meaning they only select "high quality" artists ... they don't push loads of dross from self promoting artists that suck like the old (RIP) did. "Brad Sucks" is (non-exclusively) on the Magnatune label, but his music doesn't suck.

Hopefully in the future Amarok will include some generic API to interface with other enlightened music stores and repositories of Creative Commons music, so that Magnatune doesn't get accused of monopolising :). For instance, I'd like to be able to add say, ccMixter and maybe IUMA in addition to Magnatune. An open web services API for music stores would make this possible, and while I haven't looked "under the hood" of the new Amarok-Magnatune browsing feature yet, I suspect this is what they have already created.

Anyway, there doesn't seem to be a backported version of Amarok 1.4.4 in the Ubuntu / Kubuntu Dapper in the repositories (yet). There are some Edgy Eft packages, but I don't want to upgrade to Edgy at the moment.

Instead, I've compiled my own and have made some deb packages, using the official deb source packages. I haven't tested this version heavily yet, but it seems to work. I had to override one dependency, since it complained that the Dapper "Common Debian Build System" (cdbs package) was not recent enough .... hopefully this was a safe thing to do.

You can download my packaged versions here:

amarok_1.4.4-0ubuntu1_i386.deb (link fixed .. Thanks victor !!)



Install them by typing:

$ sudo dpkg -i amarok_1.4.4-0ubuntu1_i386.deb amarok-xine_1.4.4-0ubuntu1_i386.deb amarok-engines_1.4.4-0ubuntu1_i386.deb
Yah, I should probably GPG sign these and try to get them included in Dapper backports or something .... but no time to do the job properly at the moment.

Update - if you have trouble with some missing dependencies, this may help:

$ sudo apt-get install ruby python-qt3 kdelibs4c2a libifp4 libnjb5 libpq4 libqt3-mt libtunepimp3 libvisual-0.4-0 libxine-main1

Hopefully that catches most of the dependencies that are likely to be missing, particularly for those running Ubuntu Dapper and not Kubuntu Dapper.