Petition grapher

The houses of parliament in the UK host a website of petitions. When a particularly popular petition is trending it can be addictive to refresh the page and watch the numbers going up behind your eyes. But of course what one really wants is a graph.

So I built this tool which regularly queries the parliament API and stores historical petition signatures in a database which it uses to draw graphs.

The Up-Goer Five Text Editor

When Randall Monroe released the amazing Up-Goer Five comic, I was inspired to hack together a customised editor so that I could explain my own research in the limited vocabulary of the thousand most common words.

For me the most exciting bit about this was that I got an email from Mr. xkcd himself. It also became a bit of a science-communication craze. A lot of scientists got in on the action (some kind people have made a collection here).

The editor has featured in The Guardian (and again). More recently it’s even been used for conference sessions, which are pretty fantastic. (The 9th talk in that playlist is particularly excellent). It’s also quite popular as a science communication training exercise, although it goes without saying that no-one is suggesting that this is the best way to communicate.

iGEM

The international genetic engineered machine competition (iGEM) was my first taste of proper experimental science, and I still have a fondness for synthetic biology. I was part of the Cambridge Team for 2010. This was an exciting team project where we got to define our own genetic engineering project and work on it over a summer.

We focused on bioluminescence, building modular genetic components (BioBricks) from firefly luciferase, in a number of colours, and also from the bacterium Vibrio fischeri. The exciting thing about the bacterial luciferase is that this permits ‘autoluminescence’, i.e. the bacteria produce light without adding any other chemicals. We exploited this to light ourselves in the photo below.

In the project we achieved a Gold Medal, were finalists in the competition and won the prize for Best Wiki, which I designed. As part of the project I built BioBrick2GenBank, a small tool which converts BioBricks to GenBank format for editing in standard cloning software. This has been used >350,000 times to date.

Our BioBricks have been used by a number of future teams, including by a team from Peking, who used this part in one bacterium, combined with a light sensitive-system in bacteria in a separate tube, to allow cell-cell communication!

Gibson assembly

We were also early users of the revolutionary Gibson Assembly protocol, and I penned the lyrics to the embarassing music-video we made to promote it, earning us the (dubious?) distinction of a Craig Venter tweet.

Media

On the back of this project I was quoted in New Scientist, and later by the BBC.

Book chapter

Ben Reeve and I later wrote a chapter about the application of bioluminescence in synthetic biology.