The Manchester Microbe Map is now a thing!

I finally managed to find a few hours to sort out the Manchester Microbe Map, it turned out pretty nicely:

I'd written most of the code a few months back, but visually it was a little boring. Luckily, at the last meetup I got talking to the very talented Sam Hodges, who just so happens to be a design student. He whipped up a nice design for it, and we managed to get it nailed in a weekend. There's still a lot of data missing, but you get the idea.

For those interested, it's built in Flash (mainly so I can put it out as a desktop app without having to screw around). The data all comes in from a laboriously put together XML document, as we had to piece the results together by hand from all the teams (I'm not kidding around!). The actual microbe shots are hosted on Flickr, which completely made my day by already providing ready-made 150x150 thumbnails that I can access via the API. Handy.

We need to finish putting the data in, neaten it up, and hopefully it'll be on some sort of screen/installation at FutureEverything. We've also had some VERY exciting news on another possible use for it that's cropped up, but it's a secret for now.

Anyway, check the map out here.

For Science! OpenPCR @ Madlab

Last week's DIYBio was a special event, to get stuck into building a couple of PCR machines. In addition to our home-made one, we also got our hands on what we think is the first OpenPCR machine in the UK.

Getting a bit ahead of myself though. What is PCR?

PCR is a relatively simple and inexpensive tool that you can use to focus in on a segment of DNA and copy it billions of times over. So, even with a small DNA sample, such as from spitting in a tube, or tearing off a piece of a leaf of lettuce, PCR allows to you make a bunch of copies of the DNA so you have enough to analyze. PCR is used every day to diagnose diseases, identify bacteria and viruses, match criminals to crime scenes, and in many other ways.

The OpenPCR is a really neat idea: it's the first example of truly open-source hardware I've ever seen. I was confused about how hardware can be 'open source', but what this essentially means is that the precise schematics of all the machine components are readily and freely available. So, if you had the time/materials and tools, you could build yourself one. The kit itself is supplied as an awesome box of bits (wood! Arduino! Metal things!) and costs something like $500 (ish). It then hooks up to a nice AIR app and you can do what you like with it.

In addition to the OpenPCR, the clever chaps at Madlab have put together a fantastic home-grown PCR machine, which is made of pipe, polystyrene, a filament lightbulb, and a plastic lunchbox full of electronics. Really. I didn't note down the cost at the time, but it's significantly less than five hundred dollars... I assume it's also significantly more likely to burn your house down, but that's all part of the fun, right? Science!

The Madlab version was built by the Hacman experts, so it was only fair that we were allowed to get stuck into building the OpenPCR. On paper it says one person can build it in three or four hours: we decided that as a group we could do far better than that, so we tipped the box out and got stuck in:

Anyway, the plan is to see how the OpenPCR stacks up against the Madlab budget version, and then hopefully we can then see how both machines compare to an actual, cost-lots-of-money, proper PCR machine. We've not decided as yet what the criteria for 'best machine' will actually be, but it should be really interesting to see how it all turns out anyway.

Oh, and the BBC's science correspondent turned up too, along with a big camera and a microphone:

I managed to stay out of the firing line as much as possible, but a couple of the guys there made the rookie mistake of sounding knowledgeable and ended up being interviewed. I didn't escape completely though, and ended up explaining the Microbe Map repeatedly down a microphone, probably for the radio. It was pretty nice to see an event like this being covered anyway, I'm not sure entirely how it's all being used, but as soon as I find anything out I'll stick it on here.

There are lots more photos on the Madlab flickr feed, next time we should hopefully have some experiments going and maybe even some idea of how our PCR kit stacks up against expensive kit. For science!

'Enter the amateur!' - DIYbio @ Madlab

Photo: madlabuk

On Wednesday night I managed to get down to the first Manchester DIYbio event at Madlab. It was the kind of event I wouldn't usually have been instinctively drawn to, but after Lia at Madlab suggested I check it out and get my thoughts down I decided to get in there and see what the project was about. I was initially there on a whim and wasn't expecting to be hugely involved, but I came out of it with every intention of getting stuck into the project first-hand.

DIYBio "is an organization dedicated to making biology an accessible pursuit for citizen scientists, amateur biologists and biological engineers who value openness and safety". The movement covers a wealth of community-driven projects all over the world, spanning a wide range of disciplines, with a focus on bringing biology out of the lab and into the hands of people who wouldn't ordinarily have access to these fields.

Going into the event I was a little apprehensive that I'd be in a minority of techies in a large group of terribly knowledgeable biologist types. It was quite nice to find out that actually the group was comprised of more tech folks than scientists, and after chatting to a few people it quickly became clear there is a great range of practitioners involved, both from Team Digital and Team Science. :)

The overall plan is that any future project ideas will be open to the group for discussion and planning, but as a introductory project the organisers have come up with The Manchester Microbe Map: an investigation into the microbes on ATM machines all over the city. I think this is a great starting point: it's an interesting idea that will allow the group to establish who can do what, both in terms of who's willing get out there and get stuff done, and also who can bring particular skills to the table. My interest with this project is definitely the data visualisation end of things: once we have our data, what can we do with it digitally? I love the idea of getting this stuff mapped out and visualising things like physical factors, proximity to certain places of interest, time of day etc: there's a lot of factors we might consider, and it might even turn out we discover more factors once we get stuck into the data. The final piece is being shown (I think) at FutureEverything, so it would be great to be involved from the outset. Hopefully there'll be some data vis ninjas involved that I can learn from.

As part of the Microbe Map project involves swabbing for samples, we also ran through a highly entertaining demo on DNA extraction "tiki-style", using pineapple juice, washing up liquid, salt, and a sample of saliva. Bonus points to those who drank the shot afterwards ("in the name of science!"), I wasn't remotely man enough to try it.

DIYBio MCR looks like it could turn out to be hugely interesting anyway, there's a ton of talented people involved, and a massive scope to do, well, anything. Once again, the Madlab guys have allowed this to happen in a really great environment, and I couldn't be happier that Manchester is involved in another awesome project like this. The DIYBio meetups are once a month, hopefully this initial project will kickstart something brilliant. Looking forward to the next one!