Weeknote #43

Last week Naomi and I travelled down to Bristol for a network meeting of the EPSRC Bridging the Gaps projects. Our NanoInfoBio project has now technically finished, although we do have £50K of continuation funding to take us into 2012. We were hosted by the University of the West of England BTG project, and the meeting went very well. Several projects offered a single slide on "The Good, the Bad and the Beautiful", and ours were as follows:

Good: The use of seed-corn funding (eg. £5K) to nurture ideas from initial "blue sky" sessions, through to prototyping and then subsequent large funding.

Bad: Nobody came to coffee. We had real trouble getting people to socialise and mix on an informal basis. Several projects reported similar problems with both real and virtual interactions.

Beautiful: The realisation of one of our stated aims, which was to "grown our own" researchers. We are now seeing MMU undergrads working on NIB-supported Ph.D. projects, and they will hopefully stay on to become valued members of staff, and help to train a next generation of inter-disciplinary researchers.

It was an inspiring meeting, and it helped me to realise just how much we've accomplished with the project in two short years. The real challenge now is to embed the lessons we've learned into institutional thinking, and the targeted continuation funding will make a significant impact on research activities ahead of the REF in 2014.

On a personal level, it was also a pleasure to catch up with Mike Luck, who's now Head of Department at King's College London (a post recently held by my Ph.D. supervisor, Alan Gibbons, until his retirement). I first met Mike as a potential Ph.D. student, when he was showing around applicants at University College London. When I eventually fetched up at the University of Warwick, Mike had, by then, taken an academic post there, and remembered me from the tour. He does great work on multi-agent systems, and I'm pleased to see him doing so well.

Weeknote #18 (w/e 12/9/10)

A big week in the Ashby-Amos household, as the little one started primary school on Tuesday. She was a lot braver than her father, who tried to use the excuse of "worms on the path" in order to avoid going on his first day.

Various commitments meant that I was only able to pay a fleeting visit to the BIC-TA conference in Liverpool. It was really just a question of turning up, presenting the paper and shooting off again, although it was good to briefly catch up with Dave Reid, a colleague from my time at the University of Liverpool.

A story with NanoInfoBio connections attracted quite a lot of attention this week; Gavin Bingley, a Ph.D. student working with Jo Verran, presented some work on microbial degradation of historical cine film, and it was covered quite extensively. Jo and her team will be working with MMU chemists Craig Banks and Lindsey Munro to develop the nano-sensor mentioned in most reports. This project is one of the three 25K "Large Projects" supported by NIB.

Yesterday, I took the little one bike shopping in Halifax, and we made a detour on the way back so that she could have a little snooze in the car. I decided to drive home via Cragg Vale, which is an interesting place, not only for the views, but for the fact that it is the location of the longest continuous gradient in England.

Weeknote #6 (w/e 20/6/10)

We (three colleagues and myself) were recently successful in obtaining funding from the NanoInfoBio project to test an idea that's been rattling around for a while. DNA hash pooling is a technique that Dennis Shasha developed, with some assistance from me, while I was visiting him. Dennis is an incredibly sharp and prolific Professor of Computer Science at the Courant Institute of New York University. He was the Series Editor for my first book, and we kept in touch since its publication. Justine, the little one and I visited Dennis while he was in Paris on sabbatical with his family, in the summer of 2007. While Tyler, Dennis and Karen's son, played American football, we walked round and round an athletics track on the edge of the city, knocking around our own particular problem.

The task of analysing large populations of mixed DNA strands is of particular relevance to the emerging field of metagenomics, which is concerned with understanding, in genetic terms, the vast complexity of the planet's biosphere. Methods for looking at environmental samples often require a lot of genetic sequencing; although new ways of doing this are constantly driving down the cost, it can still be expensive to sequence large populations, as well as time-consuming. Dennis and I developed a technique that combines computational analysis with simple rounds of laboratory steps, based on the computer science idea of hashing. The idea is to associate "labels" with individual sub-populations of genetic sequences, such that the number of different genomes with the same label is relatively low. In this way, each genome (or genomic fragment) is associated with its own "fingerprint", which we can then use to confirm its presence (or otherwise) in a sample. Our hope was that this technique would offer a cheap, quick and simple pre-processing step before any sequencing was required, thus reducing the cost and complexity of analysing a sample.

We finally published the theoretical paper last year, but have only just obtained the funding to actually test the idea in the lab. I floated the concept at one of the NIB brain-storming meetings, and it was picked up by a talented team of biologists (Trish Linton, Mike Dempsey and Robin Sen). We put together a proposal to NIB for a small amount of support (£25K), and we were fortunate enough to be one of three projects funded in the last round. The nine-month post-doctoral position is currently going through the MMU approval process, so watch this space if you're interested.

Weeknote #1 (w/e 16/5/10)

In an effort to blog more regularly, I've decided to adopt the Weeknote model of short seven-day updates on what's been going on.

The weekend was dominated by my inability to leave the country; I was due to fly to Madrid to give a series of lectures on molecular and cellular computing to Masters and Doctoral students at the Universidad Politécnica de Madrid. It was also an opportunity to take a couple of days of much-needed time with my wife and daughter, who'd be travelling with me. As the airspace in Northern Ireland had already been closed, we checked the status of the flight before we set off for Liverpool Airport. Everything was ok, but by the time we got there a couple of hours later, they'd shut down. A maudlin hen party, wearing mandatory pink fluffy stetsons, were told that the next available flight was on Thursday; we just returned home, where I quickly rescheduled the lectures for two weeks time. My host, Alfonso Rodríguez-Patón, was incredibly understanding and helpful, managing to book a new hotel for us, despite the fact that my new schedule coincides with a major festival on the Thursday (making hotel rooms extremely rare).

Another significant event this week was the Future Everything festival, which was (if you read the various reviews and tweets) wildly successful. I contributed to a panel discussion on New Creativity, which also featured Anab Jain, a TED Fellow who talked about her Power of 8 project, Kerenza McClarnan of Buddleia, who's facilitating artist-led enquiry into urban spaces, and Adrian Hon of award-winning games company Six to Start, who talked about the purpose of play. It was a fascinating session, with a lot of dynamic connections made between the panelists (none of whom really knew anything in advance about what the others would say). The session was recorded, so I'll post a link if and when the video is made available.

In mid-week we had our latest brain-storming "away"-day for our Bridging the Gaps: NanoInfoBio (NIB) project. This is a two-year initiative, supported by the EPSRC, to encourage cross-disciplinary research within MMU (with specific focus on the life sciences/engineering/computing/maths/nanotechnology interface(s)). We're almost ten months into the project now, and are beginning to develop a coherent set of themes around which we can coalesce. We're giving out a few project grants of £25K in order to boot-strap small feasibility studies, so we arranged an afternoon at a Manchester hotel to generate some ideas. Experience has shown that it's best to get everyone away from the distractions of email, and the temptation to "just pop back to the office", and I think everyone was happy with how it went. Rather than dividing everyone into groups, as might seem natural, we first performed a general "audit" of possible project ideas (this first pass generated 12), and then "drilled down" as a whole group to examine each idea in turn. Once a page or so of flip-chart paper had been filled for each project, only then did we split up in order to go over the fine details of costings and so on. The group-level discussion led to some surprising contributions, which would have been lost if we'd split up too quickly. I think it worked.