Who says Universities aren't forward thinking?

Our local hospitality operation has recently put in place an automated booking system, which allows grant holders to request and approve catering for meetings, etc. This is great, as it avoids (in principle) orders going missing, and so far it seems to have worked well.

Each request is assigned a "ticket number", and I noticed that the system designers appear to have learned the lessons of the Millennium Bug, and allowed plenty of room for new requests. The order I approved today, for example, is request number

REQ000000000721

which, assuming there were 720 previous requests since the system began, allows for 1,000,000,000,000 unique requests (that's a trillion).

Even if we assume a million requests a day, 365 days a year, we've still got over 2,700 years before the system runs out of space.

By which time we might have introduced some variety into the menu.

Weeknote #37

These weeknotes are turning into monthnotes, but I shall persevere...

Lots to report, starting with a trip down south at the end of April to visit the Bristol Robotics Laboratory. This is a joint venture between the Universities of West of England and Bristol; I was in touch with the Director, Chris Melhuish a few years ago in relation to some ant work, but I'd never before had the chance to visit. One of their most high-profile projects is the EcoBot, an energetically autonomous robot that uses microbial fuel cells, and the meeting was semi-related to that. I was there at the invitation of Ioannis Ieropoulos, who met our post-doc Angel and forged a connection between our respective groups. The meeting went very well, and there will definitely be much to discuss in the coming months.

The beginning of May saw a number of COBRA project members in Budapest, for the European Commission FP7 FET11 conference. We organized a special session on "biological and chemical IT", which was well attended. We're currently drafting a summary paper for the forthcoming open-access meeting proceedings. The next COBRA event will be another special session, this time at the European Conference for Artificial Life, held in Paris this August.

This month has also seen a lot of activity on the DIYbio front, with the initial "swabfest" (taking samples from Manchester bus stops in order to ascertain the level of bacterial contamination) closely followed by a session at the hugely-influential FutureEverything conference in Manchester. We showed a couple of movies during the presentation, and these will hopefully be made available shortly, as well as footage of the event as a whole.

I'm very excited by the announcement of a new volume of fiction, to which I've made a small contribution. Litmus is edited by Ra Page at Comma Press, and has the subtitle "Short Stories from Modern Science". From the blurb: "This anthology draws out and distills science’s love of narrative from a wide range of scientific disciplines, weaving theory into very human stories, and delving into the humanity of theorists and experimenters as they stood on the brink of momentous discoveries: from Joseph Swan’s original light-bulb moment to the uncovering of ‘mirror neurons’ lighting up empathy zones in the human brain; from Einstein's revelation on a Bern tram, to Pavlov’s identification of personality types thanks to a freak flood in his St Petersburg lab.

Each story has been written in close consultation with scientists and historians and is accompanied by a specially written afterword, expanding on the science for the general reader."

Our story was written by the BAFTA-nominated novelist and scriptwriter Jane Rogers, and it focusses on an often overlooked aspect of the work of Alan Turing; his studies of morphogenesis.

The only other big bit of news is that I've accepted an invitation to coordinate the computer science research activities of our School, in preparation for the 2014 Research Excellence Framework. I'll be responsible for our return in the Computer Science and Informatics Unit of Assessment; we did pretty well last time around, in 2008, so the pressure's on.

In terms of papers, today Angel and I submitted a revised journal version of our population-based oscillator paper, and last week we submitted an abstract to the ECAL workshop (on a different, but related subject). I'm also working on a BACTOCOM technical paper, as well as a short paper on a fun topic (a proof of the NP-completeness of a game I've studied in the past).

Virtual Futures 2.0

With regret, I have had to cancel my appearance at VF2.0. Sorry.

Weeknote #36 (w/e 17/4/11)

A rather frantic month has unfortunately left the weeknotes at the bottom of the priority pile. However, teaching's now finished (apart from the small matter of honours projects to mark...), so now's the time to pick up all the loose ends.

At the end of last month we were in Brussels for the first BACTOCOM annual review. Until we receive the formal report from the European Commission, we can't say too much about this, but we all felt that it generally went very well.

Last week, both Jo Verran and I attended the Spring meeting of the Society for General Microbiology. I gave an invited lecture on "bacterial random search (BACTOCOM, basically) in the "Maths and Microbes" session, and Jo gave an open lecture in the evening, on biofilms. I was only able to stay for the first day, and would have liked to have seen more of what seemed like a very interesting conference. The next one is in York at the start of September, and I'll definitely try to get to that.


Last Tuesday we were treated to the rather surreal sight of Dolly Parton discussing the implications of one of our NanoInfoBio projects. Jo and her team were recently filmed by the BBC's One Show for a piece about their work on fungal deterioration of cine film, in association with the North West Film Archive. It went out last week, and was marvellous publicity for the project, the University, and the NWFA.

On Thursday we had the pleasure of hosting a public lecture by Ian Stewart. Ian and I met once or twice during my time at Warwick in the mid-1990s, but credit for his visit goes entirely to Naomi Jacobs, who set it all up via one of her many side projects. As well as being a well-respected catastrophe theorist, Ian is a world-renowned author and populariser of science and mathematics. He gave an excellent talk, based on his new book Mathematics of Life, a conjunction of subjects that is obviously close to the heart of many NIBbers.

United Utilities are threatening me.

I love this letter that arrived the other day from United Utilities. Ostensibly they're trying to get me to buy their HomeServe insurance, but the way they've phrased it is just this side of sinister. "How would you cope without fresh water at address?" sounds, to me, like a corporate version of "Lovely taps you've got there. Shame if something were to... happen to them."

And they can leave the washing machine out of this, it's done nothing wrong.

Weeknote #35 (w/e 20/3/11)

Lots of public engagement activity to report from the last two weeks. The first item is that the BACTOCOM piece is now up in the new Revolution Manchester gallery at MOSI (the Manchester Museum of Science and Industry). It's a great gallery, and we're delighted to be featured, but the use of "Bactocom" as a noun (as opposed to an acronym) means that we now have to rig up a fake machine made out of petri dishes, computer parts and moss, just in case anyone asks to see "the bactocom". (Photo by Ade Hunter.)

We also launched DIYbio Manchester last week. This is a one-year project, funded by the Wellcome Trust public engagement programme, with the aim of encouraging citizen scientists to become more actively involved in biology.

Dan Hett wrote a nice blog post about the launch party, and Hwa Young and I were briefly interviewed on BBC Radio Manchester's breakfast show (which you can hear below).



Alice and I also had great fun at Saturday's 'Hands on Science' family fun day, organised at MMU as part of National Science and Engineering week. Her personal favourites were the "memory metal" and the "magic sand", the robots and the racing car. I think she also enjoyed "talking to the computer" (the Turing Test, run by Ben and Matthew).



Once again, there was strong representation from the Novel Computation Group, with Naomi and Zarka manning demo stands, as well as Ben and Matthew helping out. Not sure what's happening with Alice's right hand in that picture, though.

Weeknote #34 (w/e 6/3/11)

Slight shift of focus this week, as the previous seven days have been utterly dominated by arrangements for the fifth birthday party of a certain someone. Anyway, we hired the Fielden Centre in Todmorden (which will mean nothing to 99.7% of my readership), and couldn't fault them (specifically, Bridie) for helpfulness, friendliness and downright reasonable pricing (this is not product placement, BTW).

Anyway, this was the first party we'd organised where everything was up to us; catering and entertainment. On top of this, we decided that such an occasion deserved a healthy turn-out, and invited around 30 kids, on the assumption that roughly 20 would be able to make it. As opposed to the 30 that turned up.

I learned some important lessons this weekend, and I offer them to you now, in ascending order of importance.

5. Check the facilities in your venue. Our place was kitted out with an oven, which allowed us to indulge our wildest, almost Blumenthal-esque food fantasies (ie. pizza, and fish fingers and chips). However, we weren't warned that, after being turned on, the temperature of the oven would rise by about 3 degrees every half hour.

4. Dress as a pirate. Never fails.

3. Corollary to (4). When dressing as a pirate, ensure that arriving parents are aware of your true identity (ie. father of party girl), lest they mistake you for a particularly shoddy hired entertainer (happened).

2. Check your music. I'd vaguely heard about this Glee thing that the kids were into, and thought that music from the series would make an appropriate soundtrack to a party full of 4 and 5-year-olds. Wrong. After rashly picking up two CDs without checking the tracklisting, I got them home to discover that the second track on one of them was a cheery cover of Amy Winehouse's Rehab. Cue frantic last-minute iTunes purchases. Also, check your equipment. An iPod/docking station combo that can be unbearably loud in a kitchen with quarry tile flooring will suddenly sound like a wasp trapped under a beer glass when placed in a cavernous hall full of small children hyped up on blue pop.

And the absolute, number 1 lesson I've learned from organizing a kid's party is don't be the baddy. Specifically, under no circumstances plan games that involve you making semi-arbitrary decisions about who is "out". You will never remember all of the names, and will end up looking pretty evil as you point at some quivering 4-year-old and shout across the room "You! No! Yes, you! You're out!"

I thought I'd be clever and organize a game of "Islands", which is a variant of "musical chairs", using sheets of newspaper as the islands onto which the kids must jump when the music stops. "Very clever," thought I. "Fits well with the 'Under the Sea' party theme." I was so very wrong to be in any way self-satisfied, as the game swiftly descended into Lord of the Flies-type chaos, with refusals to leave swiftly followed by the emergence of factions, and then all out war declared (mainly on me).

Pick games, like "Four corners" (from the link above), or "Pass the parcel". In that way, the decision on who is "out" is taken completely out of your hands, it's utterly unambiguous, and you can simply shrug at the tearful toddler as they shuffle sadly to the margins of the room, and say, apologetically, "Look, I don't make the rules."

Weeknote #33 (w/e 27/2/11)

I've been very bad at updating my weeknotes over the past few...umm...weeks, so here's a quick run-down of what's happened since the last one.

At the start of February I sat on my first EPSRC panel. I can't go into too much detail, as I'm not sure the results have been released yet, but we basically had a day-and-a-half, locked in a hotel in Swindon, to rank a load of funding proposals. It was quite an exhausting experience, but very useful, in that it was my first insight into the process as a reviewer (as opposed to proposer). Top tip: drive, don't take the train. That way, you get to take along the several KG of paperwork, instead of relying on the summary you've prepared, and avoid embarrassment when you have to repeatedly ask to use the copies brought along by your far more experienced colleague. Lesson learned for next time.

Last week I had a nice couple of days near Paris, visiting the group of Alfonso Jaramillo. Alfonso is the technical lead on our BACTOCOM project, and I believe he currently has an open post-doc position. On the subject of European projects, I was pleased that our COBRA project managed to secure the organization of special sessions at both FET11 in Budapest this May, and the European Conference on Artificial Life, in Paris this August. Busy times ahead.

In terms of papers, Matthew and I finally had the "zombie paper" accepted, and there's a preprint version available here. Matthew spent most of last week at MOSI, participating in their half-term Turing test. By all accounts, it was a huge success, so well done to him.

The New Scientist Cupcake

Yesterday, I received an intriguing package at work. A square box, marked "FRAGILE". Guesses in the lab ranged from "a mug" (about the right size, but far too light) to...something more sinister.

There was a sense of anti-climax when I opened the box to find that it was from the New Scientist.

Specifically, from the arm of their operation that deals with job adverts. I've placed a few ads with them in the past, and now they were touting for repeat business.

With a cupcake.

The enclosed note very kindly said that they're sending me "a little something in the post to sweeten up my day", but I was staggered by the amount of packaging it required. One cardboard box, a large sheet of bubble wrap, another small box (tied with ribbon), the cupcake itself (wrapped in plastic), and the note.

It certainly did its job, which was to get my attention, but I'm not sure the overall impression is what they intended.

I still ate it, though.

Weeknote #32 (w/e 16/1/11)

A (belated) Happy New Year to my tens of readers!

I spent a lovely evening last Monday, as the guest of the Bollington SciBar. This event was set up by Naomi, and took place in the civilised surroundings of the Vale Inn. I spoke for about half an hour on synthetic biology to a gratifyingly large audience, before we opened things up for discussion. There were many insightful questions, and everyone seemed to enjoy themselves. The drive back was much less fun, due to the failure of my windscreen wipers, but that's another story.

Just before Christmas we said goodbye to Jose Cecilia (Chema), who was visiting the group from his University in Murcia, supported by Andy Nisbet and his participation in the HiPEAC Network of Excellence. Chema spent three months working on an implementation of ant colony optimisation for the GPU, and we've just had a conference paper accepted (preprint version is here).

Weeknote #31 (w/e 19/12/10)

I delayed this week's note until the details of a couple of publications were confirmed.

The first has resulted from Naomi's work on our NanonInfoBio project, and concerns the "problem" of interdisciplinarity. A lot of interesting and important contemporary research occurs where the boundaries between academic disciplines become blurred (synthetic biology being a good example), and we decided to investigate how it might be encouraged. The resulting paper (written largely by Naomi, with a relatively minor contribution from me) has been submitted to a journal, and is now available as a preprint. The title and abstract are as follows:

---

Removing Barriers to Interdisciplinary Research
Naomi Jacobs and Martyn Amos

A significant amount of high-impact contemporary scientific research occurs where biology, computer science, engineering and chemistry converge. Although programmes have been put in place to support such work, the complex dynamics of interdisciplinarity are still poorly understood. In this paper we interrogate the nature of interdisciplinary research and how we might measure its "success", identify potential barriers to its implementation, and suggest possible mechanisms for removing these impediments.

---

I'm also delighted to announce the second instalment of the Synthesis Lectures on Synthetic Biology that I edit for Morgan and Claypool. Within this publishing model, libraries pay a one-off subscription charge, and are then given perpetual access to a growing list of lectures (in this context, "lecture" means a short book, in the region of 100 pages), although they may also be bought individually, either in electronic form, or as paperbacks.

The first lecture was published by Natalie Kuldell and Neal Lerner of MIT in 2009, and has already been downloaded nearly 300 times.

The second lecture has just been published, and is titled Bacterial Sensors: Synthetic Design and Application Principles. It's written by Jan Roelof van der Meer from the University of Lausanne in Switzerland, and is an in-depth treatment of the engineering of living cells for the purpose of biosensing.

The first two lectures have got the series off to a flying start, which I hope I can maintain as the third runner in the relay (my own lecture is due next year). I'm also happy to consider proposals for lectures, so if you work in synthetic biology and would like to consider writing a short book, do please drop me a line.

That's it for the blog for 2010, so I'll just wish you a happy and peaceful holiday, and a productive new year.

Weeknote #30 (w/e 12/12/10)

This week's big news is that we've completed the final formalities on a new European grant. COBRA stands for Coordination of Biological and Chemical IT Research Activities, and it's a three-year coordination action funded by the European Commission Seventh Framework Programme (FP7).

The project is one of several funded under the Future and Emerging Technologies Proactive initiative, and the constituent projects are NEUNEU, MATCH-IT, BACTOCOM and ECCell.

The main objectives of the project are to create a sustainable European research community in the emerging area of "biological and chemical-based IT", and to write a definitive roadmap document on how this field might develop, its main challenges and opportunities, and how its potential impact on society at large.

MMU will coordinate the overall project activity, and our first meeting will be held in Manchester next January.

Separated at birth?

Weeknote #29 (w/e 5/12/10)

I'm delighted to have confirmed the details of my talk at the Spring Meeting of the Society for General Microbiology (SGM), in Harrogate next April. The SGM is the largest microbiological society in Europe, and was founded in 1945. Its first President was Sir Alexander Fleming, and he's been followed by an impressive list of luminaries. The current President is Hilary Lappin-Scott, with whom I worked briefly at Exeter, and our own Jo Verran is the Education and Public Affairs Officer. I'll be talking about "Massively-parallel microbial search: a new platform for synthetic biology" (BACTOCOM, basically...)

Weeknote #28 (w/e 28/11/10)

We had a meeting of the Faculty Science Communication and Engagement Group last Monday, which was a good chance to take stock after a highly-successful Manchester Science Festival. I was particularly proud of my Group, as they threw themselves whole-heartedly into various activities, which are summarised here. Naomi and Zarka were invaluable event organizers, Pete and Matthew were honorary Girl Geeks during the robot building sessions, and then Pete stepped in at the last minute to give a Teawitter talk on evacuation. We all enjoyed our involvement in this year's Festival, and are already looking forward to National Science and Engineering Week next year.

Fake Biologist Alert!: I was featured in the Autumn edition of the MMU Success magazine, talking about BACTOCOM. If you want to see the full story, including me in an unnecessary labcoat, it's here.

Finally, this week was not a good week in which to be an Ipswich Town supporter. I was all for giving Roy Keane the benefit of the doubt at first, but yesterday's clueless capitulation at the hands of our fiercest rivals is giving me pause for thought.

Weeknote #27 (w/e 21/11/10)

Frank Swain's article on the New Scientist website (see last week's note) appears to have attracted quite a lot of notice, although I'm not entirely sure that the Tokyo team's preliminary results justify the media attention. The idea of distributing a computation across a population of bacteria using targetted information exchange (as opposed to a more general, untargetted chemical signal) is certainly novel, and is one we've been actively pursuing over the last year with BACTOCOM. My small appearance as a commentator has led to some interest from various parties, none of which I'll expand on now, since it's all still very tenuous. Still, it's nice that this sort of research is gaining the sort of attention that I think it needs.

Work pressures meant that I resigned today as a founder Director of ArcSpace, the Community Interest Company I joined a year-and-a-bit ago. The organisation's growing quite quickly right now, and I think it's time to stand aside and let someone else have a go. Although there'll be some tough times ahead in the sector, they have access to the best possible resource - committed, passionate individuals - and I wish them well.

Finally, some words of support to my friends Rob and Nadine, who are going through a tough time with their son, Keifer, right now. As Rob said, "Joy comes in small doses", and a sick child immediately puts into perspective the trivialities of everyday life. The Ashby-Amos clan send their love.

Weeknote #26 (w/e 14/11/10)

Bit tardy again this week. Yesterday afternoon I spoke to Frank Swain, after he tracked me down via Twitter. He wanted to chat about the recent Tokyo iGEM work on bacterial sudoku solvers, and the resulting piece appeared today. It was good to see BACTOCOM getting another plug.

Speaking of BACTOCOM, we're currently working on the definitive design document for our system, which will be submitted as a position paper shortly. It's taken a while to get going, what with delays in appointing staff, and so on, but I think the project's in good shape now. We're expecting to be able to announce further good news on the project support front any day now, so stay tuned.

In other news, Pete, Steve and I finally submitted the journal version of our paper on mutual information for crush detection. This work forms the core of Pete's Ph.D. thesis, which he's currently in the process of writing up. I think it's a solid paper, which has actually been improved due to an earlier draft being picked up by the MIT Technology Review blog. We did some extra work in response to criticisms made in the article, and I think it's much stronger as a result.

The only other thing of note to report is that I'm now officially a member of the EPSRC College. This is made up of around 4,000 individuals, whose job it is to evaluate research proposals and serve on prioritisation panels. Given the turbulent state of research funding right now, I guess it's an interesting time to become involved.

Blatant plagiarism

I've seen my work plagiarised in the past, but I get particularly irritated when I see it being done badly. Here are some pretty wretched examples, by way of illustration. This is the first page of a paper I wrote with colleagues in 1996, before I even had my Ph.D., and when I was still at Liverpool. Note the phrase "Today's supercomputers still employ the kind of sequential logic used by the mechanical dinosaurs of the 1930s." Now, see these course materials, this article, and this article. In each case, they've taken my own words (and not just the sentence highlighted above, often whole paragraphs from the paper), and presented them as their own.

This got me annoyed, so I decided to do a little random digging. By googling random phrases from my Ph.D. thesis (PDF download) from 1997, I was able to uncover wholesale theft of my material.

This example is particularly galling; G.P. Raja Sekhar of the Indian Institute of Technology is presenting whole swathes of my own work as his own. Before proceeding, I should point out that I have asked Sekhar to remove his version, but he has apparently declined to do so.

In the illustrations below, I've presented the original (thesis) version on the left, and the stolen versions on the right. As you can see, no attempt has been made to hide the plagiarism in any way, and it's extensive (click on the thumbnails for a closer look).





It's not just the reuse of the odd figure here and there; it's systematic theft of figures (some of which took me hours to draw) and large sections of text.

C. Saravanan of Vel Sri Ranga Sanku College, Bing Hu, QiKai Xu, Chenjue Wang and Xiaoyang Kuang of City College of New York, and Tankut Yalcinoz of The Fountain; you are all plagiarists. But G.P. Raja Sekhar; if you want to use my material, I'll happily share the Powerpoint with you. Just don't pretend you wrote it.

Update (12/11/10, 13:38): Dr Raja Sekhar has been in touch. He offers the following statement: "This is to state that the Lecture Notes DNA Computing - Graph Algorithms published by POSTECH, South Korea is a result of some joint work with my students listed in the preface whom I have acknowledged. Some of the material contains the work of Martyn Amos and was not cited and we deeply regret this and withdraw this article from anywhere it appears."

Weeknote #25 (w/e 7/11/10)

This week we welcomed the latest addition to the Novel Computation Group; Dr. Ing. Ángel Goñi Moreno joins us as a post-doc on the BACTOCOM project. He originally visited for three months last year, from our collaborators at UPM (Madrid), and has obviously not been put off by the Mancunian weather. His recent Ph.D. work has attracted a fair bit of attention; he'll be working on modelling and simulation aspects of the project, and we're delighted to have him. Angel's arrival brings the group numbers up to 15 (4 academics, 2 post-docs, 2 administrators and 6 Ph.D. students, plus a visitor). We've pretty much run out of space in the lab, but it makes for a vibrant atmosphere.

Top tip: When trying to impress family by lighting two adjacent fireworks, one after the other in quick succession, remember that the gas stream from the first will inevitably knock over the second, leading to an unpredictable trajectory. Shortest. Display. Ever.

Weeknote #24 (w/e 31/10/10)

Last week we held our synthetic biology event as part of the Manchester Science Festival. Over 130 people turned up for Artificial Life: Perils and Pitfalls, and we heard from Ron Weiss of MIT, Maureen O'Malley from Exeter, and Steve Yearley from Edinburgh. Gerry Kelleher, our Deputy Vice-Chancellor, also said a few words at the start. The overall feedback from the audience was excellent, and I think we can class it a success, although I might have hoped for a little more intellectual "argy bargy" (the audience members who asked questions were generally already quite sympathetic to the synbio "cause"). All in all, a great evening, and we thank the panelists, audience members (and, of course, our sponsors at the EPSRC) for making it so.

I was also booked in to talk at another event over the weekend, but found myself double-booked (my own silly fault). A fifth birthday party regretfully trumped a fourth Teawitter Party, although my Ph.D. student, Pete, came to the rescue, for which I am eternally grateful. His talk on crowds was, by all accounts, very well-received, so maybe he's one to watch in the public engagement stakes...


It was also, of course, Halloween this weekend, so no post would be complete without a picture of our very own little witch. She's been super-cute in the last few days; we're big fans of The Cube, and she solemnly informed us, while we were watching it yesterday, that if she won £25K she would give it straight to daddy, because she's "not big enough to have pounds." Awwww. Like I'm any better with money!