Mark Read

Research Associate, Department of Electronics, The University of York

Electronics departmental seminar

I have in the past presented at conferences, special interest and research groups, but yesterday was my first departmental seminar. There was some initial concern about low numbers – the suitability of speaking to electronics researchers about simulating the immune system had previously been raised, but I felt that the motivation, potential impact and issues of computational immunology could be conveyed without excess immunological detail. Many in Electronics use simulation, and there was interest in simulating systems that are themselves not well understood.

The drive of my seminar was to demonstrate how computational simulation could aid drug discovery (which is challenging and very expensive), but that simulation results are not necessarily representative of the real immune system, and to highlight the techniques I employ to build confidence that they are. I’m pleased to say it was very well received. The next might actually be on swarm robotics!

CD200-modelling abstract accepted to ICARIS 2012


I received the excellent news that an abstract concerning the modelling of CD200, a molecule implicated in modulating dendritic cell activity and recovery from EAE, has been accepted as an oral presentation at this year’s ICARIS conference. This work was conducted by Bjorn and James over the Christmas holiday – both are starting PhDs with Jon Timmis in October, we have high hopes for them both!

CoSMoS Workshop 2012

This year marks the last of the CoSMoS project’s workshops on complex system modelling and simulation. I am undertaking some of the administrative duties as one of the workshop chairs. The workshop will take place as a satellite workshop of the Unconventional Computation and Natural Computation (UCUN) at the University of Orléans, France between 3-7 September 2012. It welcomes submissions that explore all aspects of complex systems modelling and simulation with a special focus on the theme of how complex systems simulations can be used to simulate unconventional computation and natural computation.

These workshops have always been engaging in the past, and I’m sure this year will be no exception.

“Best PhD Award”, 2nd Prize

I’m very pleased to learn that my PhD thesis has been awarded 2nd prize in Computer Science’s “Best PhD Thesis” award for the year 2011 (when it was submitted)! I’m told there’s a certificate and a cash prize – sounds like something nice to hang in my house, and a celebratory dinner with my girlfriend.

This opens the door for submission at a national level… fingers crossed.

Mark & Jon in San Diego

I’m writing this at LAX airport as I await my flight out of California, at the end of another successful visit to my collaborator, Vipin Kumar. Jon has been with me this week, and we’ve had a fantastic time – its always a bit dull, even in a place as nice as La Jolla, to be visiting on your own.

As always, its been a hugely positive meeting. The CD200 modelling work that was largely conducted by Bjorn and James recently was well received, and we have submitted an abstract describing the preliminary findings. We’ve also made excellent progress on the Nature Biotech, now Methods, paper. And I have a stack of material to look at and distill into some interesting grant proposals; Jon pointed out that, incredibly, all the progress made within his lab on modelling EAE, Payers Patch development and Leishmaniasis has received not one cent of direct funding from any funding council. This is not for want of trying, and with a promising Nature Methods paper in the works, a Science Signalling paper already accepted, and two other high quality publications in review, it’s astonishing that the lab has accomplished so much on money scraped together from disparate sources. Just think what we could achieve with some hard backing!

Trips like this always highlight to me the value of face-to-face collaboration in interdisciplinary endeavours. Technologies like Skype are impressive in facilitating collaborations, and my own carbon footprint is nothing to boast about, but what we seem to accomplish in a few hours of meeting in person can dwarf months of work over conference calls. I think it comes down to the huge separation between computer science/engineering and immunology disciplines. A passing comment from Vipin concerning some aspect of immunology has decades of highly specialised experience backing it, and other immunologists can follow the thought process, However to a computer scientist dabbling in immunology I often find at least 5 interpretations for what Vipin has said, and this needs extensive clarification. There are aspects of communication across these subjects that is very difficult to cram into packets and send half-way across the globe and have arrive intact. We have been writing the (now) Nature Methods paper for nearly 2 years now, and I can quite happily believe that without this visit it could be another 2. Thankfully the paper is now in a state where we think submission within the next few months is possible. A big part of it is also building the relationship, which is hard to do across boarders. Like many walks of life, I see success in science as being largely due to the people undertaking it. Building good collaborations with good people who you can trust is essential (I’ll keep my observations concerning the other side of this line to myself…).

I will be sad to see the back of the beautiful blue cloudless skies, ocean, sand and sun. The 25-30 degree climate is about to be replaced with the half meter of snow that I hear has fallen on my holiday destination of Calgary. I’ll be out of the loop for a week, back just in time for the CoCoRo general assembly in Stuttgart in 9 days. In the meantime, I will be visiting one of my childhood friends who emigrated to Canada a few years ago, and raves about how good it is. I hear that horse riding (in half a meter of snow?) is on the cards.

Dr. Mark Read!


Last week marked the end of an era for me, I received the official email from the university that my thesis has been accepted!

Statistical and Modelling Techniques to Build Confidence in the Investigation of Immunology through Agent-Based Simulation.

Has a nice ring to it… This is by far the most expensive and exclusive book I have ever bough. There are only 3 physical copies worldwide, and there are no current plans to go into mass-print :)

There’s a huge amount of content here that I have yet to publish, and that will be a high priority for 2012. For those who are interested, my external examiner was Pietro Lio from the University of Cambridge.

I’m looking forward to wearing a graceful gown and a silly hat in the summer, and spending a special day with fiends and loved ones.

York University Robot Lab Launched

Wednesday was an exciting day for the robotics guys at the university – it was the official launch of the £250K robot lab built on the new “Heslington East” campus. We kicked off with a press event that attracted Look North, ITV Calendar, York press and more. It’s quite an experience having reporters, photographers all over the place! That was chased up with a VIP tour with representatives from the uni and from industry. Our demos included flying drones “dancing” and tracking a moving target, epucks running the omega algorithm, a walling 6-legged robot, simulations from CoCoRo and from Symbrion, and controlling a robot using the Xbox Kinect. To end the day, Jon gave a fantastic talk to a fully packed 250-people lecture hall on immunity in robotics.

We had some drama in the lab in the days leading up to the event 0 Monday night we had a fire! This prompted more media attention, with some interesting stories circulating around the York press concerning activities in our “Robot Wars Arena”. Overstated perhaps. We do some cool stuff, but have yet to venture into robots (deliberately) attacking one another! The actual cause was a faulty battery that was left to charge overnight, and failed to stop charging when it was full; the result was it overheated and caught fire. York Uni were brilliant, the entire lab was given a deep clean to remove soot and then repainted in less than 36 hours.

I shall leave you with this video, which shows three drones flying and “dancing” to a nice waltz, created by my CoCoRo colleague, James Hilder.

Here are some of the videos and stories – though I don’t know how long these links will stay live for: York Press (video story), Calendar (video, 22 min in)

UPDATE 03/02/12: Luis Fuente, another of Jon’s students, has found a video from BBC look north of the robot lab launch. Its a large file (35M), so click here to download it any play it in a player of your choice (I like VLC).

 

Submission to IPCAT 2012 accepted

Starting the new year off with some fantastic news, a paper first-authored by Richard Greaves has been accepted to IPCAT 2012! Richard submitted his excellent MSc thesis in autumn, and this will be an added bonus for him. The paper examines the issues in extending an established and calibrated simulation when the influence of new pathways/cells are to be investigated – a common pattern in many strands of research. Extension of simulations with new components can have a profound effect on its behaviour, and the logical course of action is to re-calibrate. However, this in itself can have substantial implications on existing results and predictions. The paper calls for the investigation of more principled simulation design and calibration methodologies that, it is hoped, can indicate when influential pathways or components are absent from a simulation in the first place. Richard has been working with my ARTIMMUS simulation, and the paper is tied to a case study in extending this EAE simulation. (The paper presenting ARTIMMUS to the world has been a very long work in progress… I’m looking forward to its publication, hopefully this year!).

PhD Viva Success!

Last Friday (25th Nov) I successfully defended my PhD, which was accepted subject to (quite!) minor corrections. I was examined by Dr Pietro Lio of the University of Cambridge, and Prof John Clark of the University of York. The subject of my fairly meaty thesis is “Statistical and Modelling Techniques to Build Confidence in the Investigation of Immunology through Agent-Based Simulation”. I look forward to completing the corrections and uploading a complete version here.

Understandably this lead to some celebration, and a very happy collection of colleagues, family and friends. I’m still waiting for the full feeling to sink in, but nonetheless, its a great (near… corrections still to be made) end to an engaging 4 years of research. I owe a lot to the many people who have helped me get to where I am now, so thank you all!

CoCoRo General Assembly

Yesterday the CoCoRo project held its first general assembly meeting, marking 6 months since the start of the project. The meeting was a success, with all partners presenting interesting aspects of work conducted in the early stages of the project.

James Hilder and myself, representing the Uni of York, presented initial ideas concerning the operating system design, and early work on porting algorithms into the CoCoRo simulation. AUVs flocking based on Reynold’s Boids algorithm is particularly interesting to watch (at least I think so!)… here’s a video. The algorithm represents one of several possible solutions that allow swarms of AUVs to explore their environment as a group without losing contact with one another.