Dr. Mark Read

Research Fellow, Charles Perkins Centre, The University of Sydney
Research Gate
My Research Gate

CoSMoS book draws closer

The CoSMoS project may have concluded, but its research output certainly has not. Members and affiliates of the project met this week to discuss the current state of the CoSMoS book. CoSMoS is the “complex systems modelling and simulation infrastructure” (the “i” is AWOL), and the years of experience in how (and how not) to create representative simulations of complex systems that CoSMoS supported is now culminating in a book. It’s a patterns book – a familiar computer science concept – where each pattern tries to encapsulate and advise on some key concept or technique relating to the messy endeavour that in silico complex systems research can be. Its in good shape, despite the numerous “text to go here” placeholders: the structure and content seems strong to me. Of course the “stuff here” placeholders persist because the many authors, myself included, have yet to venture that far down the proverbial todo lists. Susan Stepney has done a tremendous job getting the book to where it is now, but we are each responsible for providing text for patterns that we either suggested or hold experience in. We’re all willing participants, yet I don’t envy Susan’s job. Studying the organisation and dynamics of complex systems through simulation is highly challenging, and so too is the job of organising the dynamics of academics tasked with writing about it. The current drive is to have the completed draft by end of summer, and the tweaked and polished final book by Christmas.

NB. CoSMoS does have a webpage, but it currently displays a charming “fatal error” communiqué.

Slides of Awareness

Last week I had the pleasure of visiting Barcelona (well, Castelldefels), where in a hotel right on the beach, a collection of representatives from the Awareness project engaged in a hugely productive few days of slide writing.

Labelled a ‘slides factory’, the meeting tasked us with creating a 2 hour laymans seminar and an academic course comprising around 15 lectures on self-awareness in autonomic systems. Awareness is an EU funded coordination action focusing on this very subject, and supports the CoCoRo project on which I myself am employed. My angle was awareness in the immune system – how it functions to maintain the health of the host, without incurring autoimmunity, and where autoimmunity does occur how it can be self-regulated.

The slides factory experience was interesting, and far more productive than I would have thought possible. Both the lecture and the academic course were near completion by the end of the few days. The format was 11 people spinning ideas concerning content and message, writing sections individually, and then collecting feedback from the group. The slides have to be finalised (dotted i’s, crossed t’s) by the end of October, and at some point in the future, you may find these lectures and seminars rolled out on academic and popular science circuits!

Oh… almost forgot the beach. These guys wave-boarding with kites were quite a sight!

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.

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.