Dr. Mark Read

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

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!

ICARIS in progress!

This year’s ICARIS conference (international conference on artificial immune systems) is held in Taormina, Sicily. The university of York has 6 delegates here, covering both the computational immunology and engineering concerns of the conference.

Richard Williams’ had the “grave yard” shift, presenting his position on the limitations of UML in capturing the stochastic aspects of the immune system, and how he has used statistics to model the distributions of immune behaviour that result from this stochasticity. Jon Timmis presented on day 2, arguing that if immunological simulations are to inform drug discovery and design, and clinical trial design as we all hope, then they must be viewed as safety critical systems (the safety of patients depending on this information). As as result, the processes through which they are constructed, tested for bugs, documented and demonstrated as reliable must all become more rigorous. This is a message that has been emanating from our lab for some time now (my own thesis addresses some of these issues), and its very encouraging to see the audience being receptive to the message. The same “grave yard” shift of day 2 (at the end of a long day, with a completely dark room) saw my own presentation on possible cellular mechanisms through which CD200 inhibits DC function (work performed by Bjorn and James). This too was well received, though I learnt that talking over a live video of ARTIMMUS that is already annotated with text can be tricky to time correctly!

We have just, literally just now, had Tiong’s paper on sensor networks. There was some comedy as Tiong tried to start his presentation on a Chinese chap’s computer – only to find that he could not full screen the presentation as all the menus were in Chinese symbols!

I leave you with this lovely picture of Taomina…

Update: the conference is now coming to a close. Its been fantastic to see colleagues in the field again, who have been very social – 18 of us went to dinner together last night, where the following photo was taken of the day’s plenary speakers, Prof. Stephanie Forrest. She delivered an outstanding presentation on “The Biology of Software”, where she described research on using evolutionary methods to fix bugs in computer code (amongst other things). She was very happy at dinner.

PS. There has been a conspicuous gap in my own publication record for the last two years, being the bulk of my research that resulted in the construction of the ARTIMMUS simulation. This is not dead, its just turning out to be an extremely hard paper to write given where we are trying to send it. Its on the 10th complete re-write in 2 years. We found some time to look at it again in the conference, and this draft is looking good, so hopefully there will be more news on that soon enough…


I have just had the privilege of attending ICARIS 2011 in Cambridge, a conference dedicated to the computational modelling of the immune system, and taking immune system inspiration in solving engineering problems.

One of Jon Timmis’ research students who I helped supervise last summer, Richard Williams, was presenting an abstract of his work on EAE. His presentation was excellent, and he won the computational immunology best paper award!

Though I was not first author on any paper in this year’s proceedings, and hence not presenting, I did end up presenting some work. There were a number of cancelations and speakers who did not show, and I was asked by one of the organisers if I would like to present some results. I took the opportunity to talk about establishing confidence in simulation results being genuinely representative of the real immune system, an aspect of the field that I believe is hugely¬†under-appreciated. Most of the talk’s content was lifted from my recent MCMDS journal paper, currently in press. The talk was hugely well received, which is always encouraging! It was great to see old friends again, I hope I have the opportunity to attend ICARIS 2012. which will be in Italy.