Dr. Mark Read

Research Fellow, Charles Perkins Centre, The University of Sydney
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Invited Talk Season

Life has become suddenly hectic, I’m giving three talks in 4 weeks, and I’m discovering again how much preparing for talks occupies your mental space. The desire not to make a fool of ones self is a powerful motivator!

The first talk was to the Discipline of Physiology here at the University of Sydney. As a computer scientist, giving a talk concerning biology to a room of biologists is a little nerve wrecking, but it went well. My aim was to demonstrate how mechanistic simulation (simulation’s that explain not only what the biology is doing, but how and why it is doing it) is a valuable complement to traditional techniques in trying to understand biological systems. I found the room hard to read, but I am told it was a successful talk. It did not inspire a shower of requests for collaboration, but I think it got the audience thinking. I tried to be honest about the limitations and pitfalls of simulation, having to program the environment and physics in addition to the experiments themselves leave a lot of scope for error. I’m a big fan of the argumentation structures that Kieran Alden has been pioneering at the University of York, which I feel is a key component to demonstrating that simulation results are faithful representations of the biology. Incidentally, this work culminated in a tool written by Paul Andrews, also at York, to support the creation of such arguments – Artoo. Kieran and Paul are preparing a manuscript on these techniques, and I’ll create a post about it when it hits the press.

The second talk was at the Computer Graphics International (CGI) conference hosted here in Sydney. Jinman Kim organised a workshop at the conference, and asked me to present my work. I was honoured, and somewhat nervous again as the work on neutrophil swarming is still very much under construction. Still, its a great case study, and very visually appealing. Essentially, I’m working with Tatyana Chtanova of the Garvan Institute,¬†Jon Timmis and Peter Kim to try and explain what cases this swarming behaviour in neutrophils (immune system cells that respond very rapidly to injury, you will need quicktime installed to see the movie, click it to play) [1]:

That video shows how neutrophils in a mouse ear respond to a sterile injury caused by a very fine laser burn (causing a single cell to burst) over the course of 50 minutes. It’s striking how quickly cells respond, and how coordinated their movement is. It came from reference [1]. This talk too was very well received, possibly in part because I littered it with videos and images. I have one more talk to give in a week, but that’s to a lab that I work with here, so less pressure. I’m really starting to wish that there were about 48 hours in a day!

REFS:

[1] T Lammerman et al. Neutrophil swarms require LTB4 and integrins at sites of cell death in vivo. Nature 498(7454):371-5. doi: 10.1038/nature12175. URL.

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!