Dr. Mark Read

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

New year, new student

A new year is upon us. We are now 14 months from the end of CoCoRo, not quite time to panic, but not impossibly far off either. Its time to knuckle down to some AIS (artificial immune system)-oriented fault tolerance in our shoals of AUVs.

Over the past year I’ve done some work on shoaling in underwater swarm robotics. Communication and distance sensing underwater is problematic, electromagnetic signals are hugely attenuated. Our robots don’t have the capacity for sophisticated visual processing, so we rely on bluelight systems (blue LEDs and photodiodes) to detect distances between AUVs. The range of bluelight and radio frequency systems underwater will be 50cm at best. This equates to about 5 AUV body lengths. Our studies to date have shown that creating well-aligned shoals without communication of velocities between members of the shoal is incredibly difficult (if not impossible). This work is going to be carried on by Sophie Alexander, an Engineering MEng student who is going to investigate shoaling algorithms in this challenging underwater context. To the left is a nice picture of 15 CoCoRo AUVs, well aligned (but not shoaling) on the table.

Journal paper accepted to BioSystems

We have just had word that our paper, first authored by Richard Greaves, has been accepted for publications in BioSystems. It is an extension of the conference paper presented at IPCAT this year, firth authored by Richard Greaves, and includes work that Bjorn and James did on modelling CD200 regulation of dendritic cells in EAE. Bjorn and James were placement students from Leeds university who are both starting PhDs under Jon Timmis (and others). It is truly remarkable that the placement students’ work would end up in a journal, and a testament to their potential.

The paper examines several possible mechanistic models of how CD200 negative signalling of DCs suppresses their ability to promote autoimmune T cell responses, and clearly motivates further work in the computational immunology field on principled approaches to designing and building simulations. As luck would have it, this is work that is on our horizons.

Manuscript accepted by BMC Bioinformatics

During their respective Masters degrees, Richard Williams and Richard Greaves conducted some very elegant experiments using the ARTIMMUS simulation that elucidated the nature of regulation in EAE. Richard Williams’ work won the Best Immunological Modelling Paper award at ICARIS 2011, and it was his abstract that lead to the current journal submission. Richard W’s work was combined with work from Richard G, and yesterday the manuscript was accepted for publication in the BMC Bioinformatics journal. Winning a best paper prize and then being accepted for publication in this very respectable journal is a fantastic testament to the very high quality of work that these two have conducted (as Master’s students, no less)!

The paper reports three experiments, all excellent exemplars of how simulation facilitates work that could not be conducted in vivo. Manipulation of dendritic cell peptide presentation demonstrates that the regulation mediating recovery from autoimmunity in this model of EAE does not require regulatory T cells and their autoimmunity-inducing targets to be primed by the same dendritic cells. The paper reports that although CD4Th cells are invaluable in facilitating the cytotoxic T cell response, their physical presence and the temporal aspects of signals they deliver to dendritic cells modulate the magnitude of this response. Artificial means to deliver the signals that CD4Th cells are responsible for could yield more aggressive CTL responses that might overcome otherwise persisting disease.

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!

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!).


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.