Dr. Mark Read

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

“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.

update (12/10/12): Alas I did not win at the national level. Never mind, it was an honour to have been put forward and to to recognised in my department!

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.

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.