Dr. Mark Read

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

Sydney Bioinformaticians Get Together

Towards the end of one excellent conference (ANZOS 2014) I saw the call for another workshop, and so threw in an abstract. The abstract was accepted as a post-grad talk, and so I would be presenting at the Sydney Bioinformatics Research Symposium 2014. This was a smaller, though still well-attended affair hosted at the CPC.

There were some noteworthy highlights. Prof Andreas Zankl (a clinician) give a stunning talk littered with computer science, he and his team (of 3!) are designing a new database and user interface to collate together data and opinion on bone dysplasia. It was just so strange to have a GP tell me about the semantic web. As with last year, this year’s gathering had a “fast forward” hour wherein those with posters were given 2 minutes (exactly, you were cut short the second you overran) to draw attention to their work. It’s an adrenaline fuelled experience for the presenters, well aided by David Lovell’s considerable talent as an MC.

My own talk was on neutrophil swarming, and specifically how automated calibration can be integrated into the simulation development cycle to help refine the model. It was very well received, moreso than I think most other talks I’ve given thus far in my career. My approach in using simulation to test biological hypotheses differs from typical bioinformatics work, which is concerned with making sense of large quantities of high throughput data. I think both communities enjoyed learning a bit more about how the other’s approach works.

This year has not lacked for interesting conferences and workshops, though I’ve barely left Sydney. Its fantastic here, but I suppose the downside of living in an exotic place is that the conferences tend to come to you, rather than giving your the opportunity to head abroad.

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.

Awareness Summer School 2013

This week I have been in Lucca, Italy, for the Awareness Summer School 2013. I had a dual role at this meeting, I was both invited speaker and mentor. The former entailed delivering a lecture on using immune inspiration to build novel algorithms and robotic systems. The latter, guiding two teams of summer school students in solving an underwater swarm robotics problem. Having found it thoroughly challenging myself, I was intrigued as to what 10 other brains would come up with in creating an algorithm for relay chain formation. A swarm of underwater robots have to configure themselves to form and maintain a communication chain between the water’s surface and an `exploratory’ shoal that searches the sea for some target.

The teams were very creative, and both managed to solve the bulk of the problem in just the week available (which included breaks for keynotes, coffees and lunches). The week culminated in each team giving a sales pitch presentation to industry. One of my teams got very imaginative, and pitched their algorithm as a way of identifying lost submarines beached on the sea bed. The comical edge that gave their presentation was very well received.

Other keynote talks were given by Alan Winfield, Peter Lewis, Rene Doursat and Martin Wirsing, and all offered interesting perspectives on self-awareness in autonomous systems. Alan delivered a very convincing argument that robots operating in a noisy and unpredictable environment cannot be safe (for humans) unless they are self-aware. It was great to see them all again, all had attended the awareness slides meeting in Barcelona last year.

Lucca is a fantastic city. The walls are great, you can try to work off the pizzas and fine wine by running around them. And there is of course, delicious pizza and fine wine.

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…

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!

CoSMoS Workshop 2012

This year marks the last of the CoSMoS project’s workshops on complex system modelling and simulation. I am undertaking some of the administrative duties as one of the workshop chairs. The workshop will take place as a satellite workshop of the Unconventional Computation and Natural Computation (UCUN) at the University of Orléans, France between 3-7 September 2012. It welcomes submissions that explore all aspects of complex systems modelling and simulation with a special focus on the theme of how complex systems simulations can be used to simulate unconventional computation and natural computation.

These workshops have always been engaging in the past, and I’m sure this year will be no exception.

ICARIS 2011

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.