Dr. Mark Read

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

Professional

In August 2014, I became a founding member of a committee comprising early- & mid-career researchers (EMCR) charged with setting up and organising initiatives to support EMCR professional development, social integration and career progression within the Charles Perkins Centre (CPC). The committee organises workshops, seminars, panel sessions and networking events, and intermediates between CPC EMCRs, and the CPC executive who funds us. I currently chair this committee.

 

Reviewing and Program Committee Duties

I have refereed for the following journals:

  • Applied Soft Computing Journal.
  • Computers in Biology and Medicine Journal.
  • Frontiers in Microbiology.
  • IEEE Transactions on Evolutionary Computation.
  • The ISME Journal.
  • Natural Computing.
  • Robotica.
  • Science of Computer Programming Journal.
  • Swarm Intelligence Journal.

I have sat on the programme committee for the following conferences and workshops:

  • AIS and Biological & Biomedical Applications track at GECCO 2015.
  • Complex Systems Modelling and Simulation Workshop (CoSMoS) 2015, hosted at ECAL 2015 in York, UK.
  • Genetic and Evolutionary Computation Conference (GECCO) 2015.
  • Complex Systems Modelling and Simulation Workshop (CoSMoS) 2014, hosted at ALife 2014 in New York.
  • AIS track at GECCO 2014.
  • Workshop organiser for Confidence in Simulations for Science, hosted at SummerSim 2013.
  • Summer Computer Simulation Conference (SCSC) 2013, part of SummerSim.
  • International Conference on Artificial Immune Systems (ICARIS) 2013.
  • International Conference on Artificial Immune Systems (ICARIS) 2012.
  • Workshop Chair for the 2012 CoSMoS workshop.
  • I held the position of Publicity Chair for the BIONETICS 2011 conference.
  • The Complex Systems Modelling and Simulation Infrastructure (CoSMoS) 2010 workshop.
  • International Conference on Engineering Complex Computer Systems (ICECCS) 2010.
  • International Conference on Artificial Immune Systems (ICARIS) 2009.

 

Supervision of Research Students

I have assisted in the supervision of the following students:

  • Madison Hartill-Law, an honours student who is conducting both simulation and in vivo studies on how diet influences the gut microbiota.
  • Christopher Saunders, a PhD student on York’s CidCat’s programme who is completing a placement. Chris is simulating the administration of MBP-coated micro-beads as a possible means of protecting from EAE.
  • Sophie Alexander, an electronics MEng student, who is investigating shoaling in underwater swarm robotics.
  • Magnus Tripp, a computer science MEng student, who is extending Hannah’s work on heuristic-based calibration of agent-based systems.
  • Hannah Leonova, a Computational Biology MRes student, is investigating automated heuristic-based calibration of immunological agent-based simulations. Dissertation.
  • Bjorn Gerckens (again), who is investigating the effect that 2D versus 3D space can have on simulation results in ARTIMMUS.
  • Bjorn Gerckens, James Butler and Steve Goode, three students from Leeds university who completed DTC placements with Jon Timmis, and extended the CD200 modelling in ARTIMMUS.
  • Richard Greaves. Computational Modelling of Treg Networks in Experimental Autoimmune Encephalomyelitis. MRes, completed 2011. Thesis.
  • Richard Williams. In Silico Experimentation of Experimental Autoimmune Encephalomyelitis. MRes, completed 2010. Thesis.

 

Invited Talks and Participation in Seminars

I have been invited to present my research or participate in the following research forums (PDFs are supplied for most, please allow time for download):

  • I presented my work on modelling the gut microbiome at a workshop aimed at establishing a research alliance between the University of Sydney, and the Shaghai Jiao Tong University. 1st April 2015.
  • Delivered a talk on the analysis and simulation of complex biological data to a hand-selected group of farmers from New South Wales, Australia, who are seeking data-driven ways to optimise their farming processes. Talk took place on 1st December 2014.
  • Delivered a guest lecture to 3rd year Veterinary Science students, studying Animal Biotechnology, on the 25th September 2014. The lecture concerned the advantages and challenges of studying biological systems using computational simulation.
  • At the Computer Graphics in Biomedical and Biological Imaging Data workshop, co-located with Computer Graphics International (CGI) 2014 in Sydney, I gave an invited talk: “In Situ Imaging & Mechanistic Simulation of Cellular Swarming”.
  • In 2014 I gave an invited talk to the Discipline of Physiology at the University of Sydney: “Providing an integrative perspective of biological systems using computer simulations”.
  • I delivered a guest lecture at the 2013 Awareness Summer School held in Lucca, Italy, from 24th – 28th June. My lecture concerned the adoption of immune system principles into swarm robotic systems. Further to this, I organised a case study for students to work on. The case study entailed deriving, in simulation, an algorithm run on underwater swarm robotic platforms that would organize the swarm into a dynamic communication chain that connected two (possibly moving) points in space.
  • I was invited to give a 25 minute presentation at the BSI Mathematical and Computational Modelling in Immunology meeting held at Microsoft Research, Cambridge, on the 8th May 2013.  My talk was on simulating intervention strategies.
  • I participated in the Awareness (EU funded coordination action) slides factory, a meeting of representatives from projects examining self-awareness in autonomic systems who collectively wrote a popular science seminar and an academic course on the subject. The meeting was held in Barcelona, 24-26 September.
  • I delivered the Electronics Departmental Seminar, at the University of York, on the 14th May 2012: The power of investigating immunology through simulation, and the problem of believing the results.
  • I was invited to present at ICARIS 2011 (with about 24 hours notice!): Confidence in Computational Immunology
  • I participated in the 2011 Dagstuhl seminar on artificial immune systems. A position paper on AIS resulting from this seminar is still in preparation.
  • In June 2010 I gave a talk to the High Integrity Systems Engineering research group in the University of York’s Computer Science department: The benefits and challenges of modelling and simulating complex systems.
  • I gave a talk to the Non Standard Computation research group in the Computer Science department at the University of York in Feb 2010: Simulation to inform immunology: the tale of a programmable lab rat.
  • in January 2010 I gave a talk to the Non-Standard Computation research group in the University of York’s Computer Science department: Out of the frying pan, into the fire: the applicability of UML for modelling autoimmune and regulatory T cell networks.

 

Teaching and Demonstration

Since starting my RA on the CoCoRo project, I have been gaining experience in lecturing. So far, I have delivered material on the following courses and subjects:

  • Agent-Based Modelling of Biological Systems (2012). I presented updated material to the next cohort of CidCats students (see below for the first cohort).
  • Swarm Intelligence (2012). I prepared and presented material on: shoaling in underwater swarm robotics; statistical and sensitivity analysis techniques; simulation in swarm robotics. I delivered a further lecture on collective behaviour.
  • Agent-Based Modelling (2011). I presented material concerning ARTIMMUS to the CidCats students, doctoral students in YCCSA’s recently awarded doctoral training centre.
  • Swarm Intelligence (2011). Material on the use of simulation in swarm robotics.

I have extensive experience in demonstrating a wide variety of computer science modules during my PhD at the University of York’s Computer Science department, assisting undergraduate and postgraduate students in learning. These include:

  • Theory and Practice of Programming (2010).
  • Practical Programming Skills (2009, 2010).
  • Object Oriented Design (2009).
  • Introduction to Computer Systems (2009).
  • Cryptography, Attacks and Countermeasures (2007).

 

Awards

 

Public Engagement

Communicating research activities to the general public is important for the future of academia; the public has a right to know what research is funded by the taxpayer, and their support is important for its continuity. I held a role in the EPSRC funded public engagement scheme, New Outlooks in Science and Engineering (NOISE), though which I took part in the following public engagement exercises:

  • Judge at the 2013 York Rotary competition, where teams from local schools competed to build a cart capable of propelling itself up an inclined ramp using only gravity and a weight for propulsion.
  • Sat on a panel of 3 computer scientists at the 2010 Cheltenham Science Festival, and engaged the audience in a discussion concerning the future of computers, and how they have aided modern day life.
  • Demonstrated principles of science and engineering to the general public at the 2009 Manchester Science Fair.