Dr. Mark Read

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

Resources & Software

This page contains links to software, tools, or websites relating to my work.

My google scholar profile.

 

GutSim

My simulation of gut microbial community response to diet was featured in Andrew Holmes’s 2017 Cell Metabolism paper. This will also be released once the main manuscript describing the simulation work is published; I anticipate this to be mid-2017.

 

3D Leukocyte Motility Simulator

In 2016 I published a paper in PLOS Computational Biology that proposed a combination of simulation and multi-objective optimisation as a means to determine the search strategies that leukocytes (cells of the immune system) employ. The simulation can be downloaded here. It includes an implementation of NSGA-II, a multi-objective optimisation engine, that was used to fit motility models to real-world cellular motility data.

A modified version of this multi-objective optimisation technology was used in my 2016 Journal of the Royal Society Interface paper on calibration of biological simulations.

 

ARTIMMUS

The Artificial Murine Multiple Sclerosis simulation (ARTIMMUS) can be downloaded here.

There is a supporting information PDF which provides details on its biological underpinning and construction.

This simulation is largely the product of my doctoral research, it is the world’s first (to my knowledge) agent-based simulation of experimental autoimmune encephalomyelitis (EAE). The model of EAE simulated here is a T cell-mediated autoimmune disease in mice, used as a model for multiple sclerosis. This simulation has lead to a number of publications: Read 13, Greaves 13, Williams 13, Read 11, and others – see my Publications page.

 

CoCoRo Underwater Swarm Robotics Project

Their website.

The CoCoRoSim 3D underwater simulation is available for download here.

The CoCoRoSim simulator is an 3D agent-based simulation of the underwater swarm robotic system being developed as part of the CoCoRo project. One of my responsibilities on the project was to develop and maintain this simulation.

 

Statistical Software

The following files provide implementations of statistical tests or distributions that can be difficult to find elsewhere.

 

CoSMoS Project

The CoSMoS website.

The Complex Systems Modelling and Simulation infrastructure (CoSMoS – don’t ask where the ‘i’ went…) project was an EPSRC-funded research project held between the universities of York and Kent. The project aim was to provide capacity in the simulation of complex systems, from both a simulation programming language infrastructure perspective (occam-π, a process oriented langauge), and a more philosophical simulation development angle. The latter culminated in the “CoSMoS process”, a guide to developing simulations of complex systems that are well grounded in their complex system domains. This was achieved through explicit modelling at various stages of simulation conceptualisation and development, and the tracking of assumptions relating the simulation to the domain. A book consolidating the major research output of CoSMoS is currently being written.

 

AWASS 13 Summer School

The CoCoRoSim simulation, used for development of your chain formation algorithm, can be downloaded here. It’s a ZIP file.

The presentation explaining the problem is available here.

You will need to download NetLogo first (you need 3D, not 2D, but it looks like they are downloaded in the same package). When you have installed that, you can open the simulation in NetLogo, by opening the “CoCoRoSim.nlogo” file in the source zip file available above.

NetLogo documentation is very good. If you google “netlogo dictionary” and “netlogo 3d dictionary”, the first hit is nearly always the code dictionary. Most NetLogo 2D commands work in NetLogo 3D also.

2D dictionary

3D dictionary