Engineering Simulations to Understand and Gain Inspiration From Biological Systems

In several areas of biological science, computer simulation is increasingly providing researchers with relevant tools to interrogate human biology, rather than a continued reliance on predictions from animal experiments. Our motivation for simulating biological systems is driven by three key objectives: to further understand biological systems, reduce animal experimentation, and inspire development of novel bio-inspired engineering approaches. Yet simulations designed to explore complex biological mechanisms capture a range of uncertain factors that impact the relationship between a prediction and the real world: factors that together act as a barrier to wider simulation use and acceptance in laboratory or clinical studies. Developing robust, evidence-based approaches to agent-based simulation design, implementation, and analysis has been a feature of research in the York Computational Immunology Lab for a number of years, within significant immunological case studies. In October I moved from the Centre for Immunology and Infection to the Department of Electronics, with the aim of switching the focus of our research from solely capturing individual biological systems of interest to examining the engineering processes by which agent-based simulations should be composed, implemented, and applied. In this talk I will give an overview of what we are hoping to achieve within that focus, how we are hoping to quantify, and propagate uncertain factors in simulation development, and how our work will impact bio-inspired engineering approaches in robotics and further afield. I am very interested in hearing and discussing how simulations are developed and applied outside BioSciences and exchanging experience, and look forward to discussing this with researchers at CRESS.

Tuesday, 5 April, 2016 - 13:30 to 15:00
Kieran Alden
Presenter(s) biography: 

Kieran is an interdisciplinary researcher based in the Department of Electronics and York Computational Immunology Lab at the University of York. He studied Computer Science at Royal Holloway, University of London and a Masters of Research in Computational Biology at the University of York. He then stayed at York to complete his PhD within the Centre for Immunology and Infection, focusing on the design and analysis of agent-based simulations of immune system formation and function. Following his PhD he had a spell as a Research Fellow at the School of Biosciences, University of Birmingham, funded by the National Centre for the Replacement, Refinement, and Reduction of Animals in Research (NC3R's), scoping the development of agent-based simulations of the gut microbiota. Kieran returned to York in March 2013 to facilitate the development of the York Computational Immunology Lab and create integrated approaches for modelling immune system development and function. Since October 2015 he has worked for the Department of Electronics, focusing on understanding uncertainty in models of biological systems, while assisting the management of simulation-focused research in the York Computational Immunology and York Robotics Laboratories.