Jamie Twycross
background | publicationsResearch interests: systems biology, synthetic biology, artificial life, biologically-inspired computing, artificial immune systems, computer security and networking, robotics.
I am a Research Fellow at the University of Nottingham, U.K., working jointly in the Centre for Plant Integrative Biology (CPIB) and School of Computer Science. CPIB, which brings together a team of biologists, computer scientists, engineers, informaticians, mathematicians and statisticians, is a flagship centre for Integrative Systems Biology. Integrative Systems Biology seeks to use experimental, computational, mathematical and engineering techniques to understand biological organisms in their entirety.
At CPIB we are studying the root system of the model plant Arabidopsis thaliana. In this context, my research is focused on computational modelling, specifically, the application and development of:
- novel computational modelling frameworks
- integrative multi-scale modelling frameworks
New trends in computer science have led to the development of a number of novel computational modelling frameworks. These frameworks include multi-agent systems, Petri nets, and P-systems. Of particular interest are P-systems, which are designed to capture various mechanisms present in biological cells and to mimic several of their most fundamental features. I am investigating how such frameworks can be applied to model plant root systems in order to provide an alternative approach to model formulation and to analyse what sort of emergent processes they permit. This work will lead to a better understanding of model properties such as scalability and robustness in noisy environments.
Integrative multi-scale models seek to combine models at different scales, such as the molecular, cellular, tissue and organ scales, in order to produce models of the entire root system. The goal here is to establish a multi-scale in silico framework capable of accounting for root responses to environmental cues, such as gravity, water, nutrients, temperature and obstacles. By using this framework to integrate models of primary root growth, meristem function and lateral root development produced by members of CPIB, a prototype in silico virtual root will be produced. The virtual root will be combined with the virtual shoot being developed by the Computable Plant Project at UCI/Caltech to create an in silico model of an entire plant. This model will be employed to pioneer the use of predictive modelling in Plant and Crop Sciences, and to address issues of major importance in Crop Science, such as seedling establishment and sustainability.
As part of my research effort, I have, in collaboration with other researchers at CPIB and elsewhere, developed a software suite, called the Infobiotics Workbench, for designing, simulating and evaluating executable models. Please visit http://www.infobiotics.org/infobiotics-workbench/ for more details and to download the software.
Integrated Innate and Adaptive Artificial Immune Systems applied to Process Anomaly Detection. Jamie Twycross. Ph.D. Thesis, University of Nottingham, January 2007.
An Immune System Approach to Document Classification. Jamie Twycross. Master’s Thesis, COGS, University of Sussex, U.K., August 2002.