Agent-based modelling of fungal mycelia

Complex systems and their modelling is an important area of research. There are many open questions and best practises are still being devised. This project re-conceptualises an existing Individual Based Model (IBM) representing a biological complex system, that of fungal mycelia, as an Agent Based Model (ABM). The project attempts to implement this ABM in occam-p, a process oriented programming language, in order to run simulations and compare results with those from the original IBM. Some emergent behaviours regarding phenotypic growth forms are observed in the devised ABM. Success of the re-conceptualisation, in the sense of model equivalence, can only be claimed if both the ABM is considered “equivalent” to the IBM and the implementation accurately reflects the ABM. As the occam-p language is currently under development, this project also evaluates the usability of the language for complex systems modelling.

This research represents the MMath project conducted by Matthew Harbage, under the supervision of Dr Polack. The project, run within the Department of Computer Science, University of York, was completed in 2010. The project transformed a mathematical model of fungal growth, into an individual-based model developed in the occam-pi programming language. The images below show the outputs of the mathematical model and the individual-based one respectively.

Mathematical model simulation Occam-pi simulation of the fungal model