Seminar with Simon Connely

Title: Modelling Biological Interactions with Formal Methods

Speaker: Simon Carter, PhD candidate, School of ITEE

Place: Room 621, GP South (Building 78)

Time: Thursday 6th April, 10:30 morning Tea. 11:00am seminar

"Computer science could provide the abstraction needed for consolidating knowledge of biomolecular systems." [1]

I am interested in modelling molecular biological interactions and genetic regulatory networks (GRNs) using formal methods, as distinct from approaches such as differential equations or neural networks. As an initial case study it was decided to develop models of a small and well-characterised GRN, the lac operon [2], using tools supporting several formalisms then compare the models, methods, notations, and tools in order to determine their relative advantages and disadvantages.

To date I have built models of the lac operon using two process algebras, finite state processes and the stochastic pi-calculus. Evaluation criteria have been established and applied to both. The intention is to build and compare additional models using the Petri net and Statecharts formalisms.

This seminar will feature a computer science perspective on modelling molecular biological processes, an overview of simple GRNs and issues faced in modelling them, together with a presentation of the models developed to date.

[1] Aviv Regev and Ehud Shapiro, Cellular abstractions: Cells as computation, Nature 419, p343,

[2] Wikipedia - lac operon:

Speaker bio and contact:
Simon was born in Birmingham, England quite some time ago. He grew up in northern Scotland and Sierra Leone before moving to Australia and working in a variety of software industry positions within the Australian Government and UQ. Simon has a BSc from ANU, an MSc from UQ, and is currently a PhD candidate in the School of ITEE, advised by Dr Paul Strooper and Dr Jennifer Hallinan (University of Newcastle upon Tyne).

World-class basic and applied inter-disciplinary research on questions fundamental to understanding, designing and managing complex systems
2009 The ARC Centre for Complex Systems, Australia