Petri nets for systems and synthetic biology

We give a description of a Petri net-based framework for modelling and analysing biochemical pathways, which uni¯es the qualita- tive, stochastic and continuous paradigms. Each perspective adds its con- tribution to the understanding of the system, thus the three approaches do not compete, but complement each other. We illustrate our approach by applying it to an extended model of the three stage cascade, which forms the core of the ERK signal transduction pathway. Consequently our focus is on transient behaviour analysis. We demonstrate how quali- tative descriptions are abstractions over stochastic or continuous descrip- tions, and show that the stochastic and continuous models approximate each other. Although our framework is based on Petri nets, it can be applied more widely to other formalisms which are used to model and analyse biochemical networks

Qualitative modelling and analysis of regulations in multi-cellular systems using Petri nets and topological collections

In this paper, we aim at modelling and analyzing the regulation processes in multi-cellular biological systems, in particular tissues. The modelling framework is based on interconnected logical regulatory networks a la Rene Thomas equipped with information about their spatial relationships. The semantics of such models is expressed through colored Petri nets to implement regulation rules, combined with topological collections to implement the spatial information. Some constraints are put on the the representation of spatial information in order to preserve the possibility of an enumerative and exhaustive state space exploration. This paper presents the modelling framework, its semantics, as well as a prototype implementation that allowed preliminary experimentation on some applications.Comment: In Proceedings MeCBIC 2010, arXiv:1011.005

An introduction to Biomodel engineering, illustrated for signal transduction pathways

BioModel Engineering is the science of designing, constructing and analyzing computational models of biological systems. It is inspired by concepts from software engineering and computing science. This paper illustrates a major theme in BioModel Engineering, namely that identifying a quantitative model of a dynamic system means building the structure, finding an initial state, and parameter fitting. In our approach, the structure is obtained by piecewise construction of models from modular parts, the initial state is obtained by analysis of the structure and parameter fitting comprises determining the rate parameters of the kinetic equations. We illustrate this with an example in the area of intracellular signalling pathways

A Max-Plus Model of Asynchronous Cellular Automata

This paper presents a new framework for asynchrony. This has its origins in our attempts to better harness the internal decision making process of cellular automata (CA). Thus, we show that a max-plus algebraic model of asynchrony arises naturally from the CA requirement that a cell receives the state of each neighbour before updating. The significant result is the existence of a bijective mapping between the asynchronous system and the synchronous system classically used to update cellular automata. Consequently, although the CA outputs look qualitatively different, when surveyed on "contours" of real time, the asynchronous CA replicates the synchronous CA. Moreover, this type of asynchrony is simple - it is characterised by the underlying network structure of the cells, and long-term behaviour is deterministic and periodic due to the linearity of max-plus algebra. The findings lead us to proffer max-plus algebra as: (i) a more accurate and efficient underlying timing mechanism for models of patterns seen in nature, and (ii) a foundation for promising extensions and applications.Comment: in Complex Systems (Complex Systems Publications Inc), Volume 23, Issue 4, 201

Action Stories for Counter Terrorism (extended abstract)

Due to the raised terrorist threat worldwide, there is an urgent need to research that assists security and police services to protect the public and key assets and to prevent attacks from taking place. Successful protection and prevention may require potential and known suspects to be monitored or arrested. These operations are high risk because inappropriate surveillance, interview or arrest may have damaging political, public relations and intelligence effects. In addition to better tracking information on which to base suspicions, the security and police services need to have confidence that operations will yield evidence that can demonstrate conclusively that a deceptive activity such as a terrorist attack was in the process of being planned or executed before an operation takes place