Modeling Biological Pathway Dynamics With Timed Automata

Living cells are constantly subjected to a plethora of environmental stimuli that require integration into an appropriate cellular response. This integration takes place through signal transduction events that form tightly interconnected networks. The understanding of these networks requires to capture their dynamics through computational support and models. ANIMO (Analysis of Networks with Interactive MOdelling) is a tool that enables construction and exploration of executable models of biological networks, helping to derive hypotheses and to plan wet-lab experiments. The tool is based on the formalism of Timed Automata, which can be analysed via the UPPAAL model checker. Thanks to Timed Automata, we can provide a formal semantics for the domain-specific language used to represent signalling networks. This enforces precision and uniformity in the definition of signalling pathways, contributing to the integration of isolated signalling events into complex network models. We propose an approach to discretization of reaction kinetics that allows us to efficiently use UPPAAL as the computational engine to explore the dynamic behaviour of the network of interest. A user-friendly interface hides the use of Timed Automata from the user, while keeping the expressive power intact. Abstraction to single-parameter kinetics speeds up construction of models that remain faithful enough to provide meaningful insight. The resulting dynamic behaviour of the network components is displayed graphically, allowing for an intuitive and interactive modelling experience

Multi-agent simulation: new approaches to exploring space-time dynamics in GIS

As part of the long term quest to develop more disaggregate, temporally dynamic models of spatial behaviour, micro-simulation has evolved to the point where the actions of many individuals can be computed. These multi-agent systems/simulation(MAS) models are a consequence of much better micro data, more powerful and user-friendly computer environments often based on parallel processing, and the generally recognised need in spatial science for modelling temporal process. In this paper, we develop a series of multi-agent models which operate in cellular space.These demonstrate the well-known principle that local action can give rise to global pattern but also how such pattern emerges as the consequence of positive feedback and learned behaviour. We first summarise the way cellular representation is important in adding new process functionality to GIS, and the way this is effected through ideas from cellular automata (CA) modelling. We then outline the key ideas of multi-agent simulation and this sets the scene for three applications to problems involving the use of agents to explore geographic space. We first illustrate how agents can be programmed to search route networks, finding shortest routes in adhoc as well as structured ways equivalent to the operation of the Bellman-Dijkstra algorithm. We then demonstrate how the agent-based approach can be used to simulate the dynamics of water flow, implying that such models can be used to effectively model the evolution of river systems. Finally we show how agents can detect the geometric properties of space, generating powerful results that are notpossible using conventional geometry, and we illustrate these ideas by computing the visual fields or isovists associated with different viewpoints within the Tate Gallery.Our forays into MAS are all based on developing reactive agent models with minimal interaction and we conclude with suggestions for how these models might incorporate cognition, planning, and stronger positive feedbacks between agents

BioNessie - a grid enabled biochemical networks simulation environment

The simulation of biochemical networks provides insight and understanding about the underlying biochemical processes and pathways used by cells and organisms. BioNessie is a biochemical network simulator which has been developed at the University of Glasgow. This paper describes the simulator and focuses in particular on how it has been extended to benefit from a wide variety of high performance compute resources across the UK through Grid technologies to support larger scale simulations

'BioNessie(G) - a grid enabled biochemical networks simulation environment

The simulation of biochemical networks provides insight and understanding about the underlying biochemical processes and pathways used by cells and organisms. BioNessie is a biochemical network simulator which has been developed at the University of Glasgow. This paper describes the simulator and focuses in particular on how it has been extended to benefit from a wide variety of high performance compute resources across the UK through Grid technologies to support larger scale simulations

CAST – City analysis simulation tool: an integrated model of land use, population, transport and economics

The paper reports on research into city modelling based on principles of Science of Complexity. It focuses on integration of major processes in cities, such as economics, land use, transport and population movement. This is achieved using an extended Cellular Automata model, which allows cells to form networks, and operate on individual financial budgets. There are 22 cell types with individual processes in them. The formation of networks is based on supply and demand mechanisms for products, skills, accommodation, and services. Demand for transport is obtained as an emergent property of the system resulting from the network connectivity and relevant economic mechanisms. Population movement is a consequence of mechanisms in the housing and skill markets. Income and expenditure of cells are self-regulated through market mechanisms and changing patterns of land use are a consequence of collective interaction of all mechanisms in the model, which are integrated through emergence

An improved multi-agent simulation methodology for modelling and evaluating wireless communication systems resource allocation algorithms

Multi-Agent Systems (MAS) constitute a well known approach in modelling dynamical real world systems. Recently, this technology has been applied to Wireless Communication Systems (WCS), where efficient resource allocation is a primary goal, for modelling the physical entities involved, like Base Stations (BS), service providers and network operators. This paper presents a novel approach in applying MAS methodology to WCS resource allocation by modelling more abstract entities involved in WCS operation, and especially the concurrent network procedures (services). Due to the concurrent nature of a WCS, MAS technology presents a suitable modelling solution. Services such as new call admission, handoff, user movement and call termination are independent to one another and may occur at the same time for many different users in the network. Thus, the required network procedures for supporting the above services act autonomously, interact with the network environment (gather information such as interference conditions), take decisions (e.g. call establishment), etc, and can be modelled as agents. Based on this novel simulation approach, the agent cooperation in terms of negotiation and agreement becomes a critical issue. To this end, two negotiation strategies are presented and evaluated in this research effort and among them the distributed negotiation and communication scheme between network agents is presented to be highly efficient in terms of network performance. The multi-agent concept adapted to the concurrent nature of large scale WCS is, also, discussed in this paper

On Modeling Coverage and Rate of Random Cellular Networks under Generic Channel Fading

In this paper we provide an analytic framework for computing the expected downlink coverage probability, and the associated data rate of cellular networks, where base stations are distributed in a random manner. The provided expressions are in computable integral forms that accommodate generic channel fading conditions. We develop these expressions by modelling the cellular interference using stochastic geometry analysis, then we employ them for comparing the coverage resulting from various channel fading conditions namely Rayleigh and Rician fading, in addition to the fading-less channel. Furthermore, we expand the work to accommodate the effects of random frequency reuse on the cellular coverage and rate. Monte-Carlo simulations are conducted to validate the theoretical analysis, where the results show a very close match

A survey of self organisation in future cellular networks

This article surveys the literature over the period of the last decade on the emerging field of self organisation as applied to wireless cellular communication networks. Self organisation has been extensively studied and applied in adhoc networks, wireless sensor networks and autonomic computer networks; however in the context of wireless cellular networks, this is the first attempt to put in perspective the various efforts in form of a tutorial/survey. We provide a comprehensive survey of the existing literature, projects and standards in self organising cellular networks. Additionally, we also aim to present a clear understanding of this active research area, identifying a clear taxonomy and guidelines for design of self organising mechanisms. We compare strength and weakness of existing solutions and highlight the key research areas for further development. This paper serves as a guide and a starting point for anyone willing to delve into research on self organisation in wireless cellular communication networks