9th Workshop on Membrane Computing, WMC9
Edinburgh (UK), July 28-31, 2008
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MACS at Heriot-Watt University
School of Mathematical and Computer Sciences (MACS)

International Journal on Natural Computing
International Journal on Natural Computing

Oxford University
Oxford University Press

Scottish Bioinformatics Forum
Scottish Bioinformatics Forum

Prof. V. Danos (Edinburgh, UK), about the talk;
Prof. D. Gilbert (Glasgow, UK), about the talk;
Prof. P. Hogeweg (Utrecht, The Netherlands), about the talk;
Dr. M. Kirkilionis (Warwick, UK), about the talk;
Dr. F. J. Romero-Campero (Nottingham, UK), about the talk;
Prof. S. Wolfram (Champaign - IL - USA), about the talk.

Prof. V. Danos
title: A stochastic calculus of binding with applications to the modelling of cellular signalling
abstract: Kappa is a stochastic calculus of binding and modification that handles well the modelling of complex and fine-grained regulation in biological systems. Its main usage is in the description, simulation and causal dissection of signalling pathways -where traditional methods are beset by combinatorial explosion and do not offer the same ease of description

Prof. D. Gilbert
title: Modelling and analysing the dynamic behaviour of biochemical networks
abstract: Modelling intracellular biochemical networks presents particular challenges connected with the need to reconcile the difficulty of obtaining experimental data with the requirements of providing information at a level of detail which will be useful for biochemists. Such models should be able to both explain and predict behaviour, and I will illustrate this with research undertaken in Glasgow in the area of intracellular signalling pathways. Moreover modelling is a key component in the emerging discipline of Synthetic Biology in which the activity of design as well as analysis is of prime importance. I will discuss a framework for modelling and analysing biochemical networks which unifies qualitative and quantitative approaches, and show how it has been applied in the context of a Synthetic Biology project. I will also describe a very fast model checker that has been developed at Glasgow which can be applied to biochemical systems and discuss how it can be used to drive the design of such systems.

Prof. P. Hogeweg
title: Multilevel modeling of morphogenesis
abstract: In order to study the growth and development of cellular systems one needs a formalism in which on can combine the biophysical properties of cells with the modulation of these properties by gene regulatory processes. I will argue that the multisclale CA formalism now known as the Cellular Potts Model (CPM) provides a simple yet basically sound representation of a biological cell, which can be interfaced with gene regulatory processes. It represents a cell as highly deformable object which takes its shape from internal and external forces acting upon it. I will demonstrate how within this formalism complex large scale morphodynamic processes can result from local regulation of cell, and in particular membrane, properties. I will explain morphogenetic mechanisms which tend to evolve in such systems.

Dr. M. Kirkilionis
title: Multi-Scale Modeling and Simulation of Cellular Membrane Transport and Reaction Systems
abstract: Based on the development of new experimental techniques, mainly imaging techniques like FRAP and FRET, cellular transport and reaction processes can be better understood than ever before. Cell biology in general offers a whole range of such important applications (in the end all life depends on this complex machinery) which are challenging for mathematical modeling and the performance of existing numerical algorithms. Inside the cell membrane systems like the ones involved in the secretory pathway are especially important and can be used to understand the state-of-the-art of modeling and simulation in a wider area to much advantage.
One specific property of cellular structures are their complicated geometry, here just called 'Complex Domains'. The complexity of these cellular domains can now be measured much more accurately with the help of modern imaging and image analysis techniques. It is tempting to combine methods from image analysis and numerical simulations in order to get a better understanding how different molecules, small to large (ions to protein complexes) distribute and react inside the cell. Moreover such geometries are typically 'complex' on every relevant scale. This makes their representation in a simulation typically difficult, and one must use adequate approximations. This need for averaging nicely explains why (in this case spatial) scales are important (and why all modeling is relative to a chosen scale), and therefore scale is perhaps the most important notion in this area, even before considering the appropriate choice of either a discrete or continuous state space to represent the different components of the system.
The same is true for the second part of the problem, the action (mostly binding) of macro-molecules with each other or other binding partners. This process creates events at which the system state changes, and that again needs to be represented relative to a chosen temporal scale in the model (and finally the simulation). We discuss this with the help of birth-death processes and the dynamics of Markov chains, and describe the dynamics of ion channels in a typical membrane with the help of multi-scale analysis.

Dr. F. J. Romero-Campero
title: A Multiscale Modelling Framework Based On P Systems
abstract: Cellular systems present a highly complex organisation at different scales including the molecular, cellular and colony levels. The complexity at each one of these levels is tighly interrelated to each other. Integrative systems biology aims to obtain a deeper understanding of cellular systems by focusing on the systemic integration of the different levels of organisation in cellular systems.
The different approaches in celluar modelling within systems biology have been classified into mathematical and computational frameworks. Specifically, the methodology to develop computational models has been recently called executable biology since it produces executable algorithms whose computations resemble the evolution of cellular systems.
In this work we present P systems as a multiscale modelling framework within executable biology. P system models explicitly specify the molecular, cellular and colony levels in cellular systems in a relevant and understandable manner. Molecular species and their structure are represented by objects or strings, compartmentalisation is described using membrane structures and finally cellular colonies and tissues are modelled as a collection of interacting individual P systems. The interactions between the components of cellular systems are described using rewriting rules. These rules can in turn be grouped together into modules to characterise specific cellular processes.
One of our current research lines focuses on the design of cell systems biology models exhibiting a prefixed behaviour by assembling automatically these cellular modules. Our approach is equally applicable to systems as well as synthetic biology.

Prof. S. Wolfram
title:The View from A New Kind of Science
abstract: to be defined