Stronger computational modelling of signalling pathways using both continuous and discrete-state methods

Starting from a biochemical signalling pathway model expresses in a process algebra enriched with quantitative information, we automatically derive both continuous-space and discrete-space representations suitable for numerical evaluation. We compare results obtained using approximate stochastic simulation thereby exposing a flaw in the use of the differentiation procedure producing misleading results

Computational and Mathematical Modelling of the EGF Receptor System

This chapter gives an overview of computational and mathematical modelling of the EGF receptor system. It begins with a survey of motivations for producing such models, then describes the main approaches that are taken to carrying out such modelling, viz. differential equations and individual-based modelling. Finally, a number of projects that applying modelling and simulation techniques to various aspects of the EGF receptor system are described

A logic of behaviour in context

AbstractWe present a novel temporal logic for expressing properties of behaviour in context. The logic is applied to models of continuous processes, specifically using the continuous π-calculus as a modelling language for biochemical systems.The logic allows the expression of the temporal behaviour of a system when placed in the context of another system. Here we study this in terms of biochemical reactions and the expression of temporal behaviour in the context of other biochemical processes. We present the syntax and semantics of the logic and study the model-checking problem over continuous time and continuous state-space process models, using the continuous π-calculus.We present a succinct, but naive, model-checking algorithm and then show how this can be improved. We investigate the complexity of model-checking, where repeated ODE solving emerges as a particular cost; assess some limitations of the technique; and identify potential routes to overcome these

BioSilicoSystems - A Multipronged Approach Towards Analysis and Representation of Biological Data (PhD Thesis)

The rising field of integrative bioinformatics provides the vital methods to integrate, manage and also to analyze the diverse data and allows gaining new and deeper insights and a clear understanding of the intricate biological systems. The difficulty is not only to facilitate the study of heterogeneous data within the biological context, but it also more fundamental, how to represent and make the available knowledge accessible. Moreover, adding valuable information and functions that persuade the user to discover the interesting relations hidden within the data is, in itself, a great challenge. Also, the cumulative information can provide greater biological insight than is possible with individual information sources. Furthermore, the rapidly growing number of databases and data types poses the challenge of integrating the heterogeneous data types, especially in biology. This rapid increase in the volume and number of data resources drive for providing polymorphic views of the same data and often overlap in multiple resources. 

In this thesis a multi-pronged approach is proposed that deals with various methods for the analysis and representation of the diverse biological data which are present in different data sources. This is an effort to explain and emphasize on different concepts which are developed for the analysis of molecular data and also to explain its biological significance. The hypotheses proposed are in context with various other results and findings published in the past. The approach demonstrated also explains different ways to integrate the molecular data from various sources along with the need for a comprehensive understanding and clear projection of the concept or the algorithm and its results, but with simple means and methods. The multifarious approach proposed in this work comprises of different tools or methods spanning significant areas of bioinformatics research such as data integration, data visualization, biological network construction / reconstruction and alignment of biological pathways. Each tool deals with a unique approach to utilize the molecular data for different areas of biological research and is built based on the kernel of the thesis. Furthermore these methods are combined with graphical representation that make things simple and comprehensible and also helps to understand with ease the underlying biological complexity. Moreover the human eye is often used to and it is more comfortable with the visual representation of the facts

Predicting software performance in symmetric multi-core and multiprocessor Environments

With today\u27s rise of multi-core processors, concurrency becomes a ubiquitous challenge in software development.Performance prediction methods have to reflect the influence of multiprocessing environments on software performance in order to help software architects to find potential performance problems during early development phases. In this thesis, we address the influence of the operating system scheduler on software performance in symmetric multiprocessing environments

Modulation of the Mitogen Activated Protein Kinase Pathway Spatiotemporal Signalling Components: Influence on Pathway Activation Behaviour Using an Agent Based Model

The subtleties of how the Mitogen Activated Protein Kinase works (MAPK) biochemical signalling pathway works, its emergent oscillatory behaviour and sensitivity is explained though an analysis of a computational agent based model that takes into account the distribution of the MAPK cascade components into multiple compartment