CMSB

Process algebras were originally designed for modelling concurrent computations. Over the last decade, computer scientists have explored their application to modelling bio-molecular processes, with considerable success. A predominant abstraction is ...

It is a commonly held view that life's inherent complexity renders its construction futile. The simplest known microorganisms possess hundreds of apparently essential genes, many of which provide unknown functionality. For this and other reasons, ...

Signaling and regulatory pathways coordinate multiple cellular functions in response to environmental variations. Discovering the pathways governing functionally specific responses is essential for understanding of biological systems. It aims at ...

In recent years Systems Biology has become a rich field of study, trying to encompass all the information that has become available thanks to the new high-throughput techniques of biologists, in order to build detailed models of complex systems.

Some ...

Verifying that a computational model implements the conceptual model of some dynamic biological phenomena is an important yet non-trivial task. In this paper, we discuss a variety of steps that contribute to this verification process, using the Bio-PEPA ...

In this paper we describe a method and an associated computational tool to modify and piecewise enlarge the topology of a biological network model, using a set of biochemical components, in order to generate one or more models whose behaviours simulate ...

This paper presents a generic abstract machine for simulating a broad range of process calculi with an arbitrary reaction-based simulation algorithm. The abstract machine is instantiated to a particular calculus by defining two functions: one for ...

We present a numerical approximation technique for the analysis of continuous-time Markov chains that describe networks of biochemical reactions and play an important role in the stochastic modeling of biological systems. Our approach is based on the ...

To incorporate instant effects and different timescales within a single biological system, an extension of discrete regulatory networks with short-term stimuli is proposed. By maintaining a vector of recent changes, activities initiated by a steep ...

Boolean modeling frameworks have long since proved their worth for capturing and analyzing essential characteristics of complex systems. Hybrid approaches aim at exploiting the advantages of Boolean formalisms while refining expressiveness. In this ...

A signalling network is a network of reactions that govern how a cell responds to its environment. A pathway is a dynamic flow of "signal" through the network (signal transduction), for example from a receptor to a transcription factor that enables ...

Stochastic models are becoming increasingly popular in Systems Biology. They are compulsory, if the stochastic noise is crucial for the behavioural properties to be investigated. Thus, substantial effort has been made to develop appropriate and ...

We propose a local search algorithm for structural identification of Generalized Mass Action (GMA) models from time course data. The algorithm has been implemented as part of our existing system for identification of dynamical systems.

We compare this ...