Formal Methods for Performance Evaluation
7th International School on Formal Methods for the Design of Computer, Communication, and Software Systems, SFM 2007, Bertinoro, Italy, May 28-June 2, 2007, Advanced Lectures
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61 Result(s)
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Chapter and Conference Paper
Formal Methods for Checking the Consistency of Biological Models
Formal modeling approaches such as process algebras and Petri nets seek to provide insight into biological processes by using both symbolic and numerical methods to reveal the dynamics of the process under stu...
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Chapter and Conference Paper
Fluid Model Checking
In this paper we investigate a potential use of fluid approximation techniques in the context of stochastic model checking of CSL formulae. We focus on properties describing the behaviour of a single agent in ...
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Chapter and Conference Paper
Modelling Non-linear Crowd Dynamics in Bio-PEPA
Emergent phenomena occur due to the pattern of non-linear and distributed local interactions between the elements of a system over time. Surprisingly, agent based crowd models, in which the movement of each in...
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Chapter
Translation from the Quantified Implicit Process Flow Abstraction in SBGN-PD Diagrams to Bio-PEPA Illustrated on the Cholesterol Pathway
For a long time biologists have used visual representations of biochemical networks to gain a quick overview of important structural properties. Recently SBGN, the Systems Biology Graphical Notation, has been ...
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Chapter and Conference Paper
Structural Analysis for Stochastic Process Algebra Models
Stochastic process algebra models have been successfully used in the area of performance modelling for the last twenty years, and more recently have been adopted for modelling biochemical processes in systems ...
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Article
A Reservation Optimised Advance Resource Reservation Scheme for Deploying RSVP in Mobile Environments
One of the major problems of deploying Resource ReSerVation Protocol (RSVP) in mobile environments is called the advance resource reservation (ARR) problem. Conventional solutions to this problem waste too man...
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Chapter and Conference Paper
Process Algebras for Collective Dynamics
Stochastic process algebras extend classical process algebras such as CCS [1] and CSP [2] with quantified notions of time and probability. Examples include PEPA [3], EMPA [4], MoDeST [5] and IMC [6]. These for...
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Chapter
Modelling and Analysis of the NF-κB Pathway in Bio-PEPA
In this work we present a Bio-PEPA model describing the Nuclear Factor κB (NF-κB) signalling pathway. In particular our model focuses on the dynamic response of NF-κB to an external stimulus. Each biochemical spe...
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Chapter
Formal Methods for Biochemical Signalling Pathways
We apply quantitative formal methods to a domain from the life sciences: biochemical signalling pathways. The key idea is to model pathways as stochastic continuous time distributed systems. Components of the ...
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Chapter
Deriving Differential Equations from Process Algebra Models in Reagent-Centric Style
The reagent-centric style of modeling allows stochastic process algebra models of biochemical signaling pathways to be developed in an intuitive way. Furthermore, once constructed, the models are amenable to anal...
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Chapter and Conference Paper
Equivalence and Discretisation in Bio-PEPA
Bio-PEPA is a process algebra for modelling biological systems. An important aspect of Bio-PEPA is the ability it provides to discretise concentrations resulting in a smaller, more manageable state space. The ...
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Chapter
Process Algebra Modelling Styles for Biomolecular Processes
We investigate how biomolecular processes are modelled in process algebras, focussing on chemical reactions. We consider various modelling styles and how design decisions made in the definition of the process ...
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Chapter and Conference Paper
HYPE: A Process Algebra for Compositional Flows and Emergent Behaviour
Several process algebras for modelling hybrid systems have appeared in the literature in recent years. These all assume that continuous variables in the system are modelled monolithically, often with the diffe...
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Article
Performance Modelling of Content Adaptation for a Personal Distributed Environment
In the new era of wireless, mobile connectivity the possibilities of anything, anytime, anywhere access are becoming a reality. In order to deliver services and content to users in a variety of contexts, content ...
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Article
Computational models in systems biology
A report of the 6th International Conference on Computational Methods in Systems Biology, Rostock, Germany, 12-15 October 2008.
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Chapter and Conference Paper
Integrated Analysis from Abstract Stochastic Process Algebra Models
Bio-PEPA is a novel stochastic process algebra which has been recently developed for modelling biochemical pathways [5,6]. In Bio-PEPA a reagent-centric style of modelling is adopted, and a variety of analysis...
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Chapter and Conference Paper
The Distribution of Mutational Effects on Fitness in a Simple Circadian Clock
The distribution of mutational effects on fitness (DME F ) is of fundamental importance for many questions in biology. Previously, wet-lab experiments and population genetic methods ...
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Chapter and Conference Paper
Process Algebras in Systems Biology
In this chapter we introduce process algebras, a class of formal modelling techniques developed in theoretical computer science, and discuss their use within systems biology. These formalisms have a number of ...
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Article
Formal techniques for performance analysis: blending SAN and PEPA
In this paper we consider two performance modelling techniques from the perspectives of model construction, generation of an underlying continuous time Markov process, and the potential for reduction in the Ma...
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