4,996 research outputs found
Application of a stochastic name-Âpassing calculus to representation and simulation of molecular processes
We describe a novel application of a stochastic name passing calculus for the study of biomolecular systems. We specify the structure and dynamics of biochemical networks in a variant of the stochastic P-Âcalculus, yielding a model which is mathematically wellÂdefined and biologically faithful. We adapt the operational semantics of the calculus to account for both the time and probability of biochemical reactions, and present a computer implementation of the calculus for biochemical simulations
Process Calculi Abstractions for Biology
Several approaches have been proposed to model biological systems by means of the formal techniques and tools available in computer science. To mention just a few of them, some representations are inspired by Petri Nets theory, and some other by stochastic processes. A most recent approach consists in interpreting the living entities as terms of process calculi where the behavior of the represented systems can be inferred by applying syntax-driven rules. A comprehensive picture of the state of the art of the process calculi approach to biological modeling is still missing. This paper goes in the direction of providing such a picture by presenting a comparative survey of the process calculi that have been used and proposed to describe the behavior of living entities. This is the preliminary version of a paper that was published in Algorithmic Bioprocesses. The original publication is available at http://www.springer.com/computer/foundations/book/978-3-540-88868-
Formal executable descriptions of biological systems
The similarities between systems of living entities and systems of concurrent processes may support biological experiments in silico. Process calculi offer a formal framework to describe biological systems, as well as to analyse their behaviour, both from a qualitative and a quantitative point of view. A couple of little examples help us in showing how this can be done. We mainly focus our attention on the qualitative and quantitative aspects of the considered biological systems, and briefly illustrate which kinds of analysis are possible. We use a known stochastic calculus for the first example. We then present some statistics collected by repeatedly running the specification, that turn out to agree with those obtained by experiments in vivo. Our second example motivates a richer calculus. Its stochastic extension requires a non trivial machinery to faithfully reflect the real dynamic behaviour of biological systems
Analysis of signalling pathways using the prism model checker
We describe a new modelling and analysis approach for signal
transduction networks in the presence of incomplete data. We illustrate
the approach with an example, the RKIP inhibited ERK pathway
[1]. Our models are based on high level descriptions of continuous time
Markov chains: reactions are modelled as synchronous processes and concentrations
are modelled by discrete, abstract quantities. The main advantage
of our approach is that using a (continuous time) stochastic logic
and the PRISM model checker, we can perform quantitative analysis of
queries such as if a concentration reaches a certain level, will it remain at
that level thereafter? We also perform standard simulations and compare
our results with a traditional ordinary differential equation model. An
interesting result is that for the example pathway, only a small number
of discrete data values is required to render the simulations practically
indistinguishable
Cell Cycle Control in Eukaryotes: a BioSpi model
This paper presents a stochastic model of the cell cycle control in eukaryotes. The framework used is based on stochastic process algebras for mobile systems. The automatic tool used in the simulation is the BioSpi. We compare our approach with classical ODE specications
A Process Calculus for Molecular Interaction Maps
We present the MIM calculus, a modeling formalism with a strong biological
basis, which provides biologically-meaningful operators for representing the
interaction capabilities of molecular species. The operators of the calculus
are inspired by the reaction symbols used in Molecular Interaction Maps (MIMs),
a diagrammatic notation used by biologists. Models of the calculus can be
easily derived from MIM diagrams, for which an unambiguous and executable
interpretation is thus obtained. We give a formal definition of the syntax and
semantics of the MIM calculus, and we study properties of the formalism. A case
study is also presented to show the use of the calculus for modeling
biomolecular networks.Comment: 15 pages; 8 figures; To be published on EPTCS, proceedings of MeCBIC
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Computational Modeling for the Activation Cycle of G-proteins by G-protein-coupled Receptors
In this paper, we survey five different computational modeling methods. For
comparison, we use the activation cycle of G-proteins that regulate cellular
signaling events downstream of G-protein-coupled receptors (GPCRs) as a driving
example. Starting from an existing Ordinary Differential Equations (ODEs)
model, we implement the G-protein cycle in the stochastic Pi-calculus using
SPiM, as Petri-nets using Cell Illustrator, in the Kappa Language using
Cellucidate, and in Bio-PEPA using the Bio-PEPA eclipse plug in. We also
provide a high-level notation to abstract away from communication primitives
that may be unfamiliar to the average biologist, and we show how to translate
high-level programs into stochastic Pi-calculus processes and chemical
reactions.Comment: In Proceedings MeCBIC 2010, arXiv:1011.005
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 algebra have an impact on how a modelling style can be applied. Our goal is to highlight the often implicit choices that modellers make in choosing a formalism, and illustrate, through the use of examples, how this can affect expressability as well as the type and complexity of the analysis that can be performed
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