Application of a stochastic name-passing calculus to representation and simulation of molecular processes
From MaRDI portal
Publication:1607114
DOI10.1016/S0020-0190(01)00214-9zbMath0997.92018WikidataQ56764378 ScholiaQ56764378MaRDI QIDQ1607114
Aviv Regev, William Silverman, Ehud Shapiro, Corrado Priami
Publication date: 25 July 2002
Published in: Information Processing Letters (Search for Journal in Brave)
Computing methodologies and applications (68U99) Kinetics in biochemical problems (pharmacokinetics, enzyme kinetics, etc.) (92C45) Biochemistry, molecular biology (92C40) Models and methods for concurrent and distributed computing (process algebras, bisimulation, transition nets, etc.) (68Q85)
Related Items
Formal molecular biology ⋮ Modelling biochemical pathways through enhanced \(\pi\)-calculus ⋮ BioAmbients: an abstraction for biological compartments ⋮ Modelling of DNA mismatch repair with a reversible process calculus ⋮ Flexible nets: a modeling formalism for dynamic systems with uncertain parameters ⋮ Structural operational semantics for stochastic and weighted transition systems ⋮ A process algebra framework for multi-scale modelling of biological systems ⋮ Modeling individual's aging within a bacterial population using a pi-calculus paradigm ⋮ A Computationally Fast and Parametric Model to Estimate Protein-Ligand Docking Time for Stochastic Event Based Simulation ⋮ Bounded Asynchrony: Concurrency for Modeling Cell-Cell Interactions ⋮ Communicating by compatibility ⋮ Simulation techniques for the calculus of wrapped compartments ⋮ Foundational aspects of multiscale modeling of biological systems with process algebras ⋮ Typed stochastic semantics for the calculus of looping sequences ⋮ Stochastic simulation of multiple process calculi for biology ⋮ Spatial calculus of looping sequences ⋮ Equivalences for a biological process algebra ⋮ Constructing and visualizing chemical reaction networks from pi-calculus models ⋮ Immune Systems and Computation: An Interdisciplinary Adventure ⋮ Hybrid semantics for Bio-PEPA ⋮ Modelling patterns of gene regulation in the bond-calculus ⋮ Turing universality of the Biochemical Ground Form ⋮ Refining Dynamics of Gene Regulatory Networks in a Stochastic π-Calculus Framework ⋮ Modeling biological systems in stochastic concurrent constraint programming ⋮ Brane Calculi ⋮ Stochastic transcription elongation via rule based modelling ⋮ Spatial Calculus of Looping Sequences ⋮ The Importance of Being (A Little Bit) Discrete ⋮ A Process Model of Actin Polymerisation ⋮ Some Investigations Concerning the CTMC and the ODE Model Derived From Bio-PEPA ⋮ Approximating Probabilistic Behaviors of Biological Systems Using Abstract Interpretation ⋮ Process Algebra with Hooks for Models of Pattern Formation ⋮ Modular Verification of Interactive Systems with an Application to Biology ⋮ Control Flow Analysis of Generalised Boolean Networks ⋮ Pathway analysis for BioAmbients ⋮ Computational self-assembly ⋮ Relating continuous and discrete PEPA models of signalling pathways ⋮ On the decidability and complexity of the structural congruence for beta-binders ⋮ On process rate semantics ⋮ Probabilistic model checking of complex biological pathways ⋮ nano\(\kappa\): A calculus for the modeling and simulation of nano devices ⋮ Evolving BlenX programs to simulate the evolution of biological networks ⋮ Multi-level modelling via stochastic multi-level multiset rewriting ⋮ HYPE Applied to the Modelling of Hybrid Biological Systems ⋮ Stochastic Bigraphs ⋮ Modelling Intracellular Fate of FGF Receptors With BioAmbients ⋮ A semantic equivalence for Bio-PEPA based on discretisation of continuous values ⋮ Hybrid dynamics of stochastic programs ⋮ Continuous valuations of temporal logic specifications with applications to parameter optimization and robustness measures ⋮ Pure bigraphs: structure and dynamics ⋮ Translating Stochastic CLS into Maude ⋮ External Control in Process Algebra for Systems Biology ⋮ Stochastic biological modelling in the presence of multiple compartments ⋮ Bio-PEPA: A framework for the modelling and analysis of biological systems ⋮ An intermediate language for the stochastic simulation of biological systems ⋮ A control flow analysis for Beta-binders with and without static compartments ⋮ A process model of Rho GTP-binding proteins ⋮ On the Computational Power of Biochemistry ⋮ A brief history of process algebra ⋮ Abstract interpretation based verification of temporal properties for BioAmbients ⋮ The Calculus of Looping Sequences for Modeling Biological Membranes ⋮ Structural Analysis for Stochastic Process Algebra Models ⋮ The Attributed Pi-Calculus with Priorities ⋮ Categories of Timed Stochastic Relations ⋮ Sustainability of RNA-interference in rule based modelling ⋮ Bio-PEPA with Events ⋮ Dynamical Systems and Stochastic Programming: To Ordinary Differential Equations and Back ⋮ Bio-PEPAd: a non-Markovian extension of Bio-PEPA ⋮ On the computational power of BlenX ⋮ Language-based performance prediction for distributed and mobile systems ⋮ Biological Transactions for Quantitative Models ⋮ The Decidability of the Structural Congruence for Beta-binders ⋮ Modelling of Biochemical Reactions by Stochastic Automata Networks ⋮ A Model in κ for DNA Addition ⋮ An Intermediate Language for the Simulation of Biological Systems ⋮ A Static Analysis for Beta-Binders ⋮ A Process Model of Rho GTP-binding Proteins in the Context of Phagocytosis ⋮ Bio-PEPA: An Extension of the Process Algebra PEPA for Biochemical Networks ⋮ Efficient Stochastic Simulation of Biological Systems with Multiple Variable Volumes ⋮ Qualitative analysis of gene regulatory networks by temporal logic
Uses Software
Cites Work
