Bio-PEPA: A framework for the modelling and analysis of biological systems
From MaRDI portal
Publication:2271444
DOI10.1016/j.tcs.2009.02.037zbMath1173.68041OpenAlexW1983350265MaRDI QIDQ2271444
Federica Ciocchetta, Jane Hillston
Publication date: 7 August 2009
Published in: Theoretical Computer Science (Search for Journal in Brave)
Full work available at URL: https://doi.org/10.1016/j.tcs.2009.02.037
Biochemistry, molecular biology (92C40) Models and methods for concurrent and distributed computing (process algebras, bisimulation, transition nets, etc.) (68Q85) General biology and biomathematics (92B05)
Related Items (59)
Modelling and analysing neural networks using a hybrid process algebra ⋮ Targeting Bayes factors with direct-path non-equilibrium thermodynamic integration ⋮ General patterns of interaction in stochastic fusion ⋮ An algorithm for the identification of components in biochemical pathways ⋮ Model Checking Probabilistic Systems ⋮ Model Checking of Biological Systems ⋮ Modelling of DNA mismatch repair with a reversible process calculus ⋮ A Declarative View of Signaling Pathways ⋮ Fundamental results on the reactionâdiffusion equations associated with a PEPA model ⋮ Applying Mean-Field Approximation to Continuous Time Markov Chains ⋮ On Quantitative Modelling and Verification of DNA Walker Circuits Using Stochastic Petri Nets ⋮ A process algebra framework for multi-scale modelling of biological systems ⋮ Differential Bisimulation for a Markovian Process Algebra ⋮ A collective interpretation semantics for reversing Petri nets ⋮ Process calculi for biological processes ⋮ A general overview of formal languages for individual-based modelling of ecosystems ⋮ Back to the format: a survey on SOS for probabilistic processes ⋮ Foundational aspects of multiscale modeling of biological systems with process algebras ⋮ Approximate Bayesian inference in semi-mechanistic models ⋮ Statistical inference of regulatory networks for circadian regulation ⋮ Equivalences for a biological process algebra ⋮ On reaction-diffusion equations derived from a PEPA model ⋮ Algebra, Coalgebra, and Minimization in Polynomial Differential Equations ⋮ Exact fluid lumpability in Markovian process algebra ⋮ Hybrid semantics for Bio-PEPA ⋮ Executable biochemical space for specification and analysis of biochemical systems ⋮ Modelling patterns of gene regulation in the bond-calculus ⋮ Refining Dynamics of Gene Regulatory Networks in a Stochastic π-Calculus Framework ⋮ Formal biochemical space with semantics in Kappa and BNGL ⋮ Some Investigations Concerning the CTMC and the ODE Model Derived From Bio-PEPA ⋮ Process Algebra with Hooks for Models of Pattern Formation ⋮ Relating PDEs in Cylindrical Coordinates and CTMCs with Levels of Concentration ⋮ Modular Verification of Interactive Systems with an Application to Biology ⋮ HYPE Applied to the Modelling of Hybrid Biological Systems ⋮ A semantic equivalence for Bio-PEPA based on discretisation of continuous values ⋮ A unified framework for differential aggregations in Markovian process algebra ⋮ Modelling Biological Compartments in Bio-PEPA ⋮ External Control in Process Algebra for Systems Biology ⋮ Bio-PEPA: A framework for the modelling and analysis of biological systems ⋮ Rule-Based Modeling of Transcriptional Attenuation at the Tryptophan Operon ⋮ Symbolic computation of differential equivalences ⋮ Fluid approximation of broadcasting systems ⋮ Bio-PEPA ⋮ Mean-Field Limits Beyond Ordinary Differential Equations ⋮ Quantitative Abstractions for Collective Adaptive Systems ⋮ Membrane automata for modeling biomolecular processes ⋮ Process Algebra Modelling Styles for Biomolecular Processes ⋮ Bio-PEPA with Events ⋮ Formalisms for Specifying Markovian Population Models ⋮ On fluidization of discrete event models: Observation and control of continuous Petri nets ⋮ Bio-PEPAd: a non-Markovian extension of Bio-PEPA ⋮ A Petri net view of covalent bonds ⋮ Inferring bi-directional interactions between circadian clock genes and metabolism with model ensembles ⋮ Unwinding biological systems ⋮ Component identification in biochemical pathways ⋮ Identification of components in biochemical pathways: extensive aqpplication to SBML models ⋮ Hybrid behaviour of Markov population models ⋮ Qualitative analysis of gene regulatory networks by temporal logic ⋮ Smoothed model checking for uncertain continuous-time Markov chains
Uses Software
Cites Work
- Modeling biological systems in stochastic concurrent constraint programming
- Relating continuous and discrete PEPA models of signalling pathways
- Evolving BlenX programs to simulate the evolution of biological networks
- Application of a stochastic name-passing calculus to representation and simulation of molecular processes
- Formal molecular biology
- BioAmbients: an abstraction for biological compartments
- Bio-PEPA: A framework for the modelling and analysis of biological systems
- Probabilistic model checking of complex biological pathways
- Biological Transactions for Quantitative Models
- A Simple Calculus for Proteins and Cells
- Stochastic Concurrent Constraint Programming and Differential Equations
- Bio-PEPA: An Extension of the Process Algebra PEPA for Biochemical Networks
- Rule-Based Modelling of Cellular Signalling
- Modelling Biological Compartments in Bio-PEPA
- The BlenX Language with Biological Transactions
- Some Investigations Concerning the CTMC and the ODE Model Derived From Bio-PEPA
- Abstract Interpretation of Cellular Signalling Networks
- Computational Methods in Systems Biology
- Transactions on Computational Systems Biology III
- Unnamed Item
This page was built for publication: Bio-PEPA: A framework for the modelling and analysis of biological systems