A compositional approach to performance modelling
A compositional approach to performance modelling
Information Processing Letters
Verifying Continuous Time Markov Chains
CAV '96 Proceedings of the 8th International Conference on Computer Aided Verification
Theoretical Computer Science - Special issue: Computational systems biology
BioAmbients: an abstraction for biological compartments
Theoretical Computer Science - Special issue: Computational systems biology
Biological Transactions for Quantitative Models
Electronic Notes in Theoretical Computer Science (ENTCS)
A Simple Calculus for Proteins and Cells
Electronic Notes in Theoretical Computer Science (ENTCS)
Probabilistic model checking of complex biological pathways
Theoretical Computer Science
Bio-PEPA: An Extension of the Process Algebra PEPA for Biochemical Networks
Electronic Notes in Theoretical Computer Science (ENTCS)
Modelling and simulation of biological processes in BlenX
ACM SIGMETRICS Performance Evaluation Review
Relating continuous and discrete PEPA models of signalling pathways
Theoretical Computer Science
Modelling Biological Compartments in Bio-PEPA
Electronic Notes in Theoretical Computer Science (ENTCS)
The BlenX Language with Biological Transactions
Transactions on Computational Systems Biology IX
Some Investigations Concerning the CTMC and the ODE Model Derived From Bio-PEPA
Electronic Notes in Theoretical Computer Science (ENTCS)
Scalable simulation of cellular signaling networks
APLAS'07 Proceedings of the 5th Asian conference on Programming languages and systems
The BlenX language: a tutorial
SFM'08 Proceedings of the Formal methods for the design of computer, communication, and software systems 8th international conference on Formal methods for computational systems biology
CMSB'06 Proceedings of the 2006 international conference on Computational Methods in Systems Biology
Analysis of signalling pathways using continuous time markov chains
Transactions on Computational Systems Biology VI
Modeling kohn interaction maps with beta-binders: an example
Transactions on Computational Systems Biology III
Beta binders for biological interactions
CMSB'04 Proceedings of the 20 international conference on Computational Methods in Systems Biology
Transactions on Computational Systems Biology VII
Gene regulation in the pi calculus: simulating cooperativity at the lambda switch
Transactions on Computational Systems Biology VII
Rule-based modelling of cellular signalling
CONCUR'07 Proceedings of the 18th international conference on Concurrency Theory
External Control in Process Algebra for Systems Biology
Electronic Notes in Theoretical Computer Science (ENTCS)
Stochastic Calculus of Looping Sequences for the Modelling and Simulation of Cellular Pathways
Transactions on Computational Systems Biology IX
Stochastic biological modelling in the presence of multiple compartments
Theoretical Computer Science
CMSB '09 Proceedings of the 7th International Conference on Computational Methods in Systems Biology
Equivalence and Discretisation in Bio-PEPA
CMSB '09 Proceedings of the 7th International Conference on Computational Methods in Systems Biology
Formalisms for Specifying Markovian Population Models
RP '09 Proceedings of the 3rd International Workshop on Reachability Problems
From Biochemistry to Stochastic Processes
Electronic Notes in Theoretical Computer Science (ENTCS)
Bio-PEPA for Epidemiological Models
Electronic Notes in Theoretical Computer Science (ENTCS)
From species to pathway and tissue as process
Proceedings of the 8th International Conference on Computational Methods in Systems Biology
Proceedings of the 8th International Conference on Computational Methods in Systems Biology
A generic abstract machine for stochastic process calculi
Proceedings of the 8th International Conference on Computational Methods in Systems Biology
Action-based analysis of discrete regulatory networks with short-term stimuli
Proceedings of the 8th International Conference on Computational Methods in Systems Biology
Process Algebra with Hooks for Models of Pattern Formation
Electronic Notes in Theoretical Computer Science (ENTCS)
Relating PDEs in Cylindrical Coordinates and CTMCs with Levels of Concentration
Electronic Notes in Theoretical Computer Science (ENTCS)
Modular Verification of Interactive Systems with an Application to Biology
Electronic Notes in Theoretical Computer Science (ENTCS)
A semantic equivalence for Bio-PEPA based on discretisation of continuous values
Theoretical Computer Science
Modelling non-linear crowd dynamics in bio-PEPA
FASE'11/ETAPS'11 Proceedings of the 14th international conference on Fundamental approaches to software engineering: part of the joint European conferences on theory and practice of software
Rule-based modeling of transcriptional attenuation at the tryptophan operon
Winter Simulation Conference
Design and development of software tools for Bio-PEPA
Winter Simulation Conference
Transactions on computational systems biology XIII
Refining dynamics of gene regulatory networks in a stochastic π-calculus framework
Transactions on computational systems biology XIII
Multi-scale modelling of biological systems in process algebra with multi-way synchronisation
Proceedings of the 9th International Conference on Computational Methods in Systems Biology
Equivalences for a biological process algebra
Theoretical Computer Science
On fluidization of discrete event models: observation and control of continuous Petri nets
Discrete Event Dynamic Systems
Bio-PEPAd: A non-Markovian extension of Bio-PEPA
Theoretical Computer Science
Rule-Based modeling of transcriptional attenuation at the tryptophan operon
Transactions on Computational Systems Biology XII
Modelling and analysis of the NF-κB pathway in bio-PEPA
Transactions on Computational Systems Biology XII
Foundational aspects of multiscale modeling of biological systems with process algebras
Theoretical Computer Science
Evolving Bio-PEPA process algebra models using genetic programming
Proceedings of the 14th annual conference on Genetic and evolutionary computation
Delayed continuous-time markov chains for genetic regulatory circuits
CAV'12 Proceedings of the 24th international conference on Computer Aided Verification
Fluid analysis of foraging ants
COORDINATION'12 Proceedings of the 14th international conference on Coordination Models and Languages
Analysing robot swarm decision-making with Bio-PEPA
ANTS'12 Proceedings of the 8th international conference on Swarm Intelligence
SBMF'12 Proceedings of the 15th Brazilian conference on Formal Methods: foundations and applications
CMSB'12 Proceedings of the 10th international conference on Computational Methods in Systems Biology
Modelling trafficking of proteins within the mammalian cell using Bio-PEPA
CMSB'12 Proceedings of the 10th international conference on Computational Methods in Systems Biology
A compositional approach for modeling and simulation of bio-molecular systems
Proceedings of the Winter Simulation Conference
Verification and testing of biological models
Proceedings of the Winter Simulation Conference
Multiple verification in complex biological systems: the bone remodelling case study
Transactions on Computational Systems Biology XIV
Transactions on Computational Systems Biology XIV
PCTMC models of wireless sensor network protocols
EPEW'12 Proceedings of the 9th European conference on Computer Performance Engineering
PCTMC models of wireless sensor network protocols
EPEW'12 Proceedings of the 9th European conference on Computer Performance Engineering
BioScape: A Modeling and Simulation Language for Bacteria-Materials Interactions
Electronic Notes in Theoretical Computer Science (ENTCS)
A Software Interface Between the Narrative Language and Bio-PEPA
Electronic Notes in Theoretical Computer Science (ENTCS)
Continuous approximation of collective system behaviour: A tutorial
Performance Evaluation
Simulating Anti-adhesive and Antibacterial Bifunctional Polymers for Surface Coating using BioScape
Proceedings of the International Conference on Bioinformatics, Computational Biology and Biomedical Informatics
Stochastic Modelling of the Kai-based Circadian Clock
Electronic Notes in Theoretical Computer Science (ENTCS)
Conservation of Mass Analysis for Bio-PEPA
Electronic Notes in Theoretical Computer Science (ENTCS)
Markov Chain Simulation with Fewer Random Samples
Electronic Notes in Theoretical Computer Science (ENTCS)
Electronic Notes in Theoretical Computer Science (ENTCS)
Computational and mathematical models of the JAK-STAT signal transduction pathway
Proceedings of the 2013 Summer Computer Simulation Conference
General patterns of interaction in stochastic fusion
Natural Computing: an international journal
Quantitative reactive modeling and verification
Computer Science - Research and Development
An Algorithm for the Identification of Components in Biochemical Pathways
Electronic Notes in Theoretical Computer Science (ENTCS)
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
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In this work we present Bio-PEPA, a process algebra for the modelling and the analysis of biochemical networks. It is a modification of PEPA, originally defined for the performance analysis of computer systems, in order to handle some features of biological models, such as stoichiometry and the use of general kinetic laws. Bio-PEPA may be seen as an intermediate, formal, compositional representation of biological systems, on which different kinds of analyses can be carried out. Bio-PEPA is enriched with some notions of equivalence. Specifically, the isomorphism and strong bisimulation for PEPA have been considered and extended to our language. Finally, we show the translation of a biological model into the new language and we report some analysis results.