A compositional approach to performance modelling
A compositional approach to performance modelling
Information Processing Letters
BioAmbients: an abstraction for biological compartments
Theoretical Computer Science - Special issue: Computational systems biology
CMSB'06 Proceedings of the 2006 international conference on Computational Methods in Systems Biology
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
Performance evaluation comes to life: quantitative methods applied to biological systems
ACM SIGMETRICS Performance Evaluation Review
On the Relevance of Cellular Signaling Pathways for Immune-Inspired Algorithms
ICARIS '08 Proceedings of the 7th international conference on Artificial Immune Systems
A Ticking Clock: Performance Analysis of a Circadian Rhythm with Stochastic Process Algebra
EPEW '08 Proceedings of the 5th European Performance Engineering Workshop on Computer Performance Engineering
nanoK: A calculus for the modeling and simulation of nano devices
Theoretical Computer Science
Integrated Analysis from Abstract Stochastic Process Algebra Models
CMSB '08 Proceedings of the 6th International Conference on Computational Methods in Systems Biology
CMSB '08 Proceedings of the 6th International Conference on Computational Methods in Systems Biology
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)
Analysing Biochemical Oscillation through Probabilistic Model Checking
Electronic Notes in Theoretical Computer Science (ENTCS)
Integrated Simulation and Model-Checking for the Analysis of Biochemical Systems
Electronic Notes in Theoretical Computer Science (ENTCS)
Stochastic biological modelling in the presence of multiple compartments
Theoretical Computer Science
Bio-PEPA: A framework for the modelling and analysis of biological systems
Theoretical Computer Science
Categories of Timed Stochastic Relations
Electronic Notes in Theoretical Computer Science (ENTCS)
CMSB '09 Proceedings of the 7th International Conference on Computational Methods in Systems Biology
Dynamic Compartments in the Imperative Π-Calculus
CMSB '09 Proceedings of the 7th International Conference on Computational Methods in Systems Biology
Process algebras in systems biology
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
Conceptional modeling and analysis of spatio-temporal processes in biomolecular systems
APCCM '09 Proceedings of the Sixth Asia-Pacific Conference on Conceptual Modeling - Volume 96
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
Design and development of software tools for Bio-PEPA
Winter Simulation Conference
Computational biology: a programming perspective
Formal modeling
The attributed pi-calculus with priorities
Transactions on Computational Systems Biology XII
A language for biochemical systems: design and formal specification
Transactions on Computational Systems Biology XII
Simulation techniques for the calculus of wrapped compartments
Theoretical Computer Science
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
Spatial modeling in cell biology at multiple levels
Proceedings of the Winter Simulation Conference
Survival vs. revenue: modelling and reasoning on population dynamics (WIP)
Proceedings of the Symposium on Theory of Modeling & Simulation - DEVS Integrative M&S Symposium
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In this work we introduce Bio-PEPA, a process algebra for the modelling and the analysis of biochemical networks. It is a modification of PEPA to deal with some features of biological models, such as stoichiometry and the use of generic kinetic laws. Bio-PEPA may be seen as an intermediate, formal, compositional representation of biological systems, on which different kinds of analysis can be carried out. Finally, we show a representation of a model, concerning a simple genetic network, in the new language.