Statecharts: A visual formalism for complex systems
Science of Computer Programming
Communicating and mobile systems: the &pgr;-calculus
Communicating and mobile systems: the &pgr;-calculus
An open graph visualization system and its applications to software engineering
Software—Practice & Experience - Special issue on discrete algorithm engineering
Information Processing Letters
PI-Calculus: A Theory of Mobile Processes
PI-Calculus: A Theory of Mobile Processes
Pi-Nets: A Graphical Form of pi-Calculus
ESOP '94 Proceedings of the 5th European Symposium on Programming: Programming Languages and Systems
History-dependent automata: an introduction
SFM-Moby'05 Proceedings of the 5th international conference on Formal Methods for the Design of Computer, Communication, and Software Systems: mobile computing
A compositional approach to the stochastic dynamics of gene networks
Transactions on Computational Systems Biology IV
A Chart Semantics for the Pi-Calculus
Electronic Notes in Theoretical Computer Science (ENTCS)
The crucial role of CS in systems and synthetic biology
Communications of the ACM - Web searching in a multilingual world
A Process Model of Rho GTP-binding Proteins in the Context of Phagocytosis
Electronic Notes in Theoretical Computer Science (ENTCS)
Performance evaluation comes to life: quantitative methods applied to biological systems
ACM SIGMETRICS Performance Evaluation Review
Theoretical Computer Science
External Control in Process Algebra for Systems Biology
Electronic Notes in Theoretical Computer Science (ENTCS)
A process model of Rho GTP-binding proteins
Theoretical Computer Science
Using genetic programming to synthesize monotonic stochastic processes
CI '07 Proceedings of the Third IASTED International Conference on Computational Intelligence
Parameter Tuning of a Stochastic Biological Simulator by Metaheuristics
AI*IA '09: Proceedings of the XIth International Conference of the Italian Association for Artificial Intelligence Reggio Emilia on Emergent Perspectives in Artificial Intelligence
Stochastic simulation of biological systems with dynamical compartment structure
CMSB'07 Proceedings of the 2007 international conference on Computational methods in systems biology
A formal and integrated framework to simulate evolution of biological pathways
CMSB'07 Proceedings of the 2007 international conference on Computational methods in systems biology
Efficient, correct simulation of biological processes in the stochastic pi-calculus
CMSB'07 Proceedings of the 2007 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
Visual analytics for stochastic simulation in cell biology
i-KNOW '11 Proceedings of the 11th International Conference on Knowledge Management and Knowledge Technologies
Large scale agent-based modeling of the humoral and cellular immune response
ICARIS'11 Proceedings of the 10th international conference on Artificial immune systems
A language for biochemical systems: design and formal specification
Transactions on Computational Systems Biology XII
Novel visualisation and analysis of natural and complex systems using systemic computation
Information Visualization
Hi-index | 0.00 |
This paper presents a graphical representation for the stochastic π-calculus, which is formalised by defining a corresponding graphical calculus. The graphical calculus is shown to be reduction equivalent to stochastic π, ensuring that the two calculi have the same expressive power. The graphical representation is used to model a couple of example biological systems, namely a bistable gene network and a mapk signalling cascade. One of the benefits of the representation is its ability to highlight the existence of cycles, which are a key feature of biological systems. Another benefit is its ability to animate interactions between system components, in order to visualise system dynamics. The graphical representation can also be used as a front end to a simulator for the stochastic π-calculus, to help make modelling and simulation of biological systems more accessible to non computer scientists.