Statecharts: A visual formalism for complex systems
Science of Computer Programming
Animation of plant development
SIGGRAPH '93 Proceedings of the 20th annual conference on Computer graphics and interactive techniques
A compositional approach to performance modelling
A compositional approach to performance modelling
Communicating and mobile systems: the &pgr;-calculus
Communicating and mobile systems: the &pgr;-calculus
Theoretical Computer Science
Information Processing Letters
Membrane Computing: An Introduction
Membrane Computing: An Introduction
Probabilistic Abstract Interpretation and Statistical Testing
PAPM-PROBMIV '02 Proceedings of the Second Joint International Workshop on Process Algebra and Probabilistic Methods, Performance Modeling and Verification
Control Flow Analysis for the pi-calculus
CONCUR '98 Proceedings of the 9th International Conference on Concurrency Theory
CONCUR '01 Proceedings of the 12th International Conference on Concurrency Theory
Hybrid Modeling and Simulation of Biomolecular Networks
HSCC '01 Proceedings of the 4th International Workshop on Hybrid Systems: Computation and Control
Modeling Cellular Behavior with Hybrid Automata: Bisimulation and Collapsing
CMSB '03 Proceedings of the First International Workshop on Computational Methods in Systems Biology
Abstract interpretation of mobile ambients
Science of Computer Programming - Special issue on static analysis (SAS'99)
Static analysis for systems biology
WISICT '04 Proceedings of the winter international synposium on Information and communication technologies
Probabilistic symbolic model checking with PRISM: a hybrid approach
International Journal on Software Tools for Technology Transfer (STTT) - Special section on tools and algorithms for the construction and analysis of systems
Theoretical Computer Science - Special issue: Computational systems biology
Modelling biochemical pathways through enhanced π-calculus
Theoretical Computer Science - Special issue: Computational systems biology
BioAmbients: an abstraction for biological compartments
Theoretical Computer Science - Special issue: Computational systems biology
Proceedings of the 38th conference on Winter simulation
Concurrency in Biological Modeling: Behavior, Execution and Visualization
Electronic Notes in Theoretical Computer Science (ENTCS)
A&A for modelling and engineering simulations in Systems Biology
International Journal of Agent-Oriented Software Engineering
Natural Computing: A Natural and Timely Trend for Natural Sciences and Science of Computation
CiE '07 Proceedings of the 3rd conference on Computability in Europe: Computation and Logic in the Real World
Generic Reactive Animation: Realistic Modeling of Complex Natural Systems
FMSB '08 Proceedings of the 1st international workshop on Formal Methods in Systems Biology
Modelling Intracellular Fate of FGF Receptors With BioAmbients
Electronic Notes in Theoretical Computer Science (ENTCS)
Crafting game-models using reactive system design
Future Play '08 Proceedings of the 2008 Conference on Future Play: Research, Play, Share
Information and Computation
A Bayesian Approach to Model Checking Biological Systems
CMSB '09 Proceedings of the 7th International Conference on Computational Methods 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
Modeling Biology using Generic Reactive Animation
Fundamenta Informaticae - From Mathematical Beauty to the Truth of Nature: to Jerzy Tiuryn on his 60th Birthday
Communications of the ACM
Graph-theoretic formalization of hybridization in DNA sticker complexes
DNA'11 Proceedings of the 17th international conference on DNA computing and molecular programming
Computational biology: a programming perspective
Formal modeling
A multi-agent system for modelling carbohydrate oxidation in cell
ICCSA'05 Proceedings of the 2005 international conference on Computational Science and Its Applications - Volume Part II
Modal logics for brane calculus
CMSB'06 Proceedings of the 2006 international conference on Computational Methods in Systems Biology
Simulating bacterial transcription and translation in a stochastic π calculus
Transactions on Computational Systems Biology VI
An agent-oriented conceptual framework for systems biology
Transactions on Computational Systems Biology III
Hermes: agent-based middleware for mobile computing
SFM-Moby'05 Proceedings of the 5th international conference on Formal Methods for the Design of Computer, Communication, and Software Systems: mobile computing
Graph-theoretic formalization of hybridization in DNA sticker complexes
Natural Computing: an international journal
Living cell as a universal computer
Cybernetics and Systems Analysis
Quantitative reactive modeling and verification
Computer Science - Research and Development
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Living cells are extremely well-organized autonomous systems, consisting of discrete interacting components. Key to understanding and modeling their behavior is modeling their system organization. Four distinct chemical toolkits (classes of macromolecules) have been characterized, each combinatorial in nature. Each toolkit consists of a small number of simple components that are assembled (polymerized) into complex structures that interact in rich ways. Each toolkit abstracts away from chemistry; it embodies an abstract machine with its own instruction set and its own peculiar interaction model. These interaction models are highly effective, but are not ones commonly used in computing: proteins stick together, genes have fixed output, membranes carry activity on their surfaces. Biologists have invented a number of notations attempting to describe these abstract machines and the processes they implement. Moving up from molecular biology, systems biology aims to understand how these interaction models work, separately and together.