Selected papers of the Second Workshop on Concurrency and compositionality
Communicating and mobile systems: the &pgr;-calculus
Communicating and mobile systems: the &pgr;-calculus
Information Processing Letters
Communication and Concurrency
PI-Calculus: A Theory of Mobile Processes
PI-Calculus: A Theory of Mobile Processes
Graphs for Core Molecular Biology
CMSB '03 Proceedings of the First International Workshop on Computational Methods in Systems Biology
BioAmbients: an abstraction for biological compartments
Theoretical Computer Science - Special issue: Computational systems biology
ESOP'03 Proceedings of the 12th European conference on Programming
Developing An Hierarchical Simulator for Beta-binders
Proceedings of the 20th Workshop on Principles of Advanced and Distributed Simulation
Biological Transactions for Quantitative Models
Electronic Notes in Theoretical Computer Science (ENTCS)
Timed Concurrent Constraint Programming for Analysing Biological Systems
Electronic Notes in Theoretical Computer Science (ENTCS)
The Decidability of the Structural Congruence for Beta-binders
Electronic Notes in Theoretical Computer Science (ENTCS)
Encoding Catalytic P Systems in π@
Electronic Notes in Theoretical Computer Science (ENTCS)
A Static Analysis for Beta-Binders
Electronic Notes in Theoretical Computer Science (ENTCS)
Bio-PEPA: An Extension of the Process Algebra PEPA for Biochemical Networks
Electronic Notes in Theoretical Computer Science (ENTCS)
A Spatial Extension to the π Calculus
Electronic Notes in Theoretical Computer Science (ENTCS)
Efficient Stochastic Simulation of Biological Systems with Multiple Variable Volumes
Electronic Notes in Theoretical Computer Science (ENTCS)
An Automatic Translation of SBML into Beta-Binders
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
BetaWB: modelling and simulating biological processes
Proceedings of the 2007 Summer Computer Simulation Conference
Performance evaluation comes to life: quantitative methods applied to biological systems
ACM SIGMETRICS Performance Evaluation Review
Modelling and simulation of biological processes in BlenX
ACM SIGMETRICS Performance Evaluation Review
On the decidability and complexity of the structural congruence for beta-binders
Theoretical Computer Science
Rule-Based Modelling, Symmetries, Refinements
FMSB '08 Proceedings of the 1st international workshop on Formal Methods in Systems Biology
FMSB '08 Proceedings of the 1st international workshop on Formal Methods in Systems Biology
On Beta-Binders Communications
Concurrency, Graphs and Models
On the Computational Power of Biochemistry
AB '08 Proceedings of the 3rd international conference on Algebraic Biology
HYPE Applied to the Modelling of Hybrid Biological Systems
Electronic Notes in Theoretical Computer Science (ENTCS)
Evolving BlenX programs to simulate the evolution of biological networks
Theoretical Computer Science
nanoK: A calculus for the modeling and simulation of nano devices
Theoretical Computer Science
Undecidability of Model Checking in Brane Logic
Electronic Notes in Theoretical Computer Science (ENTCS)
Integrated Analysis from Abstract Stochastic Process Algebra Models
CMSB '08 Proceedings of the 6th International Conference on Computational Methods in Systems Biology
A Language for Biochemical Systems
CMSB '08 Proceedings of the 6th International Conference on Computational Methods in Systems Biology
The Continuous π-Calculus: A Process Algebra for Biochemical Modelling
CMSB '08 Proceedings of the 6th International Conference on Computational Methods in Systems Biology
A Grid-Inspired Mechanism for Coarse-Grained Experiment Execution
DS-RT '08 Proceedings of the 2008 12th IEEE/ACM International Symposium on Distributed Simulation and Real-Time Applications
A Bounded-Optimistic, Parallel Beta-Binders Simulator
DS-RT '08 Proceedings of the 2008 12th IEEE/ACM International Symposium on Distributed Simulation and Real-Time Applications
Control Flow Analysis for Brane Calculi
Electronic Notes in Theoretical Computer Science (ENTCS)
Modelling Biological Compartments in Bio-PEPA
Electronic Notes in Theoretical Computer Science (ENTCS)
Transactions on Computational Systems Biology X
Stochastic Calculus of Looping Sequences for the Modelling and Simulation of Cellular Pathways
Transactions on Computational Systems Biology IX
The BlenX Language with Biological Transactions
Transactions on Computational Systems Biology IX
Spatial Calculus of Looping Sequences
Electronic Notes in Theoretical Computer Science (ENTCS)
Some Investigations Concerning the CTMC and the ODE Model Derived From Bio-PEPA
Electronic Notes in Theoretical Computer Science (ENTCS)
Approximating Probabilistic Behaviors of Biological Systems Using Abstract Interpretation
Electronic Notes in Theoretical Computer Science (ENTCS)
A Translation of Beta-binders in a Prioritized Pi-calculus
Electronic Notes in Theoretical Computer Science (ENTCS)
A Control Flow Analysis for Beta-binders with and without static compartments
Theoretical Computer Science
Bio-PEPA: A framework for the modelling and analysis of biological systems
Theoretical Computer Science
Agile Modelling of Cellular Signalling (Invited Paper)
Electronic Notes in Theoretical Computer Science (ENTCS)
MarCaSPiS: a Markovian Extension of a Calculus for Services
Electronic Notes in Theoretical Computer Science (ENTCS)
BlenX Static and Dynamic Semantics
CONCUR 2009 Proceedings of the 20th International Conference on Concurrency Theory
BlenX4Bio --- BlenX for Biologists
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
Exploiting non-Markovian Bio-Processes
Electronic Notes in Theoretical Computer Science (ENTCS)
Discrete Semantics for Hybrid Automata
Discrete Event Dynamic Systems
On the computational power of BlenX
Theoretical Computer Science
Rule-based programming for integrative biological modeling
Natural Computing: an international journal
A computational framework for modelling multicellular biochemistry
CEC'09 Proceedings of the Eleventh conference on Congress on Evolutionary Computation
Biomolecular Agents as Multi-behavioural Concurrent Objects
Electronic Notes in Theoretical Computer Science (ENTCS)
Bio-PEPA for Epidemiological Models
Electronic Notes in Theoretical Computer Science (ENTCS)
A core calculus for a comparative analysis of bio-inspired calculi
ESOP'07 Proceedings of the 16th European conference on Programming
A stochastic pi calculus for concurrent objects
AB'07 Proceedings of the 2nd international conference on Algebraic biology
Modeling static biological compartments with beta-binders
AB'07 Proceedings of the 2nd international conference on Algebraic biology
Deducing interactions in partially unspecified biological systems
AB'07 Proceedings of the 2nd international conference on Algebraic biology
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
The calculus of looping sequences for modeling biological membranes
WMC'07 Proceedings of the 8th international conference on Membrane computing
WMC'07 Proceedings of the 8th international conference on Membrane computing
Scalable simulation of cellular signaling networks
APLAS'07 Proceedings of the 5th Asian conference on Programming languages and systems
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
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
The calculus of looping sequences
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
Abstract interpretation of cellular signalling networks
VMCAI'08 Proceedings of the 9th international conference on Verification, model checking, and abstract interpretation
Computational thinking in biology
Transactions on computational systems biology VIII
A flexible architecture for performance experiments with the pi-Calculus and its extensions
Proceedings of the 3rd International ICST Conference on Simulation Tools and Techniques
Abstract interpretation based verification of temporal properties for BioAmbients
Information and Computation
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)
A semantic equivalence for Bio-PEPA based on discretisation of continuous values
Theoretical Computer Science
Large scale agent-based modeling of the humoral and cellular immune response
ICARIS'11 Proceedings of the 10th international conference on Artificial immune systems
Adapting rule-based model descriptions for simulating in continuous and hybrid space
Proceedings of the 9th International Conference on Computational Methods in Systems Biology
Osteoporosis: a multiscale modeling viewpoint
Proceedings of the 9th International Conference on Computational Methods in Systems Biology
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
Spatial Calculus of Looping Sequences
Theoretical Computer Science
Equivalences for a biological process algebra
Theoretical Computer Science
Some notes on (mem)brane computation
PPSN'06 Proceedings of the 9th international conference on Parallel Problem Solving from Nature
A new occurrence counting analysis for bioambients
APLAS'05 Proceedings of the Third Asian conference on Programming Languages and Systems
A formal approach to molecular docking
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
Bisimulation congruences in the calculus of looping sequences
ICTAC'06 Proceedings of the Third international conference on Theoretical Aspects of Computing
Modeling kohn interaction maps with beta-binders: an example
Transactions on Computational Systems Biology III
Operational patterns in beta-binders
Transactions on Computational Systems Biology I
A language for biochemical systems: design and formal specification
Transactions on Computational Systems Biology XII
Modelling and analysis of the NF-κB pathway in bio-PEPA
Transactions on Computational Systems Biology XII
An analysis for proving temporal properties of biological systems
APLAS'06 Proceedings of the 4th Asian conference on Programming Languages and Systems
Simulation of kohn's molecular interaction maps through translation into stochastic CLS+
PSI'09 Proceedings of the 7th international Andrei Ershov Memorial conference on Perspectives of Systems Informatics
Typed stochastic semantics for the calculus of looping sequences
Theoretical Computer Science
Control Flow Analysis of Generalised Boolean Networks
Electronic Notes in Theoretical Computer Science (ENTCS)
Electronic Notes in Theoretical Computer Science (ENTCS)
Multilevel Computational Modeling and Quantitative Analysis of Bone Remodeling
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
A stochastic semantics for bioambients
PaCT'07 Proceedings of the 9th international conference on Parallel Computing Technologies
Rule-based modelling of cellular signalling
CONCUR'07 Proceedings of the 18th international conference on Concurrency Theory
An analysis for proving probabilistic termination of biological systems
Theoretical Computer Science
A compositional approach for modeling and simulation of bio-molecular systems
Proceedings of the Winter Simulation Conference
Spatial modeling in cell biology at multiple levels
Proceedings of the Winter Simulation Conference
Complex functional rates in rule-based languages for biochemistry
Transactions on Computational Systems Biology XIV
Complex Functional Rates in the Modeling of Nano Devices (Extended Abstract)
Electronic Notes in Theoretical Computer Science (ENTCS)
An Analysis for Causal Properties of Membrane Interactions
Electronic Notes in Theoretical Computer Science (ENTCS)
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This paper presents binders and operators, in the process calculi tradition, to reason about biological interactions. Special binders are added to wrap a process just as membranes enclose some living matter and hence to mimick biological interfaces. A few operators are then added to the pi-calculus kernel to describe the dynamics of those interfaces.