Concurrent Prolog: a progress report
Concurrent Prolog
The Logix system user manual version 1.21
Concurrent Prolog: collected papers
Communicating and mobile systems: the &pgr;-calculus
Communicating and mobile systems: the &pgr;-calculus
Information Processing Letters
Membrane Computing: An Introduction
Membrane Computing: An Introduction
Graphs for Core Molecular Biology
CMSB '03 Proceedings of the First International Workshop on Computational Methods in Systems Biology
FoSSaCS '98 Proceedings of the First International Conference on Foundations of Software Science and Computation Structure
The Immune System as a Reactive System: Modeling T Cell Activation With Statecharts
HCC '01 Proceedings of the IEEE 2001 Symposia on Human Centric Computing Languages and Environments (HCC'01)
Static analysis for systems biology
WISICT '04 Proceedings of the winter international synposium on Information and communication technologies
Modeling and querying biomolecular interaction networks
Theoretical Computer Science - Special issue: Computational systems biology
Theoretical Computer Science - Special issue: Computational systems biology
Axioms for bigraphical structure
Mathematical Structures in Computer Science
Developing An Hierarchical Simulator for Beta-binders
Proceedings of the 20th Workshop on Principles of Advanced and Distributed Simulation
WSC '05 Proceedings of the 37th conference on Winter simulation
Modeling and analysis of biological processes by mem(brane) calculi and systems
Proceedings of the 38th conference on Winter simulation
Proceedings of the 38th conference on Winter simulation
Theoretical Computer Science
Logical Analysis of Biological Systems
Fundamenta Informaticae - Contagious Creativity - In Honor of the 80th Birthday of Professor Solomon Marcus
A Calculus of Looping Sequences for Modelling Microbiological Systems
Fundamenta Informaticae - SPECIAL ISSUE ON CONCURRENCY SPECIFICATION AND PROGRAMMING (CS&P 2005) Ruciane-Nide, Poland, 28-30 September 2005
Active Evaluation Contexts for Reaction Semantics
Electronic Notes in Theoretical Computer Science (ENTCS)
What is a free name in a process algebra?
Information Processing Letters
Membrane Computing and Brane Calculi (Some Personal Notes)
Electronic Notes in Theoretical Computer Science (ENTCS)
Biological Transactions for Quantitative Models
Electronic Notes in Theoretical Computer Science (ENTCS)
On Reachability and Spatial Reachability in Fragments of BioAmbients
Electronic Notes in Theoretical Computer Science (ENTCS)
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)
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)
Information flow security in Boundary Ambients
Information and Computation
A&A for modelling and engineering simulations in Systems Biology
International Journal of Agent-Oriented Software Engineering
Performance evaluation comes to life: quantitative methods applied to biological systems
ACM SIGMETRICS Performance Evaluation Review
Expressiveness Issues in Brane Calculi: A Survey
Electronic Notes in Theoretical Computer Science (ENTCS)
Theoretical Computer Science
Membrane computing and brane calculi. Old, new, and future bridges
Theoretical Computer Science
A simple calculus for proteins and cells
Theoretical Computer Science
On the decidability and complexity of the structural congruence for beta-binders
Theoretical Computer Science
Combining Intra- and Inter-cellular Dynamics to Investigate Intestinal Homeostasis
FMSB '08 Proceedings of the 1st international workshop on Formal Methods in Systems Biology
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
Process Algebra Models of Population Dynamics
AB '08 Proceedings of the 3rd international conference on Algebraic Biology
A Biologically Inspired Model with Fusion and Clonation of Membranes
UC '08 Proceedings of the 7th international conference on Unconventional Computing
A Decentralized Implementation of Mobile Ambients
ICGT '08 Proceedings of the 4th international conference on Graph Transformations
Graph Transformation for Topology Modelling
ICGT '08 Proceedings of the 4th international conference on Graph Transformations
Electronic Notes in Theoretical Computer Science (ENTCS)
HYPE Applied to the Modelling of Hybrid Biological Systems
Electronic Notes in Theoretical Computer Science (ENTCS)
On temporal logic constraint solving for analyzing numerical data time series
Theoretical Computer Science
Synapses as stochastic concurrent systems
Theoretical Computer Science
A Language for Biochemical Systems
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
The Continuous π-Calculus: A Process Algebra for Biochemical Modelling
CMSB '08 Proceedings of the 6th International Conference on Computational Methods in Systems Biology
Flow-sensitive type systems and the ambient calculus
Higher-Order and Symbolic Computation
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
Modelling Intracellular Fate of FGF Receptors With BioAmbients
Electronic Notes in Theoretical Computer Science (ENTCS)
Modelling Biological Compartments in Bio-PEPA
Electronic Notes in Theoretical Computer Science (ENTCS)
Type Disciplines for Analysing Biologically Relevant Properties
Electronic Notes in Theoretical Computer Science (ENTCS)
An Abstract Machine for the Stochastic Bioambient calculus
Electronic Notes in Theoretical Computer Science (ENTCS)
Reachability Analysis in BioAmbients
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
The BlenX Language with Biological Transactions
Transactions on Computational Systems Biology IX
Theoretical Computer Science
Spatial Calculus of Looping Sequences
Electronic Notes in Theoretical Computer Science (ENTCS)
Improved Continuous Approximation of PEPA Models through Epidemiological Examples
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)
GridSPiM: A Framework for Simple Locality and Containment in the Stochastic π-Calculus
BICoB '09 Proceedings of the 1st International Conference on Bioinformatics and Computational Biology
Computer Languages, Systems and Structures
Rewriting Logic Specification of Membrane Systems with Promoters and Inhibitors
Electronic Notes in Theoretical Computer Science (ENTCS)
Labelled Transitions for Mobile Ambients (As Synthesized via a Graphical Encoding)
Electronic Notes in Theoretical Computer Science (ENTCS)
A Control Flow Analysis for Beta-binders with and without static compartments
Theoretical Computer Science
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
An intermediate language for the stochastic simulation of biological systems
Theoretical Computer Science
A Critical Review on Modelling Formalisms and Simulation Tools in Computational Biosystems
IWANN '09 Proceedings of the 10th International Work-Conference on Artificial Neural Networks: Part II: Distributed Computing, Artificial Intelligence, Bioinformatics, Soft Computing, and Ambient Assisted Living
A compositional theory for STM Haskell
Proceedings of the 2nd ACM SIGPLAN symposium on Haskell
A Higher-Order Graph Calculus for Autonomic Computing
Graph Theory, Computational Intelligence and Thought
The Equivalence between Biology and Computation
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
Dynamic Compartments in the Imperative Π-Calculus
CMSB '09 Proceedings of the 7th International Conference on Computational Methods in Systems Biology
CoBiC: Context-dependent Bioambient Calculus
Electronic Notes in Theoretical Computer Science (ENTCS)
On the computational power of BlenX
Theoretical Computer Science
Rule-based programming for integrative biological modeling
Natural Computing: an international journal
What Can Formal Methods Bring to Systems Biology?
FM '09 Proceedings of the 2nd World Congress on Formal Methods
Flow-sensitive Leakage Analysis in Mobile Ambients
Electronic Notes in Theoretical Computer Science (ENTCS)
Biomolecular Agents as Multi-behavioural Concurrent Objects
Electronic Notes in Theoretical Computer Science (ENTCS)
Deciding reachability problems in turing-complete fragments of mobile ambients
Mathematical Structures in Computer Science
Bio-PEPA for Epidemiological Models
Electronic Notes in Theoretical Computer Science (ENTCS)
Extending the calculus of looping sequences to model protein interaction at the domain level
ISBRA'07 Proceedings of the 3rd international conference on Bioinformatics research and applications
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
On the analysis of numerical data time series in temporal logic
CMSB'07 Proceedings of the 2007 international conference on Computational methods in systems biology
Stochastic simulation of biological systems with dynamical compartment structure
CMSB'07 Proceedings of the 2007 international conference on Computational methods in systems biology
Expressive models for synaptic plasticity
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
Scalable simulation of cellular signaling networks
APLAS'07 Proceedings of the 5th Asian conference on Programming languages and systems
Formal cell biology in biocham
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
Hierarchical modeling for computational 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
Membrane computing as a modeling framework: cellular systems case studies
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
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
π@: a π-based process calculus for the implementation of compartmentalised bio-inspired calculi
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
Model revision from temporal logic properties in computational systems biology
Probabilistic inductive logic programming
Computational thinking in biology
Transactions on computational systems biology VIII
Abstract interpretation based verification of temporal properties for BioAmbients
Information and Computation
A generic abstract machine for stochastic process calculi
Proceedings of the 8th International Conference on Computational Methods in 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
On the verification of membrane systems with dynamic structure
Natural Computing: an international journal
Process Algebra with Hooks for Models of Pattern Formation
Electronic Notes in Theoretical Computer Science (ENTCS)
Modular Verification of Interactive Systems with an Application to Biology
Electronic Notes in Theoretical Computer Science (ENTCS)
Fundamenta Informaticae - From Mathematical Beauty to the Truth of Nature: to Jerzy Tiuryn on his 60th Birthday
Mobility in computer science and in membrane systems
CMC'10 Proceedings of the 11th international conference on Membrane computing
A semantic equivalence for Bio-PEPA based on discretisation of continuous values
Theoretical Computer Science
Strand algebras for DNA computing
Natural Computing: an international journal
Biochemical reaction rules with constraints
ESOP'11/ETAPS'11 Proceedings of the 20th European conference on Programming languages and systems: part of the joint European conferences on theory and practice of software
Compartmental rule-based modeling of biochemical systems
Winter Simulation Conference
Communications of the ACM
Visual analytics for stochastic simulation in cell biology
i-KNOW '11 Proceedings of the 11th International Conference on Knowledge Management and Knowledge Technologies
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
Spatial Calculus of Looping Sequences
Theoretical Computer Science
Equivalences for a biological process algebra
Theoretical Computer Science
Flow Logic for Process Calculi
ACM Computing Surveys (CSUR)
Computational biology: a programming perspective
Formal modeling
Some notes on (mem)brane computation
PPSN'06 Proceedings of the 9th international conference on Parallel Problem Solving from Nature
Modelling coordination in biological systems
ISoLA'04 Proceedings of the First international conference on Leveraging Applications of Formal Methods
A bioambients based framework for chain-structured biomolecules modelling
CIS'04 Proceedings of the First international conference on Computational and Information Science
A case study in (mem)brane computation: generating squares of natural numbers
WMC'06 Proceedings of the 7th international conference on Membrane Computing
A new occurrence counting analysis for bioambients
APLAS'05 Proceedings of the Third Asian conference on Programming Languages and Systems
Challenges for artificial immune systems
WIRN'05 Proceedings of the 16th Italian conference on Neural Nets
Reachability analysis in boxed ambients
ICTCS'05 Proceedings of the 9th Italian conference on Theoretical Computer Science
Modeling genome evolution with a DSEL for probabilistic programming
PADL'06 Proceedings of the 8th international conference on Practical Aspects of Declarative Languages
Bio-PEPAd: A non-Markovian extension of Bio-PEPA
Theoretical Computer Science
Deciding behavioural properties in brane calculi
CMSB'06 Proceedings of the 2006 international conference on Computational Methods in Systems Biology
On the computational power of the mate/bud/drip brane calculus: interleaving vs. maximal parallelism
WMC'05 Proceedings of the 6th international conference on Membrane Computing
On the computational power of brane calculi
Transactions on Computational Systems Biology VI
Machine learning biochemical networks from temporal logic properties
Transactions on Computational Systems Biology VI
Multiple representations of biological processes
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
An agent-oriented conceptual framework for systems biology
Transactions on Computational Systems Biology III
Abstract machines of systems biology
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
Model checking biological systems described using ambient calculus
CMSB'04 Proceedings of the 20 international conference on Computational Methods in Systems Biology
CMSB'04 Proceedings of the 20 international conference on Computational Methods in Systems Biology
CMSB'04 Proceedings of the 20 international conference on Computational Methods in Systems Biology
CMSB'04 Proceedings of the 20 international conference on Computational Methods in Systems Biology
Biocomputing: an insight from linguistics
Natural Computing: an international journal
The evolution of higher-level biochemical reaction models
Genetic Programming and Evolvable Machines
Operational patterns in beta-binders
Transactions on Computational Systems Biology I
Discrete event multi-level models for systems biology
Transactions on Computational Systems Biology I
A compositional approach to the stochastic dynamics of gene networks
Transactions on Computational Systems Biology IV
AMAST'06 Proceedings of the 11th international conference on Algebraic Methodology and Software Technology
Transactions on Computational Systems Biology VII
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
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
An environment aware p-system model of quorum sensing
CiE'05 Proceedings of the First international conference on Computability in Europe: new Computational Paradigms
Stochastic simulation of multiple process calculi for biology
Theoretical Computer Science
Reachability problems in BioAmbients
Theoretical Computer Science
Simulation techniques for the calculus of wrapped compartments
Theoretical Computer Science
Foundational aspects of multiscale modeling of biological systems with process algebras
Theoretical Computer Science
Measurable stochastics for Brane Calculus
Theoretical Computer Science
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)
Coordinating parallel mobile ambients to solve SAT problem in polynomial number of steps
COORDINATION'12 Proceedings of the 14th international conference on Coordination Models and Languages
A Calculus of Looping Sequences for Modelling Microbiological Systems
Fundamenta Informaticae - SPECIAL ISSUE ON CONCURRENCY SPECIFICATION AND PROGRAMMING (CS&P 2005) Ruciane-Nide, Poland, 28-30 September 2005
Logical Analysis of Biological Systems
Fundamenta Informaticae - Contagious Creativity - In Honor of the 80th Birthday of Professor Solomon Marcus
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
Panel on grand challenges for modeling and simulation
Proceedings of the Winter Simulation Conference
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
Multistate modeling and simulation forregulatory networks
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)
Simulation of Spatial P system models
Theoretical Computer Science
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Biomolecular systems, composed of networks of proteins, underlie the major functions of living cells. Compartments are key to the organization of such systems. We have previously developed an abstraction for biomolecular systems using the π-calculus process algebra, which successfully handled their molecular and biochemical aspects, but provided only a limited solution for representing compartments. In this work, we extend this abstraction to handle compartments. We are motivated by the ambient calculus, a process algebra for the specification of process location and movement through computational domains. We present the BioAmbients calculus, which is suitable for representing various aspects of molecular localization and compartmentalization, including the movement of molecules between compartments, the dynamic rearrangement of cellular compartments, and the interaction between molecules in a compartmentalized setting. Guided by the calculus, we adapt the BioSpi simulation system, to provide an extended modular framework for molecular and cellular compartmentalization, and we use it to model and study a complex multi-cellular system.