Handbook of logic in computer science (vol. 4)
Communicating and mobile systems: the &pgr;-calculus
Communicating and mobile systems: the &pgr;-calculus
Information Processing Letters
CONCUR '01 Proceedings of the 12th International Conference on Concurrency Theory
Unfolding and Event Structure Semantics for Graph Grammars
FoSSaCS '99 Proceedings of the Second International Conference on Foundations of Software Science and Computation Structure, Held as Part of the European Joint Conferences on the Theory and Practice of Software, ETAPS'99
An introduction to event structures
Linear Time, Branching Time and Partial Order in Logics and Models for Concurrency, School/Workshop
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
Graphical rule-based representation of signal-transduction networks
Proceedings of the 2005 ACM symposium on Applied computing
Rule-based modeling of biochemical networks: Research Articles
Complexity - Understanding Complex Systems: Part II
Formal Molecular Biology Done in CCS-R
Electronic Notes in Theoretical Computer Science (ENTCS)
ESOP'03 Proceedings of the 12th European conference on Programming
Beta binders for biological interactions
CMSB'04 Proceedings of the 20 international conference on Computational Methods in Systems Biology
Systems biology, models, and concurrency
Proceedings of the 35th annual ACM SIGPLAN-SIGACT symposium on Principles of programming languages
Rule-Based Modelling, Symmetries, Refinements
FMSB '08 Proceedings of the 1st international workshop on Formal Methods in Systems Biology
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
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
Stochastic Analysis of Amino Acid Substitution in Protein Synthesis
CMSB '08 Proceedings of the 6th International Conference on Computational Methods in Systems Biology
Investigation of a Biological Repair Scheme
Membrane Computing
How liquid is biological signalling?
Theoretical Computer Science
A Process Model of Actin Polymerisation
Electronic Notes in Theoretical Computer Science (ENTCS)
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)
Rule-based programming for integrative biological modeling
Natural Computing: an international journal
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
Abstract interpretation of cellular signalling networks
VMCAI'08 Proceedings of the 9th international conference on Verification, model checking, and abstract interpretation
A generic abstract machine for stochastic process calculi
Proceedings of the 8th International Conference on Computational Methods in Systems Biology
Understanding signalling networks as collections of signal transduction pathways
Proceedings of the 8th International Conference on Computational Methods in Systems Biology
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)
Fragments-based Model Reduction: Some Case Studies
Electronic Notes in Theoretical Computer Science (ENTCS)
A Framework for Modelling and Simulating Networks of Cells
Electronic Notes in Theoretical Computer Science (ENTCS)
Efficient turing-universal computation with DNA polymers
DNA'10 Proceedings of the 16th international conference on DNA computing and molecular programming
Compartmental rule-based modeling of biochemical systems
Winter Simulation Conference
Rule-based modeling of transcriptional attenuation at the tryptophan operon
Winter Simulation Conference
Design and development of software tools for Bio-PEPA
Winter Simulation Conference
Transactions on computational systems biology XIII
Refining dynamics of gene regulatory networks in a stochastic π-calculus framework
Transactions on computational systems biology XIII
Communications of the ACM
TLCA'11 Proceedings of the 10th international conference on Typed lambda calculi and applications
A hybrid factored frontier algorithm for dynamic Bayesian network models of biopathways
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
A Syntactic Abstraction for Rule-Based Languages with Binding
Electronic Notes in Theoretical Computer Science (ENTCS)
Bio-PEPAd: A non-Markovian extension of Bio-PEPA
Theoretical Computer Science
The evolution of higher-level biochemical reaction models
Genetic Programming and Evolvable Machines
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 self-assembly in BlenX
Transactions on Computational Systems Biology XII
Rule-Based modeling of transcriptional attenuation at the tryptophan operon
Transactions on Computational Systems Biology XII
Stochastic simulation of multiple process calculi for biology
Theoretical Computer Science
Foundational aspects of multiscale modeling of biological systems with process algebras
Theoretical Computer Science
An imperative language of self-modifying graphs for biological systems
Proceedings of the 27th Annual ACM Symposium on Applied Computing
Tropical Geometries and Dynamics of Biochemical Networks Application to Hybrid Cell Cycle Models
Electronic Notes in Theoretical Computer Science (ENTCS)
Containment in Rule-Based Models
Electronic Notes in Theoretical Computer Science (ENTCS)
A Hybrid Factored Frontier Algorithm for Dynamic Bayesian Networks with a Biopathways Application
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Modular modelling of signalling pathways and their cross-talk
Theoretical Computer Science
Rule-based whole body modeling for analyzing multi-compound effects
Proceedings of the ACM sixth international workshop on Data and text mining in biomedical informatics
A rule-based and imperative language for biochemical modeling and simulation
SEFM'12 Proceedings of the 10th international conference on Software Engineering and Formal Methods
Dynamic bayesian networks: a factored model of probabilistic dynamics
ATVA'12 Proceedings of the 10th international conference on Automated Technology for Verification and Analysis
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
BioScape: A Modeling and Simulation Language for Bacteria-Materials Interactions
Electronic Notes in Theoretical Computer Science (ENTCS)
A Software Interface Between the Narrative Language and Bio-PEPA
Electronic Notes in Theoretical Computer Science (ENTCS)
Simulating Anti-adhesive and Antibacterial Bifunctional Polymers for Surface Coating using BioScape
Proceedings of the International Conference on Bioinformatics, Computational Biology and Biomedical Informatics
Computational and mathematical models of the JAK-STAT signal transduction pathway
Proceedings of the 2013 Summer Computer Simulation Conference
Quantitative reactive modeling and verification
Computer Science - Research and Development
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Modelling is becoming a necessity in studying biological signalling pathways, because the combinatorial complexity of such systems rapidly overwhelms intuitive and qualitative forms of reasoning. Yet, this same combinatorial explosion makes the traditional modelling paradigm based on systems of differential equations impractical. In contrast, agentbased or concurrent languages, such as ? [1,2,3] or the closely related BioNetGen language [4,5,6,7,8,9,10], describe biological interactions in terms of rules, thereby avoiding the combinatorial explosion besetting differential equations. Rules are expressed in an intuitive graphical form that transparently represents biological knowledge. In this way, rules become a natural unit of model building, modification, and discussion. We illustrate this with a sizeable example obtained from refactoring two models of EGF receptor signalling that are based on differential equations [11,12]. An exciting aspect of the agent-based approach is that it naturally lends itself to the identification and analysis of the causal structures that deeply shape the dynamical, and perhaps even evolutionary, characteristics of complex distributed biological systems. In particular, one can adapt the notions of causality and conflict, familiar from concurrency theory, to ?, our representation language of choice. Using the EGF receptor model as an example, we show how causality enables the formalization of the colloquial concept of pathway and, perhaps more surprisingly, how conflict can be used to dissect the signalling dynamics to obtain a qualitative handle on the range of system behaviours. By taming the combinatorial explosion, and exposing the causal structures and key kinetic junctures in a model, agent- and rule-based representations hold promise for making modelling more powerful, more perspicuous, and of appeal to a wider audience.