BioAmbients: an abstraction for biological compartments
Theoretical Computer Science - Special issue: Computational systems biology
Bioinformatics
Theoretical Computer Science
A simple calculus for proteins and cells
Theoretical Computer Science
Simulation of large-scale rule-based models
Bioinformatics
CMSB'04 Proceedings of the 20 international conference on Computational Methods in Systems Biology
Graph theory for rule-based modeling of biochemical networks
Transactions on Computational Systems Biology VII
Rule-based modelling of cellular signalling
CONCUR'07 Proceedings of the 18th international conference on Concurrency Theory
CMC'10 Proceedings of the 11th international conference on Membrane computing
Adapting rule-based model descriptions for simulating in continuous and hybrid space
Proceedings of the 9th International Conference on Computational Methods in Systems Biology
Containment in Rule-Based Models
Electronic Notes in Theoretical Computer Science (ENTCS)
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
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Rule-based modeling is an approach to modeling biochemical kinetics in which proteins and other biological components are modeled as structured objects and their interactions are governed by rules that specify the conditions under which reactions occur. BioNetGen is an open-source platform that provides a simple yet expressive language for rule-based modeling (BNGL). In this paper we describe compartmental BNGL (cBNGL), which extends BNGL to enable explicit modeling of the compartmental organization of the cell and its effects on system dynamics. We show that by making localization a queryable attribute of both molecules and species and introducing appropriate volumetric scaling of reaction rates, the effects of compartmentalization can be naturally modeled using rules. These properties enable the construction of new rule semantics that include both universal rules, those defining interactions that can take place in any compartment in the system, and transport rules, which enable movement of molecular complexes between compartments.