Graphical rule-based representation of signal-transduction networks
Proceedings of the 2005 ACM symposium on Applied computing
CMSB '08 Proceedings of the 6th International Conference on Computational Methods in Systems Biology
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
CMSB '09 Proceedings of the 7th International Conference on Computational Methods in Systems Biology
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)
CMC'10 Proceedings of the 11th international conference on Membrane computing
Efficient turing-universal computation with DNA polymers
DNA'10 Proceedings of the 16th international conference on DNA computing and molecular programming
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
Communications of the ACM
SAS'11 Proceedings of the 18th international conference on Static analysis
Formal Reduction for Rule-based Models
Electronic Notes in Theoretical Computer Science (ENTCS)
Modular Modelling in Synthetic Biology: Light-Based Communication in E. coli
Electronic Notes in Theoretical Computer Science (ENTCS)
Graph theory for rule-based modeling of biochemical networks
Transactions on Computational Systems Biology VII
WMC'09 Proceedings of the 10th international conference on Membrane Computing
Lumpability abstractions of rule-based systems
Theoretical Computer Science
Containment in Rule-Based Models
Electronic Notes in Theoretical Computer Science (ENTCS)
Rule-based modelling of cellular signalling
CONCUR'07 Proceedings of the 18th international conference on Concurrency Theory
Reconstructing species-based dynamics from reduced stochastic rule-based models
Proceedings of the Winter Simulation Conference
Toward a language for the flexible observation of simulations
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)
Dynamic behavior of cell signaling networks: model design and analysis automation
Proceedings of the 50th Annual Design Automation Conference
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Summary: BioNetGen allows a user to create a computational model that characterizes the dynamics of a signal transduction system, and that accounts comprehensively and precisely for specified enzymatic activities, potential post-translational modifications and interactions of the domains of signaling molecules. The output defines and parameterizes the network of molecular species that can arise during signaling and provides functions that relate model variables to experimental readouts of interest. Models that can be generated are relevant for rational drug discovery, analysis of proteomic data and mechanistic studies of signal transduction. Availability: http://cellsignaling.lanl.gov/bionetgen