Journal of Computational Physics
Journal of Computational Physics
Approaches to complexity reduction in a systems biology research environment (SYCAMORE)
Proceedings of the 38th conference on Winter simulation
Simulation of biochemical networks using COPASI: a complex pathway simulator
Proceedings of the 38th conference on Winter simulation
Hybrid method for the chemical master equation
Journal of Computational Physics
Research Article: Hybrid stochastic simulations of intracellular reaction-diffusion systems
Computational Biology and Chemistry
Hybrid simulation of biochemical systems using hybrid adaptive Petri nets
Proceedings of the Fourth International ICST Conference on Performance Evaluation Methodologies and Tools
Automatic Parameterisation of Stochastic Petri Net Models of Biological Networks
Electronic Notes in Theoretical Computer Science (ENTCS)
Aggregation-mediated collective perception and action in a group of miniature robots
Proceedings of the 9th International Conference on Autonomous Agents and Multiagent Systems: volume 2 - Volume 2
A Continuous-Time, Discrete-State Method for Simulating the Dynamics of Biochemical Systems
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
YAMONES: a computational architecture for molecular network simulation
BSB'05 Proceedings of the 2005 Brazilian conference on Advances in Bioinformatics and Computational Biology
Symmetry-Based model reduction for approximate stochastic analysis
CMSB'12 Proceedings of the 10th international conference on Computational Methods in Systems Biology
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Motivation: To be valuable to biological or biomedical research, in silico methods must be scaled to complex pathways and large numbers of interacting molecular species. The correct method for performing such simulations, discrete event simulation by Monte Carlo generation, is computationally costly for large complex systems. Approximation of molecular behavior by continuous models fails to capture stochastic behavior that is essential to many biological phenomena. Results: We present a novel approach to building hybrid simulations in which some processes are simulated discretely, while other processes are handled in a continuous simulation by differential equations. This approach preserves the stochastic behavior of cellular pathways, yet enables scaling to large populations of molecules. We present an algorithm for synchronizing data in a hybrid simulation and discuss the trade-offs in such simulation. We have implemented the hybrid simulation algorithm and have validated it by simulating the statistical behavior of the well-known lambda phage switch. Hybrid simulation provides a new method for exploring the sources and nature of stochastic behavior in cells. Supplementary information: The SBML file for the lambda phage tests will be made available at the OUP site.