Generalizing Gillespie’s Direct Method to Enable Network-Free Simulations
| Autor: | Song Feng, William S. Hlavacek, Keesha E. Erickson, Ryan Suderman, Yen Ting Lin, Eshan D. Mitra |
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| Rok vydání: | 2018 |
| Předmět: |
0301 basic medicine
Rule-based modeling Theoretical computer science Dynamical systems theory Biochemical Phenomena Modeling language General Mathematics Immunology Models Biological Article General Biochemistry Genetics and Molecular Biology 03 medical and health sciences 0302 clinical medicine Terminology as Topic Stochastic simulation Computer Simulation Kinetic Monte Carlo General Environmental Science Pharmacology Stochastic Processes Systems Biology General Neuroscience Modelling biological systems Mathematical Concepts Kinetics 030104 developmental biology Computational Theory and Mathematics 030220 oncology & carcinogenesis General Agricultural and Biological Sciences Monte Carlo Method Algorithms Metabolic Networks and Pathways Combinatorial explosion Biological network |
| Zdroj: | Bull Math Biol |
| ISSN: | 1522-9602 0092-8240 |
| DOI: | 10.1007/s11538-018-0418-2 |
| Popis: | Gillespie's direct method for stochastic simulation of chemical kinetics is a staple of computational systems biology research. However, the algorithm requires explicit enumeration of all reactions and all chemical species that may arise in the system. In many cases, this is not feasible due to the combinatorial explosion of reactions and species in biological networks. Rule-based modeling frameworks provide a way to exactly represent networks containing such combinatorial complexity, and generalizations of Gillespie's direct method have been developed as simulation engines for rule-based modeling languages. Here, we provide both a high-level description of the algorithms underlying the simulation engines, termed network-free simulation algorithms, and how they have been applied in systems biology research. We also define a generic rule-based modeling framework and describe a number of technical details required for adapting Gillespie's direct method for network-free simulation. Finally, we briefly discuss potential avenues for advancing network-free simulation and the role they continue to play in modeling dynamical systems in biology. |
| Databáze: | OpenAIRE |
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