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An Overview of Network-Based and -Free Approaches for Stochastic Simulation of Biochemical Systems
Stochastic simulation has been widely used to model the dynamics of biochemical reaction networks. Several algorithms have been proposed that are exact solutions of the chemical master equation, following the work of Gillespie. These stochastic simulation approaches can be broadly classified into tw...
Autores principales: | , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
2018
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6013266/ https://www.ncbi.nlm.nih.gov/pubmed/29938118 http://dx.doi.org/10.3390/computation6010009 |
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author | Gupta, Abhishekh Mendes, Pedro |
author_facet | Gupta, Abhishekh Mendes, Pedro |
author_sort | Gupta, Abhishekh |
collection | PubMed |
description | Stochastic simulation has been widely used to model the dynamics of biochemical reaction networks. Several algorithms have been proposed that are exact solutions of the chemical master equation, following the work of Gillespie. These stochastic simulation approaches can be broadly classified into two categories: network-based and -free simulation. The network-based approach requires that the full network of reactions be established at the start, while the network-free approach is based on reaction rules that encode classes of reactions, and by applying rule transformations, it generates reaction events as they are needed without ever having to derive the entire network. In this study, we compare the efficiency and limitations of several available implementations of these two approaches. The results allow for an informed selection of the implementation and methodology for specific biochemical modeling applications. |
format | Online Article Text |
id | pubmed-6013266 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2018 |
record_format | MEDLINE/PubMed |
spelling | pubmed-60132662018-06-21 An Overview of Network-Based and -Free Approaches for Stochastic Simulation of Biochemical Systems Gupta, Abhishekh Mendes, Pedro Computation (Basel) Article Stochastic simulation has been widely used to model the dynamics of biochemical reaction networks. Several algorithms have been proposed that are exact solutions of the chemical master equation, following the work of Gillespie. These stochastic simulation approaches can be broadly classified into two categories: network-based and -free simulation. The network-based approach requires that the full network of reactions be established at the start, while the network-free approach is based on reaction rules that encode classes of reactions, and by applying rule transformations, it generates reaction events as they are needed without ever having to derive the entire network. In this study, we compare the efficiency and limitations of several available implementations of these two approaches. The results allow for an informed selection of the implementation and methodology for specific biochemical modeling applications. 2018-01-31 2018-03 /pmc/articles/PMC6013266/ /pubmed/29938118 http://dx.doi.org/10.3390/computation6010009 Text en http://creativecommons.org/licenses/by/4.0/ Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/). |
spellingShingle | Article Gupta, Abhishekh Mendes, Pedro An Overview of Network-Based and -Free Approaches for Stochastic Simulation of Biochemical Systems |
title | An Overview of Network-Based and -Free Approaches for Stochastic Simulation of Biochemical Systems |
title_full | An Overview of Network-Based and -Free Approaches for Stochastic Simulation of Biochemical Systems |
title_fullStr | An Overview of Network-Based and -Free Approaches for Stochastic Simulation of Biochemical Systems |
title_full_unstemmed | An Overview of Network-Based and -Free Approaches for Stochastic Simulation of Biochemical Systems |
title_short | An Overview of Network-Based and -Free Approaches for Stochastic Simulation of Biochemical Systems |
title_sort | overview of network-based and -free approaches for stochastic simulation of biochemical systems |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6013266/ https://www.ncbi.nlm.nih.gov/pubmed/29938118 http://dx.doi.org/10.3390/computation6010009 |
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