## Abstract

Models of biochemical systems with few copies of molecules should be stochastic and should account for the random interplay among networks. Despite mathematical tools to account for low-level intrinsic fluctuations are well-known, less is known about the modeling of interplay, especially in biology. Classical abstractions use extrinsic unbounded gaussian noises to model these interplays. However, recent literature showed that bounded noises are a more realistic abstraction. NOISYSIM is a JAVA library to simulate chemically reacting systems where both intrinsic stochasticity and extrinsic bounded noises are present. Intrinsic low-numbers fluctuations are accounted by a Gillespie-like approach, extrinsic noises are modeled as Langevin stochastic equations affecting the model jump rates. NOISYSIM allows to approximate the solution of the Chapman-Kolgomorov equation characterizing the system, thus allowing to asses whether biochemical noise plays a functional role for a target network.

Original language | English |
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Title of host publication | Simulation Series |

Pages | 84-89 |

Number of pages | 6 |

Volume | 45 |

Edition | 4 |

Publication status | Published - 2013 |

Event | Symposium on Theory of Modeling and Simulation - DEVS Integrative M and S Symposium, DEVS 2013, Part of the 2013 Spring Simulation Multiconference, SpringSim 2013 - San Diego, CA, United States Duration: Apr 7 2013 → Apr 10 2013 |

### Other

Other | Symposium on Theory of Modeling and Simulation - DEVS Integrative M and S Symposium, DEVS 2013, Part of the 2013 Spring Simulation Multiconference, SpringSim 2013 |
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Country | United States |

City | San Diego, CA |

Period | 4/7/13 → 4/10/13 |

## Keywords

- Chemically reacting systems
- Extrinsic noise
- Stochastic differential equation
- Stochastic simulation

## ASJC Scopus subject areas

- Computer Networks and Communications