NoisySim: Exact simulation of stochastic chemically reacting systems with extrinsic bounded noises (WIP)

Giulio Caravagna, Alberto D'Onofrio, Giancarlo Mauri

Research output: Chapter in Book/Report/Conference proceedingConference contribution

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 languageEnglish
Title of host publicationSimulation Series
Pages84-89
Number of pages6
Volume45
Edition4
Publication statusPublished - 2013
EventSymposium 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 2013Apr 10 2013

Other

OtherSymposium on Theory of Modeling and Simulation - DEVS Integrative M and S Symposium, DEVS 2013, Part of the 2013 Spring Simulation Multiconference, SpringSim 2013
CountryUnited States
CitySan Diego, CA
Period4/7/134/10/13

Keywords

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

ASJC Scopus subject areas

  • Computer Networks and Communications

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