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 publicationDEVS 13 Proceedings of the Symposium on Theory of Modeling & Simulation - DEVS Integrative M&S Symposium
Place of PublicationSan Diego, CA, USA
PublisherSociety for Computer Simulation International
Pages6
Number of pages6
ISBN (Print)978-1-62748-032-1
Publication statusPublished - 2013

Keywords

  • chemically reacting systems, extrinsic noise, stochastic differential equation, stochastic simulation

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