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 | DEVS 13 Proceedings of the Symposium on Theory of Modeling & Simulation - DEVS Integrative M&S Symposium |
Place of Publication | San Diego, CA, USA |
Publisher | Society for Computer Simulation International |
Pages | 6 |
Number of pages | 6 |
ISBN (Print) | 978-1-62748-032-1 |
Publication status | Published - 2013 |
Keywords
- chemically reacting systems, extrinsic noise, stochastic differential equation, stochastic simulation