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.
|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|
|Number of pages||6|
|Publication status||Published - 2013|
- chemically reacting systems, extrinsic noise, stochastic differential equation, stochastic simulation