NoisySIM

NoisySIM is a Java tool to simulate chemical reactions with both intrinsic and extrinsic bounded noises.

What is the "intrinsic noise" of a biochemical network?

Cells are noisy biochemical systems very sensitive to statistical fluctuations induced by molecules present in low number. In such a case, stochastic approaches (e.g. Gillespie-like) better appeal than the deterministic counterparts, instead preferable with large numbers involved.

What is a bounded "extrinsic noise"?

Networks are not isolated. Their dynamics depends on the interplay with many (often unknown) other networks and random extracellular signals. However, modelling such interactions is difficult, often impossible. Extrinsic noise are a rapid way to have an implicit abstraction of such interplays.

Noises, often modelled as white/colored processes, are here bounded to maintain an adequate physical representation of chemical kinetics.

What is NoisySIM?

It is a library where intrinsic low-numbers fluctuations are accounted by the discrete Gillespie-like Markov representation of chemical reactions, and extrinsic noises are modelled as Stochastic Differential Equations. The noise dynamics affects the model jump rates, thus linking the extrinsic noise to the intrinsic fluctuations. This allows to explicitly simulate every reaction under the influence of external noises.

NoisySIM is a library to easily assess whether biochemical noise plays a functional role for a network, i.e. the so called functional noise-induced transitions, namely the gain of biological functionality obtained by roaming into otherwise unreachable chemical states.

How do I use the library?

NoisySIM implements an abstract model. Concrete models are defined by extending some abstract classes and their simulations are performed by the Stochastic Simulation Algorithm with Bounded Noise implemented in NoisySIM. This allows to empirically evaluate the probability of the system to be in any state at any time. NoisySIM abstract classes can be implemented automatically by using the tool's compiler which parses a simple textual model syntax (see the manual). The library is modular, customizable, and can be embedded within other simulation frameworks, if required.

• NoisySIM: exact simulation of stochastic chemically reacting systems with extrinsic noises. G.Caravagna, G.Mauri, A.d'Onofrio. Proc. of the Symposium on Theory of Modeling and Simulation (TMS 2013) 12:1-6, Society for Computer Simulation Int., San Diego, CA, USA.

• The interplay of intrinsic and extrinsic bounded noises in biomolecular networks G.Caravagna, G.Mauri, A.d'Onofrio. PLoS ONE 8(2):e51174, 2013.