Summary
Software
1) Intrinsic Noise Analyzer (iNA) is an open source software for studying reaction kinetics in living cells. The software analyzes mathematical models of intracellular reaction kinetics such as gene expression, regulatory networks or signaling pathways to quantify concentration fluctuations due to the random nature of chemical reactions. iNA implements stochastic simulation, deterministic rate equation, and system size expansion methods such as Linear Noise Approximation and Effective Mesoscopic Rate Equations.
Download for Windows: FigShare (or Softpedia). Download for MacOSX: FigShare. Source Code: GitHub. Paper: Thomas, P., Matuschek, H., & Grima, R. (2012). Intrinsic noise analyzer: a software package for the exploration of stochastic biochemical kinetics using the system size expansion. PloS One 7, e38518.
Noise analysis using LNA, System Size Expansion & Stochastic Simulation Algorithm (Gillespie Algorithm)
iNA's Graphical User Interface
2) Mathematica Notebook performing small noise approximation and noise decomposition of growth rate fluctuations of coarse-grained cell models. Download: FigShare
Paper: "Sources, propagation and consequences of stochasticity in cellular growth" P Thomas, G Terradot, V Danos, AY Weisse. Nature Communications 9, 4528 (2018)
Computation of single-cell growth statistics (noise) using Mathematica