StochDecomp - Matlab package for noise decomposition in stochastic biochemical systems

TL;DR

StochDecomp is a Matlab tool that enables detailed noise decomposition in biochemical systems, allowing researchers to quantify and analyze how individual reactions contribute to overall variability, with applications demonstrated on the JAK-STAT pathway.

Contribution

It introduces the first computational tool capable of decomposing noise into contributions from individual reactions in biochemical systems.

Findings

Able to quantify noise contributions from individual reactions

Demonstrated application on JAK-STAT pathway data

Allows inference of reaction-specific noise from experimental data

Abstract

Stochasticity is an indispensable aspect of biochemical processes at the cellular level. Studies on how the noise enters and propagates in biochemical systems provided us with nontrivial insights into the origins of stochasticity, in total however they constitute a patchwork of different theoretical analyses. Here we present a flexible and generally applicable noise decomposition tool, that allows us to calculate contributions of individual reactions to the total variability of a system's output. With the package it is therefore possible to quantify how the noise enters and propagates in biochemical systems. We also demonstrate and exemplify using the JAK-STAT signalling pathway that it is possible to infer noise contributions resulting from individual reactions directly from experimental data. This is the first computational tool that allows to decompose noise into contributions resulting from individual reactions.