data & software

first-division algorithm

Agent-based simulation of cell-size-dependent gene expression noise in growing cell populations. Download the Julia source @ Github

Computation of single-cell growth statistics (noise) using Mathematica

P. Thomas, V. Shahrezaei (2021) “Coordination of gene expression noise with cell size: analytical results for agent-based models of growing cell populations” Royal Soc Interface 18, 20210274

computational noise decomposition of growth fluctuations

Code illustrating the noise decomposition in reaction-division systems & coarse-grained cell models. Download the Mathematica notebook: FigShare

Computation of single-cell growth statistics (noise) using Mathematica

P. Thomas, G. Terradot, V. Danos, A.Y. Weisse (2018) “Sources, propagation and consequences of stochasticity in cellular growth” Nat Commun 9, 4528

research data on cell size control

Fantastic dataset on cyanobacterial cell size controlled by the circadian clock and the environment produced in the Locke Lab (Cambridge): Download


B.M.C. Martins, A.K. Tooke, P. Thomas, J.C.W. Locke (2018) “Cell size control driven by the circadian clock and environment in cyanobacteria” PNAS 115, E11415-E11424

intrinsic Noise Analyzer (iNA)

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.

iNA’s Graphical User Interface

Download for Windows: FigShare (or Softpedia. Download for MacOSX: FigShare". Source Code: GitHub

iNA’s Graphical User Interface

P. Thomas, H. Matuschek, R. Grima (2012) “Intrinsic Noise Analyzer: A software package for the exploration of stochastic biochemical kinetics using the system size expansion” PloS One 7, e38518