Software available


Inferring time derivatives including growth rates using Gaussian processes
Swain et al., Nat Commun 7 (2016) 13766.
The analysis code in Python.


Unmixing of fluorescence spectra to resolve quantitative time-series measurements of gene expression in plate readers
Lichten, White, Clark, & Swain, BMC Biotechnol 14 (2014) 11.
The analysis code in Python.


A Bayesian method for inferring quantitative information from FRET data
Lichten & Swain, BMC Biophys 4 (2011) 10.
A Matlab version of the algorithm.


Scalable rule-based modelling of allosteric proteins and biochemical networks
Ollivier et al., PLoS Comput Biol 6 (2010) e1000975.
The Allosteric Network Compiler.


Analytical expressions for stochastic gene expression
Shahrezaei & Swain, Proc Nat Acad Sci USA 105 (2008) 17256.
Matlab files for probability distributions.

Colored extrinsic fluctuations and stochastic gene expression
Shahrezaei et al., Mol Syst Biol 4 (2008) 196.
The Easystoch stochastic simulator.


Facile: a command-line network compiler for systems biology
Siso-Nadal et al., BMC Syst Biol 1 (2007) 36.
Code for the compiler in Perl and Python.


A fluctuation method to quantify in vivo fluorescence
Rosenfeld et al., Biophys J 91 (2006) 759.
Matlab implementations of both methods.