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.
Facile in Perl.

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