Ensemble means and standard errors indicate that the parameters in stochastic network for single cells are tightly specified by the new fitting method.

The parameters including the initial numbers of molecules and the rate constants in Fig 1 are labeled in the first column. In the second column are the initial parameter values used from a deterministic model ensemble[28], in which WC-2 constant over time was used to initialize both the Metropolis Hastings MCMC runs (Fig 2A) and the parallel tempering MCMC runs (Fig 2B). In the third column the parameters from the deterministic model ensemble are converted into units appropriate for the stochastic network as described in Materials and Methods. The last four columns are the ensemble means and standard errors (across the ensemble) generated by parallel tempering (see Materials and methods) for a single cell experiment with 868 single cells or 1591 single cells.