Code to reproduce the figures and results in the preprint "Direct simulation of a stochastically driven multi-step birth-death process" by Gennady Gorin and Lior Pachter

gg_200921_gillespie_gou_2step_8.m is the core stochastic simulation code.

The data to reproduce Figure 2 can be generated using gg_200921_samplefig_gen_1.m or downloaded directly, and visualized using gg_200921_samplefig_viz_1.m.

The data to reproduce the following figures can be generated using gg_200921_jointfig_gen_1.m or downloaded directly, and visualized using gg_200921_jointfig_viz_1.m.

gg_200921_numint_burst_1.m implements the analytical solution for the 2-stage BDP coupled to a bursty promoter, per Singh and Bokes 2012.