harissa.simulation.pdmp module#

Perform simulations using the PDMP model

Class#

class harissa.simulation.pdmp.BurstyPDMP(a, d, basal, inter, thin_adapt=True)[source]#

Bases: object

Bursty PDMP version of the network model (promoters not described)

kon(p)[source]#: Interaction function kon (off->on rate), given protein levels p.

kon_bound()[source]#: Compute the current kon upper bound.

flow(time, state)[source]#: Deterministic flow for the bursty model.

step()[source]#: Compute the next jump and the next step of the thinning method, in the case of the bursty model.

simulation(timepoints, verb=False)[source]#: Exact simulation of the network in the bursty PDMP case.