harissa.simulation.pdmp_fast module#

Perform simulations using the PDMP model - Fast version using Numba NB: This module takes time to compile (~8s) but is much more efficient, which is typically suited for large numbers of genes and/or cells

Functions#

`flow`	Deterministic flow for the bursty model.
`kon`	Interaction function kon (off->on rate), given protein levels p.
`kon_bound`	Compute the current kon upper bound.
`simulate`	Exact simulation of the network in the bursty PDMP case.
`step`	Compute the next jump and the next step of the thinning method, in the case of the bursty model.

harissa.simulation.pdmp_fast.flow(D0, D1, S1, M, P, time)[source]#: Deterministic flow for the bursty model.

harissa.simulation.pdmp_fast.kon(basal, inter, K0, K1, P)[source]#: Interaction function kon (off->on rate), given protein levels p.

harissa.simulation.pdmp_fast.kon_bound(basal, inter, K0, K1, D0, D1, S1, M, P)[source]#: Compute the current kon upper bound.

harissa.simulation.pdmp_fast.simulate(timepoints, basal, inter, K0, K1, B, D0, D1, S1, M, P, thin, verb)[source]#: Exact simulation of the network in the bursty PDMP case.

harissa.simulation.pdmp_fast.step(basal, inter, K0, K1, B, D0, D1, S1, M, P, thin)[source]#: Compute the next jump and the next step of the thinning method, in the case of the bursty model.

Class#

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

Bases: object

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

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