harissa.simulation.ode module

Perform simulations using the ODE model

Class

class harissa.simulation.ode.ApproxODE(a, d, basal, inter)

Bases: object

ODE version of the network model (very rough approximation of the PDMP)

kon(p)

Interaction function kon (off->on rate), given protein levels p.

step_ode(dt)

Euler step for the deterministic limit model.

simulation(timepoints, verb=False)

Simulation of the deterministic limit model, which is relevant when promoters and mRNA are much faster than proteins. 1. Nonlinear ODE system involving proteins only 2. Mean level of mRNA given protein levels