harissa.model module#

harissa.model#

Main interface for the harissa package.

`NetworkModel`	Handle networks within Harissa.
`Cascade`	Particular network with a cascade structure.
`Tree`	Random network with a tree structure.

class harissa.model.NetworkModel(n_genes=None)[source]#

Bases: object

Handle networks within Harissa.

get_kinetics(data, verb=False)[source]#: Compute the basal parameters of all genes.

fit(data, l=1, tol=1e-05, verb=False, use_numba=True)[source]#: Fit the network model to the data.

simulate(t, M0=None, P0=None, burnin=None, verb=False, use_numba=False)[source]#: Perform simulation of the network model (bursty PDMP version).

simulate_ode(t, M0=None, P0=None, burnin=None, verb=False)[source]#: Perform simulation of the network model (ODE version). This is the slow-fast limit of the PDMP model, which is only relevant when promoters & mRNA are much faster than proteins. p: solution of a nonlinear ODE system involving proteins only m: mean mRNA levels given protein levels (quasi-steady state)

class harissa.model.Cascade(n_genes, autoactiv=False)[source]#

Particular network with a cascade structure.

class harissa.model.Tree(n_genes, autoactiv=False)[source]#

Random network with a tree structure.