Package BIP :: Package SDE :: Module gillespie :: Class Model

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Class Model

Instance Methods

__init__(self, vnames, rates, inits, tmat, propensity)
vnames: list of strings

source code

getStats(self)

source code

run(self, method='SSA', tmax=10, reps=1, viz=False, serial=False)
Runs the model.

source code

GSSA(self)
Gillespie Direct algorithm

source code

Method Details

init(self, vnames, rates, inits, tmat, propensity)
(Constructor)

vnames: list of strings
rates: list of fixed rate parameters
inits: list of initial values of variables
propensity: list of lambda functions of the form:

lambda r,ini: some function of rates ans inits.

run(self, method='SSA', tmax=10, reps=1, viz=False, serial=False)

Runs the model.

Parameters:

method - String specifying the solving algorithm. Currently only 'SSA'
tmax - duration of the simulation.
reps - Number of replicates.
viz - Boolean. Whether to show graph of each replicate during simulation
serial - Boolean. False to run replicate in parallel when more than one core is a vailable. True to run them serially (easier to debug).

Returns:

a numpy array of shape (reps,tmax,nvars)