loica.operators.hill1

Module Contents

Classes

Hill1

A class that represents a DNA fragment that encode a genetic operator.

class Hill1(input, output, alpha, K, n, name=None, uri=None, sbol_comp=None, color='skyblue')

Bases: loica.operators.operator.Operator

A class that represents a DNA fragment that encode a genetic operator. The Hill1 Operator is an abstraction of a repressible or inducible promoter that maps an input into an output using a Hill function.

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inputRegulator | Supplement

The input of the operator that regulates the expression of the output

outputRegulator | Reporter

The output of the operator that is regulated by the input

alphaList

[Basal expression rate, Regulated expression rate in MEFL/second]

Kint | float

Half expression input concentration in Molar

nint | float

Hill coefficient, cooperative degree (unitless)

uristr, optional

SynBioHub URI

sbol_compSBOL Component, optional

SBOL Component

namestr, optional

Name of the operator displayed on the network representation

color: str, optional

Color displayed on the network representation

characterize(flapjack, receiver, inverter, media, strain, signal, biomass_signal, gamma)

Parameterize the Operator model that maps Input concentration into Output expression rate

__str__(self)

Return str(self).

characterize(self, flapjack, receiver, inverter, media, strain, signal, biomass_signal, gamma)

expression_rate(self, t, dt)

forward_model(self, a_j, b_j, n_i=2, K_i=1, a_A=100.0, b_A=0, K_A=1, n_A=2, Dt=0.05, sim_steps=10, A=0, odval=[1] * 100, gamma=0, p0_1=0, p0_2=0, nt=100)

residuals(self, df, oddf, a_A, b_A, K_A, n_A, gamma)