`loica.operators`¶

Submodules¶

Package Contents¶

Classes¶

`Hill1`	A class that represents a DNA fragment that encode a genetic operator.
`Hill2`	A class that represents a DNA fragment that encode a genetic operator.
`Operator`	A class that represents a DNA fragment that encode a genetic operator.
`Operator`	A class that represents a DNA fragment that encode a genetic operator.
`Operator`	A class that represents a DNA fragment that encode a genetic operator.
`Operator`	A class that represents a DNA fragment that encode a genetic operator.
`Operator`	A class that represents a DNA fragment that encode a genetic operator.
`Operator`	A class that represents a DNA fragment that encode a genetic operator.
`Receiver`	A class that represents a DNA fragment that encode a genetic operator.
`Receiver`	A class that represents a DNA fragment that encode a genetic operator.
`Receiver`	A class that represents a DNA fragment that encode a genetic operator.
`Source`	A class that represents a DNA fragment that encode a genetic operator.
`Source`	A class that represents a DNA fragment that encode a genetic operator.
`Source`	A class that represents a DNA fragment that encode a genetic operator.
`Source`	A class that represents a DNA fragment that encode a genetic operator.
`Sum`

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.

…

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)¶

class Hill2(input, output, alpha, K, n, name=None, uri=None, sbol_comp=None, color='orange')¶

Bases: loica.operators.receiver.Operator

A class that represents a DNA fragment that encode a genetic operator. The Hill2 Operator is an abstraction of a set of two repressible or inducible promoters that maps an 2 inputs into an output using a Hill function.

…

inputList [Regulator | Supplement]: The inputs of the operator that regulates the expression of the output
outputRegulator | Reporter | List: 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, receiver1, receiver2, chemical1, chemical2, nor_inverter, media, strain, signal, biomass_signal, gamma, lower_bounds=[0] * 8, upper_bounds=[100000000.0, 8, 100000000.0, 8, 100000000.0, 100000000.0, 100000000.0, 100000000.0], init_x=[1, 2, 1, 2, 1, 0, 0, 0])¶

expression_rate(self, t, dt)¶

forward_model(self, rep1_K=1, rep1_n=2, rep2_K=1, rep2_n=2, alpha0=1, alpha1=0, alpha2=0, alpha3=0, a_A=100.0, b_A=0, K_A=1, n_A=2, a_B=100.0, b_B=0, K_B=1, n_B=2, Dt=0.05, sim_steps=10, A=0, B=0, odval=[1] * 100, gamma=0, rep1_0=0, rep2_0=0, fp_0=0, nt=100)¶

residuals(self, df, oddf, a_A, b_A, K_A, n_A, a_B, b_B, K_B, n_B, chem1, chem2, gamma)¶

class Operator(output, name=None, uri=None, sbol_comp=None, color='skyblue')¶