loica.operators.hill2
¶
Module Contents¶
Classes¶
A class that represents a DNA fragment that encode a genetic operator. |
- 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.
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- 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)¶