loica.genetic_network

Module Contents

Classes

GeneticNetwork

Representation of a genetic netowrk composed by a set of Operators, Regulators and Reporters.

class GeneticNetwork(vector=None)

Representation of a genetic netowrk composed by a set of Operators, Regulators and Reporters.

…

operatorsList[Operator]

List of Operators that are part of the genetic network

regulatorsList[Regulator]

List of Regulators that are part of the genetic network

reportersList[Reporter]

List of Reporters that are part of the genetic network

vectorint

Flapjack ID of the vector that is associated with the genetic network

to_graph()

Builds a graph representation of the genetic netwok

draw()

Generates a plot of the graph representation builded by to_graph()

to_sbol(sbol_doc=None)

Generates a SBOL3 Document representation of the genetic network on sbol_doc

add_operator(self, ops)

add_regulator(self, regs)

add_reporter(self, reps)

draw(self, node_shape='o', node_size=500, linewidths=0, alpha=0.5, arrowsize=10, font_size=6, font_family='Tahoma', font_weight='bold', pos=nx.kamada_kawai_layout, contracted=False)

initialize(self)

step(self, growth_rate=1, t=0, dt=0.1)

step_stochastic(self, growth_rate=1, t=0, dt=0.1)

substep_stochastic(self, t=0, dt=0.1, growth_rate=1)

to_contracted_graph(self)

to_graph(self)

to_sbol(self, sbol_doc: sbol3.Document = None) → sbol3.Document

Convert the genetic network to SBOL. :param sbol_doc: The SBOL document to add the genetic network to.