cameo.strain_design.heuristic package

Submodules

cameo.strain_design.heuristic.evolutionary_based module

class cameo.strain_design.heuristic.evolutionary_based.OptGene(model, evolutionary_algorithm=<class 'inspyred.ec.ec.GA'>, manipulation_type='genes', essential_genes=None, essential_reactions=None, plot=True, exclude_non_gene_reactions=True, *args, **kwargs)[source]

Bases: cameo.core.strain_design.StrainDesignMethod

Attributes:
manipulation_type
plot

Methods

__call__(*args, **kwargs) Call self as a function.
run([target, biomass, substrate, …])
param target:The design target :type target: str, Metabolite or Reaction :param biomass: The biomass definition in the model :type biomass: str, Metabolite or Reaction :param substrate: The main carbon source :type substrate: str, Metabolite or Reaction :param max_knockouts: Max number of knockouts allowed :type max_knockouts: int :param variable_size: If true, all candidates have the same size.
plot
manipulation_type
run(target=None, biomass=None, substrate=None, max_knockouts=5, variable_size=True, simulation_method=<function fba>, growth_coupled=False, max_evaluations=20000, population_size=200, max_results=50, use_nullspace_simplification=True, seed=None, **kwargs)[source]
Parameters:
  • target (str, Metabolite or Reaction) – The design target
  • biomass (str, Metabolite or Reaction) – The biomass definition in the model
  • substrate (str, Metabolite or Reaction) – The main carbon source
  • max_knockouts (int) – Max number of knockouts allowed
  • variable_size (bool) – If true, all candidates have the same size. Otherwise the candidate size can be from 1 to max_knockouts.
  • simulation_method (function) – Any method from cameo.flux_analysis.simulation or equivalent
  • growth_coupled (bool) – If true will use the minimum flux rate to compute the fitness
  • max_evaluations (int) – Number of evaluations before stop
  • population_size (int) – Number of individuals in each generation
  • max_results (int) – Max number of different designs to return if found.
  • kwargs (dict) – Arguments for the simulation method.
  • seed (int) – A seed for random.
  • use_nullspace_simplification (Boolean (default True)) – Use a basis for the nullspace to find groups of reactions whose fluxes are multiples of each other and dead end reactions. From each of these groups only 1 reaction will be included as a possible knockout.
Returns:
Return type:

OptGeneResult

Module contents