gapfillingpkg

GapfillingPkg()

This class constrains the sum progressions of sets of reactions:

from modelseedpy.fbapkg import ReactionUsePkg
gapfill = GapfillingPkg(model)

  • model cobra.core.model.Model: The CobraKBase model that will be constrained. The conversion from standard COBRA models to CobraKBase models is facilitated by the cobrakbase package.

build()

The model is gapfilled with default parameters

{
           "gapfill_all_indecies_with_default_templates": 1,
           "set_objective": 1
}

and specifications of the template and the minimum objective value:

gapfill.build(template, minimum_objective=0.01)

  • template list: The collection of templates that will be used to gap-fill the model.

  • minimum_objective float: The minimum permissible objective value.

build_package()

The model is gapfilled:

gapfill.build_package(parameters)

  • parameters dict: The parameters that will supplant default values

{
           "auto_sink": ["cpd02701", "cpd11416", "cpd15302"],
           "extend_with_template":1,
           "model_penalty":1,
           "default_gapfill_models":[],
           "default_gapfill_templates":[],
           "gapfill_templates_by_index":{},
           "gapfill_models_by_index":{},
           "reaction_scores":{},
           "gapfill_all_indecies_with_default_templates":1,
           "gapfill_all_indecies_with_default_models":1,
           "default_excretion":100,
           "default_uptake":-100,
           "minimum_obj":0.01,
           "set_objective":1,
           "blacklist":"default_blacklist"
}

where the default_blacklist value is a list of approximately 100 reaction IDs that will not be included while gapfilling.

extend_model_with_model_for_gapfilling()

The reactions and metabolites from a source COBRA model are introduced to the autosink and exchange reactions of the model that is initiated by this class:

gapfill.extend_model_with_model_for_gapfilling(source_model, index)

  • source_model cobra.core.model.Model: The COBRA model whose reactions and metabolites will be imposed in the initiated model of the class.

  • index int: The number that corresponds with the species, which is relevant for distinguishing species in a community model.

extend_model_with_template_for_gapfilling()

Adds new reactions and metabolites from a template to the exchange reactions of the model that is initiated by this class:

gapfill.extend_model_with_template_for_gapfilling(template, index)

  • template modelseedpy.core.mstemplate.MSTemplateBuilder: The templates that will be used to gap-fill the model.

  • index int: The number that corresponds with the species, which is relevant for distinguishing species in a community model.

binary_check_gapfilling_solution()

Redefining the objective to the minimum sum of the reaction fluxes that are in the parameterized COBRA solution:

check_solution = gapfill.binary_check_gapfilling_solution(solution=None, flux_values=None)

  • solution cobra.core.solution.Solution: The FBA solution from a simulation of the respective model.

  • flux_values dict: The forward and reverse fluxes (values) are stored within “forward” and “reverse” keys for the IDs of all reactions (keys).

Returns check_solution dict: The collection of “<” or “>” directions for all reversed reactions in the model that are described with gapfilling penalties.

run_test_conditions()

Redefining the objective to the minimum sum of the reaction fluxes that are in the parameterized COBRA solution:

gapfill.run_test_conditions(condition_list, solution = None, max_iterations = 10)

  • condition_list list: A list of simulation conditions that will be each be examined during the simulation.

  • solution cobra.core.solution.Solution: The COBRA solution that contains the reactions that will be examined in simulations for all conditions.

  • max_iterations int: The number of iterations through which the solution and conditions will be examined.

filter_database_based_on_tests()

Silencing reactions that have associated gapfilling penalties:

gapfill.run_test_conditions(condition_list)

  • condition_list list: A list of simulation conditions that are examined during the simulation to acquire the list of reactions to be silenced.

filter_database_based_on_tests()

Silencing reactions that have associated gapfilling penalties:

gapfill.run_test_conditions(condition_list)

  • condition_list list: A list of simulation conditions that are examined during the simulation to acquire the list of reactions to be silenced.

Accessible content

The FluxFittingPkg class contains a couple of accessible content that may be useful for subsequent post-processing or troubleshooting:

  • model cobra.core.model.Model: The cobrakbase model that possesses the implemented drain reactions.

  • variables & parameters dict: Dictionaries of the linear programming variables and simulation parameters, respectively.

  • gapfilling_penalties dict: A dictionary

  • new_metabolites & new_reactions dict: Dictionaries of metabolite and reaction COBRA objects (values) for all metabolite and reaction IDs (keys) that were added to the model.