ModelSEED MS Model

buildModelByLayers Definition: void ModelSEED::MS::Model->buildModelByLayers({

});
Description:

createStandardFBABiomass Definition: ModelSEED::MS::Biomass = ModelSEED::MS::Annotation->createStandardFBABiomass({ mapping => $self->mapping() }); Description: Creates a new biomass based on the annotation

testBiomassCondition Definition: ModelSEED::MS::Model = ModelSEED::MS::Model->testBiomassCondition({ condition => REQUIRED, annotation => $self->annotation() }); Description: Tests if the organism satisfies the conditions for inclusion of the compound in the model biomass reaction

addReactionToModel Definition: ModelSEED::MS::ModelReaction = ModelSEED::MS::Model->addReactionToModel({ reaction => REQUIRED, direction => undef (default value will be pulled from reaction instance), protons => undef (default value will be pulled from reaction instance), gpr => "UNKNOWN" }); Description: Converts the input reaction instance into a model reaction and adds the reaction and associated compounds to the model.

addCompartmentToModel Definition: ModelSEED::MS::Model = ModelSEED::MS::Model->addCompartmentToModel({ Compartment => REQUIRED, pH => 7, potential => 0, compartmentIndex => 0 }); Description: Adds a compartment to the model after checking that the compartment isn't already there

addCompoundToModel Definition: ModelSEED::MS::ModelCompound = ModelSEED::MS::Model->addCompoundToModel({ compound => REQUIRED, modelCompartment => REQUIRED, charge => undef (default values will be pulled from input compound), formula => undef (default values will be pulled from input compound) }); Description: Adds a compound to the model after checking that the compound isn't already there

labelBiomassCompounds Definition: void ModelSEED::MS::Model->labelBiomassCompounds(); Description: Labels all model compounds indicating whether or not they are biomass components

parseSBML

# TODO parseSBML() parse error with SIds and UUIDs currently the id field on objects COULD output a UUID if there is no alias in the prefered alias set. If this is then placed in the "id" attribute of a species or reaction, this violates the SBML SId restrictions. Need to replace '-' with '_' and prefix with "UUID_" since uuids may start with a number while SIds cannot.

Definition: void ModelSEED::MS::Model->parseSBML(); Description: Parse an input SBML file to generate the model

printSBML Definition: void ModelSEED::MS::Model->printSBML(); Description: Prints the model in SBML format

gapfillModel Definition: ModelSEED::MS::GapfillingSolution ModelSEED::MS::Model->gapfillModel({ gapfillingFormulation => ModelSEED::MS::GapfillingFormulation, fbaFormulation => ModelSEED::MS::FBAFormulation }); Description: Runs gapfilling on the model and integrates the output gapfilling solution