sbmlsim.simulation.kisaos

Working with the KISAO ontology.

Module Contents

Functions

is_supported_algorithm_for_simulation_type(kisao, sim_type)

Check Algorithm Kisao Id is supported for simulation.

integrator_from_kisao(kisao)

Get RoadRunner integrator name for algorithm KisaoID.

algorithm_parameter_to_parameter_key(par)

Resolve the mapping between parameter keys and roadrunner integrator keys.

Attributes

logger

KISAOS_CVODE

KISAOS_RK4

KISAOS_RK45

KISAOS_LSODA

KISAOS_GILLESPIE

KISAOS_NLEQ

KISAOS_STEADYSTATE

KISAOS_UNIFORMTIMECOURSE

KISAOS_ONESTEP

KISAOS_ALGORITHMPARAMETERS

sbmlsim.simulation.kisaos.logger[source]
sbmlsim.simulation.kisaos.KISAOS_CVODE = ['KISAO:0000019', 'KISAO:0000433', 'KISAO:0000407', 'KISAO:0000099', 'KISAO:0000035',...[source]
sbmlsim.simulation.kisaos.KISAOS_RK4 = ['KISAO:0000032', 'KISAO:0000064'][source]
sbmlsim.simulation.kisaos.KISAOS_RK45 = ['KISAO:0000086'][source]
sbmlsim.simulation.kisaos.KISAOS_LSODA = ['KISAO:0000088'][source]
sbmlsim.simulation.kisaos.KISAOS_GILLESPIE = ['KISAO:0000241', 'KISAO:0000029', 'KISAO:0000319', 'KISAO:0000274', 'KISAO:0000333',...[source]
sbmlsim.simulation.kisaos.KISAOS_NLEQ = ['KISAO:0000099', 'KISAO:0000274', 'KISAO:0000282', 'KISAO:0000283', 'KISAO:0000355',...[source]
sbmlsim.simulation.kisaos.KISAOS_STEADYSTATE[source]
sbmlsim.simulation.kisaos.KISAOS_UNIFORMTIMECOURSE[source]
sbmlsim.simulation.kisaos.KISAOS_ONESTEP[source]
sbmlsim.simulation.kisaos.KISAOS_ALGORITHMPARAMETERS[source]
sbmlsim.simulation.kisaos.is_supported_algorithm_for_simulation_type(kisao, sim_type)[source]

Check Algorithm Kisao Id is supported for simulation.

Returns

is supported

Return type

bool

sbmlsim.simulation.kisaos.integrator_from_kisao(kisao)[source]

Get RoadRunner integrator name for algorithm KisaoID.

Parameters

kisao (str) – KisaoID

Returns

RoadRunner integrator name.

Return type

str

sbmlsim.simulation.kisaos.algorithm_parameter_to_parameter_key(par)[source]

Resolve the mapping between parameter keys and roadrunner integrator keys.