Index

A

add_emitter_node() (bio_compose.bundles.BioBundle method)

Api (class in bio_compose.data_model)

B

bio_compose.api module bio_compose.bundles module bio_compose.composer module bio_compose.data_model module

bio_compose.processing_tools module bio_compose.runner module bio_compose.verifier module BioBundle (class in bio_compose.bundles)

C

Composer (class in bio_compose.composer)

D

data (bio_compose.composer.Composer attribute)

DynamicJson (class in bio_compose.data_model)

E

endpoint_root (bio_compose.composer.Composer attribute) error (bio_compose.data_model.RequestError attribute)

export_csv() (bio_compose.data_model.Api method) export_plot() (bio_compose.data_model.Api method)

F

fetch_job() (in module bio_compose.data_model)

G

generate_color_gradient() (in module bio_compose.processing_tools) generate_node() (bio_compose.bundles.BioBundle method) generate_port_spec() (bio_compose.bundles.BioBundle method) generate_simularium_file() (bio_compose.runner.SimulationRunner method) get_biomodel_archive() (in module bio_compose.api) get_biomodel_file() (in module bio_compose.api) get_comparison() (bio_compose.verifier.VerificationResult method) get_compatible() (bio_compose.verifier.Verifier method)

get_compatible_verification_simulators() (in module bio_compose.api) get_job_signature() (in module bio_compose.processing_tools) get_job_status() (bio_compose.data_model.Api method) get_observables() (bio_compose.data_model.Api method) get_output() (bio_compose.data_model.Api method) (in module bio_compose.api) get_output_observables() (bio_compose.verifier.VerificationResult method) get_rmse() (bio_compose.verifier.Verifier method)

M

module bio_compose.api bio_compose.bundles bio_compose.composer bio_compose.data_model bio_compose.processing_tools bio_compose.runner bio_compose.verifier

R

read_observables() (bio_compose.data_model.Api method) RequestError (class in bio_compose.data_model) run_batch_verification() (in module bio_compose.api)

run_composition() (bio_compose.composer.Composer method) run_simulation() (in module bio_compose.api) run_smoldyn_simulation() (bio_compose.runner.SimulationRunner method) run_utc_simulation() (bio_compose.runner.SimulationRunner method)

S

save_plot() (in module bio_compose.data_model) select_observables() (bio_compose.data_model.Api method)

SimulationResult (class in bio_compose.runner) SimulationRunner (class in bio_compose.runner) submitted_jobs (bio_compose.composer.Composer attribute)

T

to_dict() (bio_compose.data_model.RequestError method)

V

VerificationResult (class in bio_compose.verifier) Verifier (class in bio_compose.verifier) verify() (in module bio_compose.api) verify_omex() (bio_compose.verifier.Verifier method) verify_sbml() (bio_compose.verifier.Verifier method)

visualize() (bio_compose.runner.SimulationResult method) visualize_comparison() (bio_compose.verifier.Verifier method) visualize_observables() (bio_compose.runner.SimulationRunner method) (bio_compose.verifier.Verifier method) (in module bio_compose.api) visualize_rmse() (bio_compose.verifier.Verifier method)