API Documentation

• bio_compose
  • get_biomodel_archive()
  • get_biomodel_file()
  • get_compatible_verification_simulators()
  • get_output()
  • run_batch_verification()
  • run_simulation()
  • verify()
  • visualize_observables()
  • bio_compose.bundles
    • BioBundle
      • BioBundle.add_emitter_node()
      • BioBundle.generate_node()
      • BioBundle.generate_port_spec()
  • bio_compose.composer
    • Composer
      • Composer.data
      • Composer.endpoint_root
      • Composer.run_composition()
      • Composer.submitted_jobs
  • bio_compose.data_model
    • Api
      • Api.export_csv()
      • Api.export_plot()
      • Api.get_job_status()
      • Api.get_observables()
      • Api.get_output()
      • Api.read_observables()
      • Api.select_observables()
    • DynamicJson
    • RequestError
      • RequestError.error
      • RequestError.to_dict()
    • fetch_job()
    • save_plot()
  • bio_compose.processing_tools
    • generate_color_gradient()
    • get_job_signature()
  • bio_compose.runner
    • SimulationResult
      • SimulationResult.visualize()
    • SimulationRunner
      • SimulationRunner.generate_simularium_file()
      • SimulationRunner.run_smoldyn_simulation()
      • SimulationRunner.run_utc_simulation()
      • SimulationRunner.visualize_observables()
  • bio_compose.verifier
    • VerificationResult
      • VerificationResult.get_comparison()
      • VerificationResult.get_output_observables()
    • Verifier
      • Verifier.get_compatible()
      • Verifier.get_rmse()
      • Verifier.verify_omex()
      • Verifier.verify_sbml()
      • Verifier.visualize_comparison()
      • Verifier.visualize_observables()
      • Verifier.visualize_rmse()