biosimulators_ibiosim package

Submodules

biosimulators_ibiosim.core module

Methods for executing SED tasks in COMBINE archives and saving their outputs

Author

Myers Research Group <chris.myers@colorado.edu>

Date

2020-06-12

Copyright

2020

License

Apache-2.0

biosimulators_ibiosim.core.exec_sedml_docs_in_combine_archive(archive_filename, out_dir, report_formats=None, plot_formats=None, bundle_outputs=None, keep_individual_outputs=None)[source]

Execute the SED tasks defined in a COMBINE/OMEX archive and save the outputs

Parameters

  • archive_filename (str) – path to COMBINE/OMEX archive

  • out_dir (str) –

    path to store the outputs of the archive

    • CSV: directory in which to save outputs to files { out_dir }/{ relative-path-to-SED-ML-file-within-archive }/{ report.id }.csv

    • HDF5: directory in which to save a single HDF5 file ({ out_dir }/reports.h5), with reports at keys { relative-path-to-SED-ML-file-within-archive }/{ report.id } within the HDF5 file

  • report_formats (list of ReportFormat, optional) – report format (e.g., csv or h5)

  • plot_formats (list of PlotFormat, optional) – report format (e.g., pdf)

  • bundle_outputs (bool, optional) – if True, bundle outputs into archives for reports and plots

  • keep_individual_outputs (bool, optional) – if True, keep individual output files

biosimulators_ibiosim.core.get_ibiosim_version()[source]

Get the version of iBioSim

Returns

version

Return type

str