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        "description": "# SBMLtoODEpy\n[![DOI](https://zenodo.org/badge/194863719.svg)](https://zenodo.org/badge/latestdoi/194863719)\n[![status](https://joss.theoj.org/papers/7180dfddc52a8b3bbf13b58eaa0e6d45/status.svg)](https://joss.theoj.org/papers/7180dfddc52a8b3bbf13b58eaa0e6d45)\n\n## Overview\nSBMLtoODEpy is a software package that converts Systems Biology Markup Language (SBML) models into Python classes that can be rapidly incorporated into biomedical systems modeling projects written in Python, such as the multiscale simulation platform CompuCell3D, or used simulated directly as ordinary equations models in Python. \n\n## Authors\nSteve M. Ruggiero and Ashlee N. Ford Versypt (ashleefv@okstate.edu), School of Chemical Engineering, Oklahoma State University\n\n## Usage\nThe simplest use of this package is to use the ParseAndGenerate function to quickly create a python implementation of an SBML model.\n\n```python\nimport sbmltoodepy\nParseAndCreateModel(inputFilePath, jsonFilePath = None, outputFilePath = None, className = \"SBMLmodel\")\n```\n\nThe parameters are:\n* inputFilePath: The file path of the SBML model.\n* jsonFilePath: An optional file path that if provided is where the function will create a json file containing all of the model elements. If not provided, a json file will not be created.\n* outputFilePath: An optional file path of where the python model implementation will be created. If not provided, the output path will be assumed to be the same as the input but with a .py extension.\n* className: The name of the class defined by the file created by this function.\n\nThis creates a new python file containing a class implementing the SBML model. \n\nTo run the model, instantiate the class and call the RunSimulation method with the desired timestep deltaT and optional specification of tolerances.\n\n```python\nmodel = SBMLmodel()\nmodel.RunSimulation(deltaT, absoluteTolerance = 1e-12, relativeTolerance = 1e-6)\n```\n\n## Installation Instructions\n\nSBMLtoODEpy requires either Python version 3.5, 3.6, or 3.7.\nSBMLtoODEpy can be downloaded using pip:\n```\npip install sbmltoodepy\n```\n\nAlternatively, SBMLtoODEpy can be installed from its source code by running the setup.py file included.\n```\npython setup.py install\n```\n\nTo test the package, use the TestPackage function.\n\n```python\nimport sbmltoodepy\nsbmltoodepy.utilities.TestPackage()\n```\n\nThe TestPackage function raises a warning about trying to set a constant species and 6 numbers.\n        \n1.27949533562e-06\n\n9.42747177955e-10\n\n1.33080766722e-07\n\n9.79758065656e-08\n\n4.05696056523e-07\n\n2.66117319017e-05\n    \nThese are the average relative errors for species, parameters, and compartments between the model results generated using SBMLtoODEpy and results calculated by COPASI for six different models provided in [the sbmltoodepy/sbml_files subdirectory](https://github.com/SMRuggiero/sbmltoodepy/tree/master/sbmltoodepy/sbml_files): Smallbone2013, Borisov2009, Guyton1972, Kerkhoven2013, Waugh2006, and Zi2011, respectively. These examples are discussed in more detail in the [tutorial](https://github.com/SMRuggiero/sbmltoodepy/blob/master/Tutorial.md).\n\n## Supporting Python packages\n\nThe following Python packages were used in this project and are needed to generate and run python models:\n* [NumPy][1]\n* [SciPy][2]\n* [libSBML][3]\n\n## Links\nFor more information on using this package, [click here to see the tutorial.](https://github.com/SMRuggiero/sbmltoodepy/blob/master/Tutorial.md)\n\nFor more information on SBML, including specifications and other software that supports SBML, [click here for the SBML web site](http://sbml.org/Main_Page)\n\nFor a good source of SBML models, [the BioModels repository is a great place to search.](https://www.ebi.ac.uk/biomodels/)\n\nFor this project's code documentation, [click here.](https://sbmltoodepy.readthedocs.io/en/latest/)\n\nFor this project's github repository, [click here.](https://github.com/SMRuggiero/sbmltopyode)\n\n[1]: https://www.numpy.org/ \"NumPy\"\n[2]: https://www.scipy.org/ \"SciPy\"\n[3]: http://sbml.org/Software/libSBML \"libSBML\"\n\n## Acknowledgments\n\nThe software package described here was made possible in part by funding through the award for project number HR17-057, from the Oklahoma Center for the Advancement of Science and Technology.\n\n## Community Guidelines\n\nTo contribute a change, users can contact Ashlee Ford Versypt by email ashleefv@okstate.edu or submit a pull request.",
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