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A small package to convert ODEs specified in a YAML file to SBML/PEtab

Project description

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About

yaml2sbml is a small package in Python to convert an ODE model specified in a YAML file into SBML for ODE simulation and into PEtab for parameter fitting. yaml2sbml offers:

  • a translator of ODE models specified in YAML into SBML/PEtab via a Python and a command-line interface;
  • a format validator for the input YAML; and
  • a model editor, which provides a simplified interface to generate, import and export YAML models.

Installation

yaml2sbml can be installed from PyPI with

pip install yaml2sbml

For more info see the docs.

Getting Started

Basic Syntax

Python

A YAML model can be translated to SBML/PEtab in Python via

import yaml2sbml

# SBML conversion
yaml2sbml.yaml2sbml(yaml_dir, sbml_dir)

#PEtab conversion
yaml2sbml.yaml2petab(yaml_dir, 
                     output_dir,
                     sbml_name)

Command-Line Interface

and in the command-line via

# SBML conversion
yaml2sbml <yaml_dir> <sbml_dir>

#PEtab conversion
yaml2petab <yaml_dir> <output_dir> <sbml_name>

Format Validation

Format validation is possible in Python via yaml2sbml.validate_yaml and in the command-line via yaml2sbml_validate.

How to cite

yaml2sbml is published in the Journal of Open Source Software.

When using yaml2sbml in your project, please cite

  • Vanhoefer J., Matos, M. R. A., Pathirana, D., Schälte, Y. and Hasenauer, J. (2021). yaml2sbml: Human-readable and -writable specification of ODE models and their conversion to SBML. Journal of Open Source Software, 6(61), 3215, https://doi.org/10.21105/joss.03215
@article{Vanhoefer2021,
  doi = {10.21105/joss.03215},
  url = {https://doi.org/10.21105/joss.03215},
  year = {2021},
  publisher = {The Open Journal},
  volume = {6},
  number = {61},
  pages = {3215},
  author = {Jakob Vanhoefer and Marta R. A. Matos and Dilan Pathirana and Yannik Schälte and Jan Hasenauer},
  title = {yaml2sbml: Human-readable and -writable specification of ODE models and their conversion to SBML},
  journal = {Journal of Open Source Software}
}

Contact

If you have a question regarding the tool: Please drop us an issue or a mail, we are happy to help.

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