yaml2sbml 0.2.5

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

Table of contents

• About

• Installation

• Getting Started

• Basic Syntax

• How to cite

• Contact

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

• The documentation of the tool is hosted on Read the Docs.

• The format documentation describes the input YAML.

• Jupyter notebooks containing examples can be found under doc/examples. Most notably:

  • Lotka_Volterra.ipynb showing the Python package,
  • Lotka_Volterra_CLI.ipynb showing the command-line interface, and
  • Lotka_Volterra_Model_Editor.ipynb demonstrates the Model Editor.

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.