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## Table of contents
* [About](#about)
* [Installation](#installation)
* [Getting Started](#getting-started)
* [Basic Syntax](#basic-syntax)
* [How to cite](#how-to-cite)
* [Contact](#contact)
## About
`yaml2sbml` is a small package in Python to convert an ODE model specified in a YAML file into
[**SBML**](http://www.sbml.org/) for ODE simulation and into
[**PEtab**](https://github.com/PEtab-dev/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
```shell
pip install yaml2sbml
```
For more info see the [docs](https://yaml2sbml.readthedocs.io/en/latest/).
## Getting Started
* The documentation of the tool is hosted on [Read the Docs](https://yaml2sbml.readthedocs.io/en/latest/).
* The [format documentation](https://yaml2sbml.readthedocs.io/en/latest/format_specification.html) describes the input YAML.
* Jupyter notebooks containing examples can be found under [`doc/examples`](https://github.com/yaml2sbml-dev/yaml2sbml/tree/main/doc/examples). Most notably:
* [Lotka_Volterra.ipynb](https://github.com/yaml2sbml-dev/yaml2sbml/tree/main/doc/examples/Lotka_Volterra/Lotka_Volterra_python/Lotka_Volterra.ipynb) showing the Python package,
* [Lotka_Volterra_CLI.ipynb](https://github.com/yaml2sbml-dev/yaml2sbml/tree/main/doc/examples/Lotka_Volterra/Lotka_Volterra_CLI/Lotka_Volterra_CLI.ipynb) showing the command-line interface, and
* [Lotka_Volterra_Model_Editor.ipynb](https://github.com/yaml2sbml-dev/yaml2sbml/tree/main/doc/examples/Lotka_Volterra/Lotka_Volterra_Model_Editor/Lotka_Volterra_Model_Editor.ipynb) demonstrates the Model Editor.
## Basic Syntax
### Python
A YAML model can be translated to SBML/PEtab in Python via
```python
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
```shell
# SBML conversion
yaml2sbml
#PEtab conversion
yaml2petab
```
### 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](https://joss.theoj.org/papers/10.21105/joss.03215).
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](https://github.com/yaml2sbml-dev/yaml2sbml/issues/new) or a [mail](mailto:jakob.vanhoefer@uni-bonn.de), we are happy to help.