A small package to convert ODEs specified in a YAML file to SBML/PEtab
Project description
Table of contents
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
.
Contact
If you have a question regarding the tool: Please drop us an issue or a mail, we are happy to help.
Project details
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