• Introduction

• Installation

• Usage

  • Command line interface

  • Python

• Known issues and limitations

yaml2sbml is a small package to convert an ODE model specified in a yaml file into an SBML for ODE simulation and into PEtab for parameter fitting. These file formats can be used with other packages.

• format_documentation.md provides a documentation of the format of the input yaml.

• Examples can be found in the examples folder.

To install go to the main folder and do:

pip install .

• Python 3.6+
• python-libsbml>=5.18.0
• PyYAML>=5.3
• pandas >= 1.0.1
• PEtab >= 0.1.4

• requirements.txt

If you don't have Python 3.6 or higher in your system, the best way to get it is either using pyenv or conda.

With conda you can create a virtual environment with a specific python version. To do so start by installing miniconda if you don't have any sort of conda installed yet, and then create a virtual environment using a specific version of python:

conda create -n <virtual_env_name> python=3.7

To activate the virtual environment do

source activate <virtual_env_ńame>

To install packages use either pip or conda:

conda/pip install <package_name>

You can either call yaml2sbml via its command line interface or within your python code:

To convert an ODE model encoded in a yaml file to SBML using the terminal, go to the yaml2sbml folder and run:

 yaml2sbml <yaml_input_file> <sbml_output_file>

For instance, using the yaml file in the examples folder:

 yaml2sbml ../examples/ode_input1.yaml ../examples/sbml_out.xml

If you want to generate PEtab parameter, observable and condition tables, additionally to the SBML file using the terminal, go to the yaml2sbml folderand run:

 yaml2petab <yaml_input_file> <petab_output_directory> <model_name>

For instance, again using the yaml file in the examples folder:

 yaml2petab ../examples/ode_input1.yaml ../examples/ example_model.xml

Alternatively you can call yaml2sbml within your python code via

import yaml2sbml

yaml2sbml.yaml2sbml(yaml_file, sbml_file)

Here all inputs ar given as strings.

To generate PEtab files call yaml2petab via

import yaml2sbml

yaml2sbml.yaml2petab(yaml_file,
                     output_dir,
                     model_name)

Here yaml_file, output_dir and model_name are strings.

• Compartments are not supported.
• Units are not supported, all quantities are dimensionless.
• Specification of PEtab data tables are not in the scope of this tool.