SED-ML Builder from PEtab Files

This project provides a set of Python scripts to generate SED-ML files from PEtab data, allowing for streamlined modeling and simulation setup for biological experiments. The tools help automate the process of loading PEtab data, extracting relevant parameters, and building a SED-ML file for further computational analysis.

Project Structure

• builders.py: Constructs elements, classes, and objects necessary for the SED-ML file from PEtab data.
• extractors.py: Extracts essential details such as simulation times for building SED-ML files.
• loader.py: Loads PEtab files and extracts SBML models, parameters, and experimental conditions.

Installation

1. Clone the repository:

   git clone git@github.com:JonahRileyHuggins/PEtabToSEDML.git
   cd PEtabToSEDML

2. Requirements are provided in both a TOML file:

   pip install -r pyproject.toml

   As well as an Anaconda environment yaml, located in the 'env' directory.

conda env create -f env/environment.yml

Dependencies

The project requires the following Python packages:

• pandas
• lxml
• libsbml
• yaml
• phrasedml

Usage

Build SED-ML File

Use builders.py to build SED-ML elements and output a SED-ML file:

import source.builders as builders
builders.build_sedml_file(yaml_file='test_benchmark/test_benchmark.yml')

License

This project is licensed under the MIT License.