autoreduce 0.3.0

Python based automated model reduction tools for SBML models

AutoReduce: An automated model reduction tool

Python toolbox to automatically obtain reduced model expressions using time-scale separation, conservation laws, and other assumptions.

Overview

AutoReduce is a Python package for automated model reduction of SBML models. It provides tools for:

• Automated model reduction using QSSA (Quasi-Steady State Approximation)
• Hill function approximation
• Integration with BioCRNPyler for synthetic biology models
• Analysis of gene expression models

Refer to the bioRxiv paper and Journal of Robust and Nonlinear Control paper for more details.

Quick Start

from autoreduce.converters import load_sbml

# Load your SBML model
sys = load_sbml('your_sbml_file.xml', outputs=['your_output'])

# Solve conservation laws
conservation_laws = sys.solve_conservation_laws(
    conserved_sets=[
        ['species1', 'species2', 'species3'],  # First conserved set
        ['species4', 'species5']               # Second conserved set
    ],
    states_to_eliminate=['species_to_eliminate1', 'species_to_eliminate2']
)

# Solve timescale separation using QSSA
reduced_qssa_model = sys.solve_timescale_separation(
    ['fast_species1', 'fast_species2']
    )

For more examples, check out the documentation.

Installation

Install the latest version of AutoReduce:

pip install autoreduce

Install with all optional dependencies:

pip install autoreduce[all]

For development installation:

git clone https://github.com/ayush9pandey/autoreduce.git
cd autoreduce
pip install -e ".[all]"

Documentation

Full documentation is available at autoreduce.readthedocs.io.

Contributing

We welcome contributions! Please see our contributing guide for details.

Versions

AutoReduce versions:

• 0.3.0 (current release): Major updates including improved API and documentation
• 0.2.0 (alpha release): pip install autoreduce==0.2.0
• 0.1.0 (alpha release): pip install autoreduce==0.1.0

Contact

For questions, feedback, or suggestions, please contact:

• Ayush Pandey (ayushpandey at ucmerced dot edu)
• GitHub Issues

License

Released under the BSD 3-Clause License (see LICENSE)

Copyright (c) 2025, Ayush Pandey. All rights reserved.