Welcome to AutoReduce’s documentation!

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

Installation

You can install AutoReduce using pip:

pip install autoreduce

For development installation with all optional dependencies:

pip install -e ".[all]"

Quick Start

Here’s a simple example of using AutoReduce to reduce a model using conservation laws and timescale separation:

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 detailed examples, see the Examples section.

Contents

Indices and tables