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A Web Tool for Generating High Quality Machine-readable Biological Pathways

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PyRates-A code-generation tool for modeling dynamical systems in biology and beyond.

Richard Gast^1,2, Thomas R Knösche³, Ann Kennedy^1,2

¹Department of Neuroscience, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, United States of America.

Plos Computational Biology

|December 27, 2023

Summary

PyRates is a new Python software for modeling complex biological systems using differential equations. It simplifies model creation and analysis, supporting various interaction delays and backend languages for dynamic systems research.

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Area of Science:

Computational Biology
Mathematical Modeling
Systems Biology

Background:

Dynamical systems in biology are often modeled using differential equations.
Analyzing complex biological systems requires robust numerical methods.
Existing tools may not fully address the complexity and modularity of biological networks or interaction delays.

Purpose of the Study:

To introduce PyRates, a Python-based software for modeling and analyzing differential equation systems.
To provide a user-friendly language for defining modular biological models.
To facilitate the analysis of dynamical systems with interaction delays.

Main Methods:

PyRates utilizes a novel language for defining modular dynamical systems.
It features a code-generation system translating models to Python, Fortran, Matlab, and Julia.
Extensions like PyCoBi (bifurcation analysis) and RectiPy (parameter fitting) were developed.

Main Results:

PyRates simplifies the implementation of complex networks of interacting dynamic entities.
The software supports various forms of interaction delays common in biological systems.
Demonstrated PyRates' utility with PyCoBi and RectiPy for model analysis and fitting.

Conclusions:

PyRates offers a versatile framework for computational modeling and numerical analysis of biological dynamical systems.
The tool enhances the study of complex biological phenomena like virus spread and neural dynamics.
PyRates and its extensions streamline the application of advanced analysis methods to biological models.