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Assembly of Cell Mimicking Supported and Suspended Lipid Bilayer Models for the Study of Molecular Interactions

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Published on: August 3, 2021

Pycellerator: an arrow-based reaction-like modelling language for biological simulations.

Bruce E Shapiro¹, Eric Mjolsness²

¹Department of Mathematics, California State University, Northridge, CA 91330, USA and.

Bioinformatics (Oxford, England)

|October 28, 2015

Summary

Pycellerator is a new Python library that converts Cellerator reaction notation into Python code for solving differential equations. This tool simplifies biochemical pathway modeling and analysis without requiring Mathematica.

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Area of Science:

Computational Biology
Biochemistry
Systems Biology

Background:

Cellerator software previously used Mathematica for biochemical reaction modeling.
Reaction notation was limited to Mathematica's extended character set.
A need existed for a more accessible and independent tool for biochemical modeling.

Purpose of the Study:

Introduce Pycellerator, a novel Python library.
Enable reading Cellerator arrow notation from text files.
Facilitate conversion to differential equations and generation of Python solvers.

Main Methods:

Pycellerator parses ASCII text files containing Cellerator reaction notation.
Converts parsed reactions into Python differential equations.
Automatically generates stand-alone Python solvers for simulating reaction dynamics.

Main Results:

Pycellerator successfully translates various reaction types (mass action, MMH, GRN, MWC, KMech) into Python code.
Generated Python solvers can be executed to produce time courses.
The library offers a Python command-line interface (CLI), API, and iPython notebook interface.
Pycellerator is independent of Cellerator and Mathematica.

Conclusions:

Pycellerator provides a flexible and powerful Python-based solution for biochemical pathway modeling.
Simplifies the process of converting complex reaction mechanisms into executable code.
Enhances accessibility for researchers by removing Mathematica dependency.