BSTModelKit.jl: A Julia Package for Constructing, Solving, and Analyzing Biochemical Systems Theory Models

TL;DR

BSTModelKit.jl is an open-source Julia package that facilitates the construction, simulation, and analysis of biochemical systems models using S-system formalism, integrating advanced numerical methods for efficient analysis.

Contribution

It introduces a comprehensive Julia package for BST modeling, combining model specification, simulation, steady-state analysis, and sensitivity analysis within the Julia ecosystem.

Findings

Efficient simulation of biochemical networks using Julia's SciML tools.

Successful demonstration of model analysis with illustrative examples.

Integration of global sensitivity analysis methods like Morris and Sobol.

Abstract

We present BSTModelKit.jl, an open-source Julia package for constructing, solving, and analyzing Biochemical Systems Theory (BST) models of biochemical networks. The package implements S-system representations, a canonical power-law formalism for modeling metabolic and regulatory networks. BSTModelKit.jl provides a declarative model specification format, dynamic simulation via ordinary differential equation (ODE) integration, steady-state computation, and global sensitivity analysis using the Morris and Sobol methods. The package leverages the Julia scientific computing ecosystem, in particular the SciML suite of differential equation solvers, to provide efficient and flexible model analysis tools. We describe the mathematical formulation, software design, and demonstrate the package capabilities with illustrative examples.