BSTModelKit.jl: A Julia Package for Constructing, Solving, and Analyzing Biochemical Systems Theory Models
This package addresses the need for efficient and flexible analysis tools for biochemical systems modeling, primarily for researchers in computational biology, but it is incremental as it builds on existing Julia scientific computing libraries.
The authors tackled the problem of modeling biochemical networks by developing BSTModelKit.jl, a Julia package for constructing, solving, and analyzing Biochemical Systems Theory models, which provides tools like ODE integration, steady-state computation, and sensitivity analysis.
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.