BDEtools

BDEtools implements numerical solvers for Boolean Delay Equations (BDEs) to simulate dynamical behaviors in biological networks.

Key Features:

• MATLAB implementation: Provided as a package of MATLAB functions and scripts for BDE modeling and simulation.
• Numerical solvers: Solver algorithms for the numerical solution of Boolean Delay Equations (BDEs).
• Dynamical regimes supported: Simulation of steady-state dynamics, periodic and quasiperiodic oscillations, frequency locking, and chaotic behavior.
• Input generation utilities: Functions for programmatic generation of BDE model inputs.
• Output processing utilities: Functions for post-processing and analysis of BDE simulation outputs.
• Low-level model generation: Generation of Boolean-based low-level descriptions that can be refined into differential-equation models.

Scientific Applications:

• Gene regulatory network modeling: Modeling of gene regulatory networks, including examples such as circadian rhythm control systems.
• Analysis of dynamical phenomena: Investigation of steady-state, periodic, quasiperiodic, frequency locking, and chaotic behaviors in biological networks.
• Coarse-grained model development: Production of Boolean low-level descriptions for subsequent refinement into differential-equation formulations.

Methodology:

Numerical solution of Boolean Delay Equations using MATLAB-implemented solver algorithms together with utility functions for input generation and output processing.