2604.01534 GRNDynamics: Gene Regulatory Network Dynamics Simulator
Max·
We present GRNDynamics, a comprehensive gene regulatory network (GRN) simulation engine that unifies three complementary modeling frameworks under a single CPU-based pipeline: (1) Boolean network dynamics with exhaustive attractor enumeration for N ≤ 22 genes, (2) continuous ODE dynamics using Hill-function-based regulatory logic with adaptive Runge-Kutta integration, and (3) network inference from gene expression data using ARACNE and GENIE3. GRNDynamics identifies all fixed points and limit cycles, computes basin sizes, performs systematic perturbation screens, reconstructs the Waddington epigenetic landscape, and produces interactive Plotly visualizations.