Models molecular biology gene regulatory networks using signed graphs for activation and inhibition logic.
CatColab Regulatory Networks is a specialized modeling tool designed for systems biologists and researchers to map complex molecular interactions. By utilizing signed category theory, it represents biological control logic through positive (activating) and negative (inhibiting) edges between genes, proteins, and metabolites. The skill allows users to define and analyze sophisticated network motifs—such as feedforward loops and toggle switches—while providing capabilities for steady-state analysis, Boolean dynamics simulation, and SBML export, making it essential for precise topological modeling of biological systems.
Key Features
01Models signed biological interactions for activation and inhibition
02Simulates Boolean dynamics and identifies steady states
03Supports model export to standard SBML format for interoperability
04Analyzes complex network motifs like feedforward and feedback loops
057 GitHub stars
06Built on rigorous mathematical foundations using double category theory
Use Cases
01Simulating metabolic switches such as the Lac Operon in bacteria
02Modeling tumor suppressor networks like p53 for oncology research
03Identifying statistically enriched motifs in large-scale genomic datasets
