switches

switches catalogs and analyzes bistable biochemical reaction network topologies to support systematic exploration of bistability and parameter dependence in biochemical systems.

Key Features:

• Exhaustive topology enumeration: All possible bistable biochemical reaction networks involving up to six reactions among three molecules or three reactions among four molecules are enumerated.
• Topology catalog: The enumeration yields over 35,000 unique reaction topologies.
• Parameterization: Each topology is populated with kinetic rates sampled within a biologically realistic range.
• Model repository: The populated topologies generate more than seven million distinct models available for analysis.
• Analytical capabilities: Bistability and parameter analysis are performed across the model set.
• Visualization support: Graphviz is used for visualization of reaction topologies.

Scientific Applications:

• Theoretical analysis of stability: Enables systematic investigation of stability and bistability in complex chemical reaction networks.
• Synthetic biology design: Informs the design and evaluation of robust synthetic biochemical switches and motifs relevant to cellular state decisions and long-term memory storage.

Methodology:

Exhaustive enumeration of reaction topologies (up to six reactions among three molecules or three reactions among four molecules), sampling of kinetic rates within biologically realistic ranges to populate topologies, generation of >7 million models, and computational bistability and parameter analysis; implemented using PHP, MariaDB, Graphviz, and Apache.