BioNetCAD

BioNetCAD enables the design, simulation, and in silico validation of cell-free biochemical networks to support synthetic biology construction and analysis of novel biochemical pathways.

Key Features:

• Design Phase: Conceptualizes abstract biochemical networks and assembles synthetic biology parts from CompuBioTicDB into novel network configurations.
• Simulation Capability: Predicts network dynamics using HSim software and classical Ordinary Differential Equations (ODE).
• Experimental Validation Support: Rationalizes designs and simulation outputs to reduce the need for extensive experimental validation and to guide experimental implementation.

Scientific Applications:

• Engineering novel biochemical pathways: Enables design and analysis of cell-free biochemical networks for constructing pathways not present in nature.
• Pre-experimental validation: Provides in silico prediction of network behavior to prioritize constructs before laboratory implementation.

Methodology:

Design of abstract biochemical networks using parts from CompuBioTicDB; simulation with HSim and classical Ordinary Differential Equations (ODE); and use of simulation outputs to inform experimental validation.