SYNBADm

SYNBADm performs automated optimal design of de novo gene circuits in MATLAB by jointly exploring structural and kinetic parameter spaces to satisfy predefined performance functions.

Key Features:

• Global Optimization: Employs global optimization techniques to explore structural and kinetic parameter spaces simultaneously.
• Multiobjective Optimization: Implements multiobjective optimization to balance multiple design criteria and trade-offs among performance metrics.
• High Complexity Handling: Manages high levels of circuit complexity enabling design of multi-functional circuits.
• Flexible Design Framework: Allows definition of custom modeling frameworks, selection from libraries of components, and specification of target performance functions.
• MATLAB Integration: Operates as a toolbox within the MATLAB environment.

Scientific Applications:

• Complex gene circuit design: Design of de novo synthetic gene circuits that perform multiple functions or exhibit sophisticated behaviors.
• Metabolic engineering: Design and optimization of genetic systems for metabolic engineering applications.
• Biosensing: Design of biosensing circuits and sensory-response architectures.
• Programmable cellular behaviors: Engineering programmable cellular behaviors via optimized gene circuits.
• Model-to-experiment translation: Facilitates transition from computational models to wet lab implementations.

Methodology:

Uses global and multiobjective optimization within MATLAB to search structural and kinetic parameter spaces, and supports user-defined modeling frameworks, component libraries, and specification of target performance functions.