Gener

Gener implements DNA strand displacement programming using a simplified two-domain strand displacement algebra to design and analyze DNA-based computations and chemical controllers.

Key Features:

• Two-domain strand displacement algebra: Implements the simplified two-domain strand displacement algebra as the core computational formalism.
• Stepwise computation: Performs step-by-step execution of computations according to strand displacement algebra rules.
• Exhaustive search capability: Supports exhaustive exploration of computation spaces and options for analysis and visualization of potential outcomes.
• Export to DSD and LaTeX: Exports programs to Microsoft Research's DSD tool and to LaTeX formats.

Scientific Applications:

• Synthetic biology: Design and analysis of chemical controllers implemented via DNA strand displacement.
• Biosensing: Construction and evaluation of DNA-based biosensing systems.
• Molecular computation: Engineering molecular computation circuits using strand displacement mechanisms.
• Dynamic regulation: Design of DNA-based controllers for dynamic regulation of biological pathways and biochemical reactions.

Methodology:

Employs a simplified two-domain strand displacement algebra as the foundational computational framework to construct DNA-based programs that perform logical operations and control biochemical reactions.