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- Feature, Signal, and Part Matching
- Matchmaker is a Clotho app for translating an abstract genetic regulatory network into a specific sequence of genetic parts.
- Schematic-based Visual Design
- Spectacles is a Clotho App which acts as a genetic regulatory network schematic design tool.
- Design algorithms
- Algorithm Manager is a Clotho App which houses a variety of design algorithms.
- Invertase placement algorithms
- Trumpet is a Clotho App for placing invertases to explore configurations of genetic circuits.
- Design for X
- DFX examines how genetic designs can be automatically analyzed to improve robustness, reliability, and testability.
- Ontology/Family Classification of Synthetic Biological Designs
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