The Phoenix project describes a framework to design complex genetic systems where the focus is on how the system behaves over time instead of its behavior at steady-state. Using Signal Temporal Logic (STL) -- a formalism used to specify properties of dense-time real-valued signals, biologists can specify very precise temporal behaviors of a genetic system.
The framework describes how genetic circuits that are built from a well characterized library of DNA parts, can be scored by quantifying the 'degree of robustness' of in-silico simulations against an STL formula. Using formal verification, experimental data can be used to validate these in-silico designs. In this framework, the design space is also explored to predict external controls (such as approximate small molecule concentrations) that might be required to achieve a desired temporal behavior.
Key Features
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Users can specify the temporal behavior
of their circuits using STL -
Users can also derive STL formulae from
time-series data using GridTLI -
Users can use this tool to explore the
solution space and identify experiment
Funding
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Office of Naval Research MURI Award
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Program Manager: Linda Chrisey
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NSF Program: CYBER-PHYSICAL SYSTEMS (CPS)
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Program Manager: Gurdip Singh
