Design, Build, Test, Learn

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

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

Office of Naval Research MURI Award
Program Manager: Linda Chrisey

NSF Program: CYBER-PHYSICAL SYSTEMS (CPS)
Program Manager: Gurdip Singh
Award Abstract

Phoenix is free to use, and the Grid TLI can be accessed by clicking the button below:

GRID TLI

Representative Publications

Selected Phoenix Publications:

E. Appleton, E. Oberortner, P. Vaidyanathan, Z. Chapasko, Y. Pacheco Alan andAgarwal, N. Roehner, T. Haddock, and D. Densmore, Phoenix: An automated design-build, poster presented at the International Workshop on Bio-Design Automation (IWBDA) , August, 2015.

E. Appleton, P. Vaidyanathan, A. Pacheco, I. Haghighi, C. Vasile, C. Madsen, N. Roehner, Y. Agarwal, Z. Chapasko, C. Belta, and D. Densmore, Phoenix: A Design-Build-Test-Learn Tool, talk presented at the Synberc 2015 Fall Retreat , September, 2015.

D. Densmore, C. Madsen, and P. Vaidyanathan, Bio Design Automation & Synthesis of Functional Specification, presented at the NSF Kickoff meeting for bioCPS , February, 2016.

C. Belta, D. Densmore, V. Kumar, and R. Weiss, CPS: Frontier: Collaborative Research: bioCPS for Engineering Living Cells, poster presented at the NSF CPS PI Meeting 2015 , November, 2015.

P. Vaidyanathan, R. Ivison, G. Bombara, N. A. DeLateur, R. Weiss, D. Densmore, and C. Belta, “Grid-based temporal logic inference,” in 2017 IEEE 56th Annual Conference on Decision and Control (CDC), 2017, pp. 5354-5359.

G. Misirli, T. Nguyen, J. A. McLaughlin, P. Vaidyanathan, T. Jones, D. Densmore, C. J. Myers, and A. Wipat, “A computational workflow for the automated generation of models of genetic designs,” ACS synthetic biology, 2018.

C. Madsen, P. Vaidyanathan, S. Sadraddini, C. I. Vasile, N. A. DeLateur, R. Weiss, D. Densmore, and C. Belta, "Metrics for Signal Temporal Logic Formulae" in 2018 IEEE Conference on Decision and Control (CDC), 2018, pp. 1542-1547.