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Design, Build, Test, Learn

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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.

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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

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  • NSF Program: CYBER-PHYSICAL SYSTEMS (CPS)

  • Program Manager: Gurdip Singh

  • Award Abstract

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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.

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  • 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.

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

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  • 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.

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  • 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.

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  • 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.

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  • 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.