Design, Build, Test, Learn

Phoenix is a tool where users are guided through an iterative, hierarchical design-build-test cycle with sets of building and testing instructions.

Given a functional specification and a structural specification, Phoenix helps break down the Structural Module, test available parts in the library, predict behavior using simulation tools, assign parts to the Genetic network and learn from results derived from empirical data.

Key features

  • Verification of Structural Specification
  • Producing Assembly Instructions for testing (using Raven)
  • Storing all data in Clotho
  • Data analytics for Cytometry data
  • Predicting behavior of a genetic network using simulation tools
  • Verifying results using Model checking
  • Generating datasheets (using Owl)

Funding

  • Office of Naval Research MURI Award
  • Program Manager: Linda Chrisey
  • NSF Program: CYBER-PHYSICAL SYSTEMS (CPS)
  • Program Manager: Gurdip Singh
  • Award Abstract


Accessing Phoenix

Phoenix is currently in development, and is not available to the general public.

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Try Phoenix

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.
    [BibTeX] [Download PDF]
    @Misc{AppletonPhoenixIWBDA2015,
    Title = {Phoenix: An automated design-build},
    Author = {Appleton, Evan and Oberortner, Ernst and Vaidyanathan, Prashant and Chapasko, Zachary and Pacheco, Alan andAgarwal, Yash and Roehner, Nicholas and Haddock, Traci and Densmore, Douglas},
    HowPublished = {poster presented at the International Workshop on Bio-Design Automation (IWBDA)},
    Month = {August},
    Year = {2015},
    Owner = {Evan Appleton},
    Timestamp = {2015.09.17},
    URL = {http://cidarlab.org/wp-content/uploads/2015/09/IWBDA_Poster.pdf}
    }

  • 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.
    [BibTeX]
    @Misc{AppletonSynBERCPhoenix2015,
    Title = {Phoenix: A Design-Build-Test-Learn Tool},
    Author = {Evan Appleton and Prashant Vaidyanathan and Alan Pacheco and Iman Haghighi and Christian-loan Vasile and Curtis Madsen and Nicholas Roehner and Yash Agarwal and Zachary Chapasko and Calin Belta and Douglas Densmore},
    HowPublished = {talk presented at the Synberc 2015 Fall Retreat},
    Month = {September},
    Year = {2015},
    Keywords = {phoenix, cidar}
    }

  • D. Densmore, C. Madsen, and P. Vaidyanathan, Bio Design Automation & Synthesis of Functional Specification, presented at the NSF Kickoff meeting for bioCPS , February, 2016.
    [BibTeX] [Download PDF]
    @Misc{NSFbioCPSKickoff,
    Title = {Bio Design Automation \& Synthesis of Functional Specification},
    Author = {Douglas Densmore and Curtis Madsen and Prashant Vaidyanathan},
    HowPublished = {presented at the NSF Kickoff meeting for bioCPS},
    Month = {February},
    Year = {2016},
    Keywords = {biocps, phoenix},
    URL = {http://cidarlab.org/wp-content/uploads/2016/02/BDA_STL.pptx}
    }

  • 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.
    [BibTeX]
    @Misc{nsfcps2015,
    Title = {CPS: Frontier: Collaborative Research: bioCPS for Engineering Living Cells},
    Author = {Calin Belta and Doug Densmore and Vijay Kumar and Ron Weiss},
    HowPublished = {poster presented at the NSF CPS PI Meeting 2015 },
    Month = {November},
    Year = {2015}
    }

  • P. Vaidyanathan, E. Appleton, C. Madsen, C. Vasile, A. Pacheco, I. Haghighi, N. Roehner, R. Ivison, J. Wang, Y. Agarwal, Z. Chapasko, C. Belta, and D. Densmore, Genetic Systems Engineering, poster presented at the International Workshop on Bio-Design Automation (IWBDA) , August, 2016.
    [BibTeX] [Abstract] [Download PDF]
    http://cidarlab.org/wp-content/uploads/2016/09/phoenix.pdf

    @Misc{vaidyanathan2016genetic,
    author = {Prashant Vaidyanathan and Evan Appleton and Curtis Madsen and Cristian-Ioan Vasile and Alan Pacheco and Iman Haghighi and Nicholas Roehner and Rachael Ivison and Junmin Wang and Yash Agarwal and Zachary Chapasko and Calin Belta and Douglas Densmore},
    title = {Genetic Systems Engineering},
    howpublished = {poster presented at the International Workshop on Bio-Design Automation (IWBDA)},
    month = {August},
    year = {2016},
    abstract = {http://cidarlab.org/wp-content/uploads/2016/09/phoenix.pdf},
    url = {http://cidarlab.org/wp-content/uploads/2016/09/PhoenixPosterFinal-1.pdf}
    }

  • 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. doi:10.1109/CDC.2017.8264452
    [BibTeX]
    @InProceedings{vaidyanathan2017grid,
    author = {Vaidyanathan, Prashant and Ivison, Rachael and Bombara, Giuseppe and DeLateur, Nicholas A. and Weiss, Ron and Densmore, Douglas and Belta, Calin},
    title = {Grid-based temporal logic inference},
    booktitle = {2017 IEEE 56th Annual Conference on Decision and Control (CDC)},
    year = {2017},
    pages = {5354--5359},
    month = {Dec},
    organization = {IEEE},
    doi = {10.1109/CDC.2017.8264452},
    keywords = {Clustering algorithms;Genetics;Inference algorithms;Optimization;Robustness;Training},
    }

  • C. Madsen, E. Appleton, P. Vaidyanathan, R. Mardian, C. Vasile, K. Elkind, A. Bennett, F. Cao, M. Nagata, C. Belta, and D. Densmore, Phoenix: A Systems Engineering Approach to Genetic Circuit Synthesis, Poster presented at the 9th International Workshop on Bio-Design Automation (IWBDA) , August, 2017.
    [BibTeX] [Download PDF]
    @Misc{madsen2017phoenix,
    author = {Curtis Madsen and Evan Appleton and Prashant Vaidyanathan and Rizki Mardian and Cristian-Ioan Vasile and Katherine Elkind and Alexander Bennett and Fan Cao and Masakazu Nagata and Calin Belta and Douglas Densmore},
    title = {Phoenix: A Systems Engineering Approach to Genetic Circuit Synthesis},
    howpublished = {Poster presented at the 9th International Workshop on Bio-Design Automation (IWBDA)},
    month = {August},
    year = {2017},
    url = {***},
    }

  • C. Madsen, E. Appleton, P. Vaidyanathan, R. Mardian, C. Vasile, K. Elkind, A. Bennett, F. Cao, M. Nagata, C. Belta, and D. Densmore, Phoenix: A Systems Engineering Approach to Genetic Circuit Synthesis, Poster presented at the 9th International Workshop on Bio-Design Automation (IWBDA) , August, 2017.
    [BibTeX] [Download PDF]
    @Misc{madsen2017phoenix,
    author = {Curtis Madsen and Evan Appleton and Prashant Vaidyanathan and Rizki Mardian and Cristian-Ioan Vasile and Katherine Elkind and Alexander Bennett and Fan Cao and Masakazu Nagata and Calin Belta and Douglas Densmore},
    title = {Phoenix: A Systems Engineering Approach to Genetic Circuit Synthesis},
    howpublished = {Poster presented at the 9th International Workshop on Bio-Design Automation (IWBDA)},
    month = {August},
    year = {2017},
    url = {***},
    }

  • G. M{i}s{i}rl{i}, 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.
    [BibTeX]
    @Article{misirli2018computational,
    author = {M{\i}s{\i}rl{\i}, G{"o}ksel and Nguyen, Tramy and McLaughlin, James Alastair and Vaidyanathan, Prashant and Jones, Timothy and Densmore, Douglas and Myers, Chris J and Wipat, Anil},
    title = {A computational workflow for the automated generation of models of genetic designs},
    journal = {ACS synthetic biology},
    year = {2018},
    publisher = {ACS Publications},
    }

CIDAR Project Leads:

Prashant Vaidyanathan
Curtis Madsen

CIDAR Collaborators:

Nicholas DeLateur
Evan Appleton