research-clotho Store, Exchange, and Interact with Synthetic Biological Data
Clotho is a framework for engineering synthetic biological systems and managing the data used to create them. It serves as both a centralized location to store synthetic biological information — such as genetic parts, nucleic acid sequences, and physical samples– as well as a framework for applications (apps) which interact with said data.

Clotho provides software developers with a robust API, facilitating the development of new apps that aid synthetic biologists in the specification, design, and construction of novel biological systems. These apps provide Clotho users with new computational tools for performing many tasks, from data entry to genetic device visualization.

Clotho also aids in the exchange of information between applications, allowing users to utilize different apps to access and interact with the same pool of data.

Click to visit the official Clotho site.

Key features

  • Storage and exchange of biological data using the Clotho data model.
  • Built-in and user-developed apps for synthetic biological engineering.
  • Robust API for app development.

Funding

  • NSF Advances in Biological Informatics Program (ABI)
  • Program Manager: Anne Maglia
  • Award Abstract

Download Clotho

Clotho 3.0 can be downloaded by clicking the button to the right.

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Selected Clotho publications:

  • E. Appleton, S. Bhatia, T. Haddock, V. Vasilev, R. Ghamari, R. Ganguly, and D. Densmore., Specify, Design, and Assemble: A Top-Down Design Flow Using Clotho, talk presented at Cold Springs Harbor Asia Series 2011 Symposium: Design & Synthesis of Biological Systems , November, 2011.
    [BibTeX] [Download PDF]
    @MISC{appletonColdSpring2011,
    author = {Appleton, Evan and Bhatia, Swapnil and Haddock, Traci and Vasilev,
    Viktor and Ghamari, Roza and Ganguly, Rishi and Douglas Densmore.},
    title = {Specify, Design, and Assemble: A Top-Down Design Flow Using Clotho},
    howpublished = {talk presented at Cold Springs Harbor Asia Series 2011 Symposium:
    Design \& Synthesis of Biological Systems},
    month = {November},
    year = {2011},
    __markedentry = {},
    keywords = {clotho, synthetic biology},
    owner = {Aaron Heuckroth},
    timestamp = {2013.08.13},
    url = {http://cidarlab.org/wp-content/uploads/2013/09/appletonColdSpring2011.pdf}
    }

  • D. Densmore, A. Van Devender, M. Johnson, and N. Sritanyaratana, “A platform-based design environment for synthetic biological systems,” in The Fifth Richard Tapia Celebration of Diversity in Computing Conference: Intellect, Initiatives, Insight, and Innovations, New York, NY, USA, 2009, pp. 24-29. doi:10.1145/1565799.1565806
    [BibTeX] [Download PDF]
    @INPROCEEDINGS{Densmore:2009:PDE:1565799.1565806,
    author = {Densmore, Douglas and Van Devender, Anne and Johnson, Matthew and
    Sritanyaratana, Nade},
    title = {A platform-based design environment for synthetic biological systems},
    booktitle = {The Fifth Richard Tapia Celebration of Diversity in Computing Conference:
    Intellect, Initiatives, Insight, and Innovations},
    year = {2009},
    series = {TAPIA '09},
    pages = {24--29},
    address = {New York, NY, USA},
    publisher = {ACM},
    acmid = {1565806},
    doi = {10.1145/1565799.1565806},
    isbn = {978-1-60558-217-7},
    keywords = {clotho, design, platform-based design, synthetic bclotho, synthetic
    biology},
    location = {Portland, Oregon},
    numpages = {6},
    owner = {Aaron Heuckroth},
    timestamp = {2013.09.16},
    url = {http://doi.acm.org/10.1145/1565799.1565806}
    }

  • E. Oberortner, D. Densmore, and J. C. Anderson, “An Interactive Pattern Story on Designing the Architecture of Clotho,” in 19th Conference on Pattern Languages of Programs (PLoP), 2012, cidarlab_conference_papers.
    [BibTeX] [Download PDF]
    @INPROCEEDINGS{oberortnerClothoPattern2012,
    author = {Oberortner, Ernst and Densmore, Dougls and Anderson, J. C.},
    title = {An Interactive Pattern Story on Designing the Architecture of Clotho},
    booktitle = {19th Conference on Pattern Languages of Programs (PLoP)},
    year = {2012},
    note = {cidarlab_conference_papers},
    __markedentry = {},
    keywords = {clotho, synthetic biology},
    owner = {Kirrei},
    timestamp = {2013.08.13},
    url = {http://cidarlab.org/wp-content/uploads/2013/09/oberortnerClothoPattern2012.pdf}
    }

  • B. Xia, S. Bhatia, B. Bubenheim, M. Dadgar, D. Densmore, and J. C. Anderson, “Developer’s and user’s guide to Clotho v2.0 A software platform for the creation of synthetic biological systems,” Meth. Enzymol., vol. 498, pp. 97-135, 2011.
    [BibTeX] [Download PDF]
    @ARTICLE{pmid21601675,
    author = {Xia, B. and Bhatia, S. and Bubenheim, B. and Dadgar, M. and Densmore,
    D. and Anderson, J. C.},
    title = {{{D}eveloper's and user's guide to {C}lotho v2.0 {A} software platform
    for the creation of synthetic biological systems}},
    journal = {Meth. Enzymol.},
    year = {2011},
    volume = {498},
    pages = {97--135},
    keywords = {clotho, synthetic biology},
    owner = {Aaron Heuckroth},
    timestamp = {2013.09.16},
    url = {http://www.ncbi.nlm.nih.gov/pubmed/21601675}
    }

Team:

Prashant Vaidyanathan
Nicholas Roehner
Alex Vahid
David Tran
Jacob Kozol

Past Clotho 3.0 Collaborators:

Maxwell Bates
Stephanie Paige
Mina Li
Bill Cao