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BioBrick Open Language

BioBrick Open Language. Cesar Rodriguez, Doug Densmore, Drew Endy. Outline. Introduction Specification Implementation Future Work. Introduction  Abstraction Hierarchy. Devices. Standard Parts. Introduction.

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BioBrick Open Language

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  1. BioBrick Open Language Cesar Rodriguez, Doug Densmore, Drew Endy

  2. Outline • Introduction • Specification • Implementation • Future Work

  3. Introduction Abstraction Hierarchy Devices Standard Parts

  4. Introduction • English-like language for the formal specification of standard biological devices. • Intended for forward engineering of DNA-based devices. • Targeted for use by biological engineers. • XML version of the language for the purpose of data exchange over the internet. • Graphical version  • Visual BioBrick Open Language (vBOL)  • Encourage and support model-driven engineering.  • Analogous to the relationship between C# and UML

  5. Introduction • Open Standard • Balance top-down control with bottom-up community development • Open communication  • Rigorous definition of symbols, syntax, and grammar. • Abstract tool for solving concrete problems. • Balance a philosophically consistent framework with utility for solving concrete problems.  • Rigorous and consistent structure  • Concrete software tools • Concrete Synthetic Biology projects

  6. SpecificationData Model

  7. Specification English-like Syntax • Berkeley Approach • Stanford Approach

  8. Stanford Syntax Registry "partsregistry.org"; New Device {       Parts      {        PrimerSite BBa_X1;        Promoter BBa_X2;        ORF BBa_X3;        ORF BBa_X5;        Terminator BBa_X6;        Terminator BBa_X7;        PrimerSite BBa_X8;       }       Input BBa_X2;       Output BBa_X3,BBa_X4; } 

  9. SpecificationGraphical Syntax 13+ Symbols Promoter Ribosome Binding Site Open Reading Frame

  10. ImplementationOverall Architecture

  11. Implementation: Flow Diagram

  12. Future Work: Spectacles

  13. Acknowledgements Barry Canton Reshma Shetty Jerome Bonnet Lance Martin Francois St. Pierre Akshay Maheshwari 2009 Berkeley iGEM Software Team 2009 Stanford iGEM Team Synthetic Biology Engineering Research Center (SynBERC) National Science Foundation National Cancer Institute/National Institutes of Health www.tinyurl.com/bolspec

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