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SBOL in Action: The BBN BioCompiler

SBOL in Action: The BBN BioCompiler. Jacob Beal. SBOL Workshop April, 2013 Newcastle upon Tyne, UK. What is BioCompiler?. High-level program  (compile against motifs & platform) Optimized GRN design Three output formats: SBOLv diagrams Matlab ODE files SBOL-ish XML

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SBOL in Action: The BBN BioCompiler

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  1. SBOL in Action: The BBN BioCompiler Jacob Beal SBOL Workshop April, 2013 Newcastle upon Tyne, UK

  2. What is BioCompiler? • High-level program  (compile against motifs & platform) • Optimized GRN design • Three output formats: • SBOLv diagrams • Matlab ODE files • SBOL-ish XML • Challenges for using SBOL: • SBOLv vs. GraphViz • Written in C++

  3. Simple Example: Inversion (green (not (aTc))) compiled for E. coli

  4. Not-Quite-So-Simple Example: XOR (blue (xor (Dox) (IPTG))) compiled for mammalian

  5. Complex Example: 4-bit Counter (4-bit-counter) compiled for mammalian

  6. Public Web Interface Anonymous access now available (but not private) Further tool integration possible via XML RPC calls

  7. Future SBOL Uses & Needs • SBOL output: • Use case: transmitting designs to other tools for visualization, editing, fabrication • Needs: • libSBOLc • Representation of species, regulatory interactions • SBOL input: • Use case: importing motif designs from other tools • Needs: • Device model with “ports” for interface • Representation of species, regulatory interactions

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