SynBERC

Synthetic Biology Engineering Research Center

Working Drafts of Slides for December Site Visit

• Devices and Device Composition – Drew Endy
  • [20 min. plus 10 min. Q/A]
  • Questions
    • Should I include example of utility of hierarchy? [e.g., Polkadorks?]
    • Should I include "process flow" meta-strategy slides?
  • Outline
    • Title Slide
    • Abstraction Hierarchy
    • Utility of Hierarchy (allows decoupling, standards, and avoidance / management of complexity)
    • Walk-through of Hierarchy Levels (Parts (reminder), Devices, Applications)
    • (Talking Point) - Devices bridge connection between basic biological functions (parts) and high level applications.
    • Introduce abstraction barriers and intefaces
    • Introduce construction of hierarchy via example 1, from Parts to Devices
    • Introduce issue of standard assembly (TK biobricks assembly scheme v1)
    • Introduce issue / challenge of functional composition (part-part junction)
    • Continue construction of hierarchy via example 2, from Devices to Systems
    • Compare [protein]-based gene-expression devices with PoPS-based devices
    • Detail PoPS and discuss issues (e.g., how do we measure PoPS)?
    • Can we extend abstraction hierarchy to post-translational devices [Get Samantha Sutton's slides here]
    • Explain issues / challenge with PTL abstraction [Wendell, we need to synch. here for sure!]
    • Can we extend abstraction hierarchy to metabolic devices [Kristala, we need to synch here!]
    • Revisit device / system interface, introduce Jason Kelly's operation definition based on ability to directly screen / select for device function, but not system / application function
    • Provide summary of foundational research [e.g., extending abstraction to post-translational devices and metabolic devices, measurement of signal carriers, coupling to genetic screening and selection]
    • Introduce applied research. As in, we will be building the following type of devices. Information Processing, Transducers (from one device family to the next), Receivers, Actuators, Metabolism
    • (~3 slides) Provide examples of devices, detailing interface with Registry (e.g., BBa_F2620)