SynBERC
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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)