Synthetic Biology:SB101

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The BioBricks Foundation was invited to run a workshop on "Synthetic Biology with BioBricks Parts" at CSB2008. Reusable educational modules about synthetic biology can be found on this page.

Skeletal draft outline of SB101

1. Intro - setting the stage for synthetic biology
   1. Overview - imagine sequencing and synthesis became free overnight. Where does that lead in terms of engineering? (Abstraction, Modularity, Standardization)
   2. History
   3. Definitions (part, device, chassis, biobrick, physical standard, functional standard, abstraction, engineering cycle)
2. Standard Parts: Goals and Tools
   1. Data sheets (goal)
   2. Measurement (path toward goal)
      1. Jason's story about telegraph cable standardization
   3. Getting & Storing parts: Registries & Repositories
   4. Legal Standards (Freedom)
   5. Production and Use - iGEM (fabs... & codon devices, ginkgo?)
3. Hands on WetLab demo:
   1. Transformation foo using real Datasheets
   2. Show off a couple of MIT Registry Binders
4. Get involved!
   1. biobricks foundation: volunteer, help steer the ship
   2. igem: do syn bio for real
   3. diybio?

Questions / Ideas

• In the history of electronics, did the pioneers begin by inventing interesting/useful devices or reusable basic parts? It seems to me they started with certain applications in mind (devices) which over time revealed a set of commonly used basic parts.

Graphics

• a technology flowchart revealing the significant events leading to the advent of synthetic biology and project what the most important advances will be 5 to 10 years into the future.
• A diagram representing available biobrick parts & devices localized to their areas of activity in a cell.

Meeting Notes Aug 3 2008

Materials

1. Paper copy of the registry (w blotted DNA)
2. Tranformation foo kit (maybe)

Teaching modules

1. Transformation foo kit - good introduction to modular biobrick parts
2. Isn't biology already standardized? "We use the same words..."

TODO

1. Compile a list of existing resources
2. Review them all for a consensus of bullet points/modules
   1. Perhaps there are some well-thought out existing introductions/organiz.
3. Follow up on email summaries:
   1. "telconf ultra-short summary" and "Open Source Registry Conference Call"

NOTES

1. Let's be interactive, have a fun breakout session, just like the $1K BioBrick challenge.
   1. Is this still in effect? Could someone from CSB go to SB4 if they win?
   2. Have a hackathon for SB tools
      1. Bring a shopping list of most desired mini-SB apps (primer designer)
      2. This would be a good way to "call to action" at the end of the wkshop
      3. Describe the software tools landscape, provide a 'hook' for hackathon
   3. Anticipate the audience:
      1. They may ask "when can we build synthetic networks?"
      2. HOW IS SYNTHETIC BIOLOGY DIFFERENT FROM SYSTEMS BIOLOGY
      3. they know a lot about computational prediction & simulation

Resources

• File:SB Primer 100707.pdf
• Berkeley Intro to Synthetic Biology
• Jason Kelly's Measurement Kit Video
• Targeted Development of Registries of Biological Parts (Peccoud lab
• Adventures in Synthetic Biology comic