Synthetic Biology:SB101: Difference between revisions
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{{Synthetic biology top}} | |||
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[[Image:SB101_blackboard.png|340px|right]] | [[Image:SB101_blackboard.png|340px|right]] | ||
The BioBricks Foundation was invited to run a workshop on "Synthetic Biology with BioBricks Parts" at [http://csb2008.org/tutabs08.html CSB2008]. Reusable educational modules about synthetic biology can be found on this page. | The BioBricks Foundation was invited to run a workshop on "Synthetic Biology with BioBricks Parts" at [http://csb2008.org/tutabs08.html CSB2008]. Reusable educational modules about synthetic biology can be found on this page. | ||
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## Overview - imagine sequencing and synthesis became free overnight. Where does that lead in terms of engineering? (Abstraction, Modularity, Standardization) | ## Overview - imagine sequencing and synthesis became free overnight. Where does that lead in terms of engineering? (Abstraction, Modularity, Standardization) | ||
## History | ## History | ||
## Definitions ( | ## Definitions (part, device, chassis, biobrick, physical standard, functional standard, abstraction, engineering cycle) | ||
# Standard Parts: Goals and Tools | # Standard Parts: Goals and Tools | ||
## Data sheets (goal) | ## Data sheets (goal) | ||
## Measurement (path toward goal) | ## Measurement (path toward goal) | ||
## Repositories | ### Jason's story about telegraph cable standardization | ||
## Getting & Storing parts: Registries & Repositories | |||
## Legal Standards (Freedom) | ## Legal Standards (Freedom) | ||
## Production and Use - iGEM (fabs... & codon devices, ginkgo?) | ## Production and Use - iGEM (fabs... & codon devices, ginkgo?) | ||
# Hands on WetLab demo: | |||
## Transformation foo using real Datasheets | |||
## Show off a couple of MIT Registry Binders | |||
# Get involved! | # Get involved! | ||
## biobricks foundation: volunteer, help steer the ship | ## biobricks foundation: volunteer, help steer the ship | ||
Line 25: | Line 33: | ||
== Graphics == | == 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 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. | * A diagram representing available biobrick parts & devices localized to their areas of activity in a cell. | ||
== Meeting Notes Aug 3 2008 == | |||
=== Materials === | |||
# Paper copy of the registry (w blotted DNA) | |||
# Tranformation foo kit (maybe) | |||
=== Teaching modules === | |||
# Transformation foo kit - good introduction to modular biobrick parts | |||
# Isn't biology already standardized? "We use the same words..." | |||
=== TODO === | |||
# Compile a list of existing resources | |||
# Review them all for a consensus of bullet points/modules | |||
## Perhaps there are some well-thought out existing introductions/organiz. | |||
# Follow up on email summaries: | |||
## "telconf ultra-short summary" and "Open Source Registry Conference Call" | |||
=== NOTES === | |||
# Let's be interactive, have a fun breakout session, just like the $1K BioBrick challenge. | |||
## Is this still in effect? Could someone from CSB go to SB4 if they win? | |||
## Have a hackathon for SB tools | |||
### Bring a shopping list of most desired mini-SB apps (primer designer) | |||
### This would be a good way to "call to action" at the end of the wkshop | |||
### Describe the software tools landscape, provide a 'hook' for hackathon | |||
## Anticipate the audience: | |||
### They may ask "when can we build synthetic networks?" | |||
### HOW IS SYNTHETIC BIOLOGY DIFFERENT FROM SYSTEMS BIOLOGY | |||
### they know a lot about computational prediction & simulation | |||
== Resources == | |||
* [[Image:SB_Primer_100707.pdf|Scott Mohr's Primer]] | |||
* [http://openwetware.org/images/f/f9/IGEM_Student_Book.pdf Berkeley Intro to Synthetic Biology] | |||
* [http://openwetware.org/wiki/The_BioBricks_Foundation:Standards/Technical/Measurement#Briefing_on_Measuring_Promoters_.26_RBSs Jason Kelly's Measurement Kit Video] | |||
* [http://www.plosone.org/article/info:doi%2F10.1371%2Fjournal.pone.0002671 Targeted Development of Registries of Biological Parts (Peccoud lab] | |||
* [http://openwetware.org/wiki/Adventures Adventures in Synthetic Biology comic] |
Latest revision as of 19:15, 29 October 2009
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
- Intro - setting the stage for synthetic biology
- Overview - imagine sequencing and synthesis became free overnight. Where does that lead in terms of engineering? (Abstraction, Modularity, Standardization)
- History
- Definitions (part, device, chassis, biobrick, physical standard, functional standard, abstraction, engineering cycle)
- Standard Parts: Goals and Tools
- Data sheets (goal)
- Measurement (path toward goal)
- Jason's story about telegraph cable standardization
- Getting & Storing parts: Registries & Repositories
- Legal Standards (Freedom)
- Production and Use - iGEM (fabs... & codon devices, ginkgo?)
- Hands on WetLab demo:
- Transformation foo using real Datasheets
- Show off a couple of MIT Registry Binders
- Get involved!
- biobricks foundation: volunteer, help steer the ship
- igem: do syn bio for real
- 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
- Paper copy of the registry (w blotted DNA)
- Tranformation foo kit (maybe)
Teaching modules
- Transformation foo kit - good introduction to modular biobrick parts
- Isn't biology already standardized? "We use the same words..."
TODO
- Compile a list of existing resources
- Review them all for a consensus of bullet points/modules
- Perhaps there are some well-thought out existing introductions/organiz.
- Follow up on email summaries:
- "telconf ultra-short summary" and "Open Source Registry Conference Call"
NOTES
- Let's be interactive, have a fun breakout session, just like the $1K BioBrick challenge.
- Is this still in effect? Could someone from CSB go to SB4 if they win?
- Have a hackathon for SB tools
- Bring a shopping list of most desired mini-SB apps (primer designer)
- This would be a good way to "call to action" at the end of the wkshop
- Describe the software tools landscape, provide a 'hook' for hackathon
- Anticipate the audience:
- They may ask "when can we build synthetic networks?"
- HOW IS SYNTHETIC BIOLOGY DIFFERENT FROM SYSTEMS BIOLOGY
- they know a lot about computational prediction & simulation