Synthetic Biology:SB101: Difference between revisions

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{{Synthetic biology top}}
<div style="padding: 10px; color: #000000; background-color: #ccccff; width:730px" >
[[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 (ex modularity, standards)
## 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
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== 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.  See slides 13 and 14 in the embedded slides below:
* 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


<html><object codebase="http://download.macromedia.com/pub/shockwave/cabs/flash/swflash.cab#version=9,0,0,0" id="doc_798565760134291" name="doc_798565760134291" classid="clsid:d27cdb6e-ae6d-11cf-96b8-444553540000" align="middle" height="500" width="450"> <param name="movie" value="http://documents.scribd.com/ScribdViewer.swf?document_id=4026697&access_key=key-e78kbtej0jx33lz2r5r&page=14&version=1"> <param name="quality" value="high"> <param name="play" value="true"> <param name="loop" value="true"> <param name="scale" value="showall"> <param name="wmode" value="opaque"> <param name="devicefont" value="false"> <param name="bgcolor" value="#ffffff"> <param name="menu" value="true"> <param name="allowFullScreen" value="true"> <param name="allowScriptAccess" value="always"> <param name="salign" value=""> <embed src="http://documents.scribd.com/ScribdViewer.swf?document_id=4026697&access_key=key-e78kbtej0jx33lz2r5r&page=14&version=1" quality="high" pluginspage="http://www.macromedia.com/go/getflashplayer" play="true" loop="true" scale="showall" wmode="opaque" devicefont="false" bgcolor="#ffffff" name="doc_798565760134291_object" menu="true" allowfullscreen="true" allowscriptaccess="always" salign="" type="application/x-shockwave-flash" align="middle" height="500" width="450"></embed> </object><div style="font-size:10px;text-align:center;width:450"><a href="http://www.scribd.com/doc/4026697/SSSB-Building-Good-Registries-for-Synthetic-Biology">SSSB: Building Good Registries for Synthetic Biology</a> - <a href="http://www.scribd.com/upload">Upload a Document to Scribd</a></div><div style="display:none"> Read this document on Scribd: <a href="http://www.scribd.com/doc/4026697/SSSB-Building-Good-Registries-for-Synthetic-Biology">SSSB: Building Good Registries for Synthetic Biology</a> </div> </html>
== 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

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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

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