SynBERC:COG: Difference between revisions
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#Produce a [[SynBERC:COG/Report|report]] with evaluation of current assembly approaches and recommendations for going forward. | #Produce a [[SynBERC:COG/Report|report]] with evaluation of current assembly approaches and recommendations for going forward. | ||
=COG:Meeting 1= | |||
Agenda: | Agenda: | ||
==What are the goals for COG?== | |||
Proposed based on SynBERC meet / conversations since: | Proposed based on SynBERC meet / conversations since: | ||
#Stay up to date with current automated cloning research projects taking place in SynBERC labs | #Stay up to date with current automated cloning research projects taking place in SynBERC labs | ||
#Get the ball rolling for solving the automated cloning problem in the short term | #Get the ball rolling for solving the automated cloning problem in the short term | ||
===Research Updates=== | |||
*1/2 the meeting? | *1/2 the meeting? | ||
*Brief updates from each of the groups? one longer presentation each month about one project? | *Brief updates from each of the groups? one longer presentation each month about one project? | ||
**Something else? | **Something else? | ||
===Getting the ball rolling for solving automated cloning=== | |||
#Define the problem we want solved | #Define the problem we want solved | ||
#Specify the possible solutions | #Specify the possible solutions | ||
#Evaluate / Act on solutions | #Evaluate / Act on solutions | ||
====Define problem==== | |||
*Combinatorial libraries of assembled parts (Wendall, UCSF iGEM team project) | *Combinatorial libraries of assembled parts (Wendall, UCSF iGEM team project) | ||
*Automation of standard BioBrick Assembly (Registry) | *Automation of standard BioBrick Assembly (Registry) | ||
*Automation of assembly independent of BBs (Synth companies?) | *Automation of assembly independent of BBs (Synth companies?) | ||
====Specify Possible Solutions==== | |||
#Decentralized approach | #Decentralized approach | ||
#*We make cloning easier by using some automation combined with "normal" individual cloning approaches. For example, each lab buys a Qiacube to partially automate minipreps and restriction digests. Then ligations and transformations are done by hand at the bench. | #*We make cloning easier by using some automation combined with "normal" individual cloning approaches. For example, each lab buys a Qiacube to partially automate minipreps and restriction digests. Then ligations and transformations are done by hand at the bench. | ||
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#*We work with a DNA synthesis company so that they can offer commercial automated cloning services. How do we ensure that such a partnership wouldn't fall apart as soon as a big synthesis order comes along? Automated cloning may be too small a market and/or too large a problem for DNA synthesis companies to tackle right now? | #*We work with a DNA synthesis company so that they can offer commercial automated cloning services. How do we ensure that such a partnership wouldn't fall apart as soon as a big synthesis order comes along? Automated cloning may be too small a market and/or too large a problem for DNA synthesis companies to tackle right now? | ||
====Evaluate / Act on Solutions==== | |||
*Registry hires more staff to do process engineering | *Registry hires more staff to do process engineering | ||
*Trial QIAcube / other "cheap" robots for distributed approach | *Trial QIAcube / other "cheap" robots for distributed approach | ||
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*Plot the cost of synth vs. assembly over time for particular length scales (drew's suggestion) | *Plot the cost of synth vs. assembly over time for particular length scales (drew's suggestion) | ||
==Meeting Frequency== | |||
*Monthly? | *Monthly? | ||
*Any weekday's particularly bad for certain groups? (Weds at MIT) | *Any weekday's particularly bad for certain groups? (Weds at MIT) | ||
==Next steps== | |||
=Communication= | =Communication= |
Revision as of 08:20, 26 October 2007
Welcome to the Construction Optimization Group (COG)!
At the last SynBERC retreat SynBERCers decided that solving the challenge of automated DNA assembly/cloning would be a priority for the center. COG will be tasked with drafting a report for the upcoming NSF visit in March(?) that evaluates current assembly approaches and proposes a path forward. This page is just getting started, please add/edit!
Goals
- Maintain communication across labs on status of automated assembly projects.
- Produce a report with evaluation of current assembly approaches and recommendations for going forward.
COG:Meeting 1
Agenda:
What are the goals for COG?
Proposed based on SynBERC meet / conversations since:
- Stay up to date with current automated cloning research projects taking place in SynBERC labs
- Get the ball rolling for solving the automated cloning problem in the short term
Research Updates
- 1/2 the meeting?
- Brief updates from each of the groups? one longer presentation each month about one project?
- Something else?
Getting the ball rolling for solving automated cloning
- Define the problem we want solved
- Specify the possible solutions
- Evaluate / Act on solutions
Define problem
- Combinatorial libraries of assembled parts (Wendall, UCSF iGEM team project)
- Automation of standard BioBrick Assembly (Registry)
- Automation of assembly independent of BBs (Synth companies?)
Specify Possible Solutions
- Decentralized approach
- We make cloning easier by using some automation combined with "normal" individual cloning approaches. For example, each lab buys a Qiacube to partially automate minipreps and restriction digests. Then ligations and transformations are done by hand at the bench.
- Centralized academic facility
- We find the resources to start an assembly facility similar to how sequencing facilities are set up on campus
- Outsource to DNA synthesis company
- We work with a DNA synthesis company so that they can offer commercial automated cloning services. How do we ensure that such a partnership wouldn't fall apart as soon as a big synthesis order comes along? Automated cloning may be too small a market and/or too large a problem for DNA synthesis companies to tackle right now?
Evaluate / Act on Solutions
- Registry hires more staff to do process engineering
- Trial QIAcube / other "cheap" robots for distributed approach
- Figure out how big an assembly order iGEM + labs using parts could put together for a Synth company (George suggestion)
- Go talk to Synth companies see if they'll do this.
- Plot the cost of synth vs. assembly over time for particular length scales (drew's suggestion)
Meeting Frequency
- Monthly?
- Any weekday's particularly bad for certain groups? (Weds at MIT)
Next steps
Communication
- Join the mailing list
Members
- Chris Anderson
- Adam P. Arkin
- Austin Che
- George Church
- Jeffrey Dietrich
- John Dueber
- Will Holtz
- Jason R. Kelly
- Tom Knight
- Sergio Peisajovich
- Randy Rettberg
- Reshma Shetty
- Lane Weaver
- Reid Williams
- Josh Kittleson
- Harris Wang
- Caroline Ajo-Franklin
- Meagan Lizarazo
- Julie Norville
- Leonard Katz
- Swapnil Chhabra