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=
=Meetings=
Agenda:
*[[SynBERC:COG/October 2007 Meeting]] - TK debrief on QIAcube
 
**[[SynBERC:COG/Homework]]:  
==What are the goals for COG?==
**#What's the cloning amount (and type) per lab ?
Proposed based on SynBERC meeting / conversations since:
**#What experiment can't we do that we'd like to do?
#Stay up to date with current automated cloning research projects taking place in SynBERC labs
*[[SynBERC:COG/December 2007 Meeting]] - Lane & Anderson research updates
#Get the ball rolling for solving the automated cloning problem in the short term
*[[SynBERC:COG/January 2008 Meeting]] - Registry research update
 
**[[:Media:SynBERC talk Reisinger.ppt|Sarah Reisinger SynBERC presentation on automated cloning]]
===Research Updates===
*[[SynBERC:COG/February 2008 Meeting]] - Sergio from the Lim Lab on combinatorial assembly
*1/2 the meeting?
*[[SynBERC:COG/April 2008 Meeting]] - Harris from the Church lab presents on MAGE
*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=
=Communication=

Latest revision as of 12:41, 5 October 2008

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

  1. Maintain communication across labs on status of automated assembly projects.
  2. Produce a report with evaluation of current assembly approaches and recommendations for going forward.

Meetings

Communication

Members

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