SynBERC:COG

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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.
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=COG:Meeting 1=
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=Meetings=
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Agenda:
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*[[SynBERC:COG/October 2007 Meeting]] - TK debrief on QIAcube
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**[[SynBERC:COG/Homework]]:  
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==What are the goals for COG?==
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**#What's the cloning amount (and type) per lab ?
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Proposed based on SynBERC meeting / conversations since:
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**#What experiment can't we do that we'd like to do?
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#Stay up to date with current automated cloning research projects taking place in SynBERC labs
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*[[SynBERC:COG/December 2007 Meeting]] - Lane & Anderson research updates
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#Get the ball rolling for solving the automated cloning problem in the short term
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*[[SynBERC:COG/January 2008 Meeting]] - Registry research update
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**[[:Media:SynBERC talk Reisinger.ppt|Sarah Reisinger SynBERC presentation on automated cloning]]
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===Research Updates===
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*[[SynBERC:COG/February 2008 Meeting]] - Sergio from the Lim Lab on combinatorial assembly
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*1/2 the meeting?
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*[[SynBERC:COG/April 2008 Meeting]] - Harris from the Church lab presents on MAGE
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*Brief updates from each of the groups? one longer presentation each month about one project?
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**Something else?
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===Getting the ball rolling for solving automated cloning===
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#Define the problem we want solved
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#Specify the possible solutions
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#Evaluate / Act on solutions
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====Define problem(s)====
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*Combinatorial libraries of assembled parts (Wendall, UCSF iGEM team project)
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*Automation of standard BioBrick Assembly (Registry)
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*Automation of assembly independent of BBs (Synth companies?)
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====Specify Possible Solutions====
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#Decentralized approach
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#*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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#Centralized academic facility
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#*We find the resources to start an assembly facility similar to how sequencing facilities are set up on campus
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#Outsource to DNA synthesis company
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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?
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====Evaluate / Act on Solutions====
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*Registry hires more staff to do process engineering
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*Trial QIAcube / other "cheap" robots for distributed approach
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*Figure out how big an assembly order iGEM + labs using parts could put together for a Synth company (George suggestion)
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*Go talk to Synth companies see if they'll do this.
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*Plot the cost of synth vs. assembly over time for particular length scales (drew's suggestion)
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==Meeting Frequency==
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*Monthly?
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*Any weekday's particularly bad for certain groups? (Weds at MIT)
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==Next steps==
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=Communication=
=Communication=

Current revision

Image:Service lab.png 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!

Contents

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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