SynBERC:COG/Report

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Contents

Single Assemblies

  • Define:

Centralized

In-house

By synth company

  • How big of an order can we put together?

Distributed

  • In house? Partnership with NEB-type/Qiagen company?

Library Assemblies

  • Define:
  • Less concern for turn-time

Pool (all library members in one tube)

Grid (individual variants are separate)

Other issues

Biobricks? Or other?

Notes from retreat

Jason R. Kelly 09:27, 18 September 2007 (EDT): These are just my notes, please feel free to add.

  • Should consider distributed vs. centralized approach
    • QIAcube could be backbone for distributed approach
  • folks would like to see the comparison between projected synthesis costs and assembly going forward 5 years.
  • synthesis companies haven't been receptive to making combinatorial libraries of pre-existing components
  • in proposing path forward should consider options ranging like NSF grants, VCs, partnering with synth companies, partnering with equip manufacturers (qiacube), etc.
    • There was suggestion that if we had a guaranteed order size, we could possible convince synth companies to add a pipeline for assembly. so could work to get a larger group together.
  • Good to continue working on both process optimization issues (e.g. work going on at Registry) as well as alternative assembly approaches that are still "in the lab".
  • We need estimates of how much SynBERCers currently clone and how that would scale given drops in assembly cost and turn-around time

To do

How do we evaluate the different approaches to automated construction?

  1. 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.
  2. Centralized academic facility
    • We find the resources to start an assembly facility similar to how sequencing facilities are set up on campus
  3. Partnership with 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?
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