SynBERC:COG/Report: Difference between revisions
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*Define: | *Define: | ||
==Centralized== | ==Centralized== | ||
===In-house=== | |||
===By synth company=== | |||
*How big of an order can we put together? | |||
==Distributed== | ==Distributed== | ||
*In house? Partnership with NEB-type/Qiagen company? | *In house? Partnership with NEB-type/Qiagen company? | ||
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=Other issues= | =Other issues= | ||
==Biobricks? Or other?== | ==Biobricks? Or other?== | ||
=Notes from retreat= | |||
'''[[User:Jason R. Kelly|Jason R. Kelly]] 09:27, 18 September 2007 (EDT)''': These are just my notes, please feel free to add. | '''[[User:Jason R. Kelly|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 | *Should consider distributed vs. centralized approach | ||
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*We need estimates of how much SynBERCers currently clone and how that would scale given drops in assembly cost and turn-around time | *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? | How do we evaluate the different approaches to automated construction? | ||
Latest revision as of 05:33, 29 October 2007
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?
- 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
- 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?
