User:Jason R. Kelly
Bio
Jason Kelly
Founder at Ginkgo BioWorks
Co-Founder of OpenWetWare, 2007
PhD in Biological Engineering @ MIT in the Endy Lab, June 2008
S.B. in Biology and Chemical Engineering @ MIT, 2003
Contact
jason AT ginkgobioworks DOT com
Activities
Thesis Project
To date, engineered biological systems have been constructed via a variety of ad hoc approaches. The resulting systems should be thought of as pieces of art. We are interested in exploring how existing forward engineering approaches might be best combined with directed evolution to make routine the construction of engineered biological systems. We have specified a procedure for construction of biological systems via screening of subcomponent libraries and rational re-assembly. We have begun development of tools to enable this approach, including a FACS-based screening system to rapidly measure the input/output function of a genetic circuit and a standard measurement kit for characterizing promoters and RBSs. Additionally, we have designed a microfluidic system that enables more sophisticated screening and selection functions. Specifically, a microfluidic chemostat integrated with a cell sorter (i.e., a sort-o-stat). This microscope-based system will enable us to evaluate whether or not more complicated screens and selections will be of practical use in service of evolving engineered biological systems.
Specific Aims
- Tools for screening and measurement
- Standard Measurement kit for promoters/RBSs
- Instructions for kit users can be found at the Registry
- PoPS device screening plasmid
- Standard Measurement kit for promoters/RBSs
- Library-based Construction
- SortoStat
Communications
- Thesis Proposal PDF
- SB3.0 Poster (2007)
- MIT BE Retreat Poster (2007)
- Synthetic Biology 2.0 Poster (2006)
- ICSB Poster (2005)
Current Project Pages
- Sortostat/Notebook
- Screening plasmid/Notebook
- Knight:Evolving Reshmaverters
- Endy:Chemostat
- Endy:Inverter composition
- Endy:Measkit draft
Publications
- Kelly JR, Rubin AJ, Davis JH, Ajo-Franklin CM, Cumbers J, Czar MJ, de Mora K, Glieberman AL, Monie DD, and Endy D. Measuring the activity of BioBrick promoters using an in vivo reference standard. J Biol Eng. 2009 Mar 20;3:4. DOI:10.1186/1754-1611-3-4 |
- Kosuri S, Kelly JR, and Endy D. TABASCO: A single molecule, base-pair resolved gene expression simulator. BMC Bioinformatics. 2007 Dec 19;8:480. DOI:10.1186/1471-2105-8-480 |
- Janes KA, Kelly JR, Gaudet S, Albeck JG, Sorger PK, and Lauffenburger DA. Cue-signal-response analysis of TNF-induced apoptosis by partial least squares regression of dynamic multivariate data. J Comput Biol. 2004;11(4):544-61. DOI:10.1089/cmb.2004.11.544 |
Popular press
Talks
Upcoming
- October, 2008, Synthetic Biology 4.0, Hong Kong, China
- Reference Standards for Characterizing Biological Parts
Previous
- June 2008, New Communication Channels for Biology Workshop, UCSD
- April 2008, Standards and Specifications in Synthetic Biology Workshop, Seattle, WA
- Measurement kit for BioBrick promoters and RBSs (delivered by Kim de Mora - thanks Kim!)
- March 2008, BioBrick Foundation Technical Standards Workshop, Berkeley, CA
- March 2008, Advanced Technologies for Agrology, Banff, Canada
- Standards for programming DNA
- July 2006, Nature/O'Reilly Science Foo Camp, Google, Mountain View, CA
Videos
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- References standards for biological engineers
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- Synchronized pipetting
OWW Pages in Progess
<google>Protocols</google>
OpenWetWare:SC coordinator torch
Synthetic Biology:BioBricks/Standardization/Functional composition
User:Jason R. Kelly/Main page copy
User:Jason R. Kelly/Interesting plant stuff
User:Jasonk/Protocols -- protocols list
Open Source Biology -- assuming such a thing exists :)
User:Jasonk/Registry of Standard Biological Parties - this seems like a good idea.
User:Jasonk/A journal worth reading - place to collect random thoughts about what I'd like to see a next-generation journal contain.
BioBricks construction tutorial - a step-by-step tutorial for a single Biobrick assembly.
Microfluidics - a page describing the endy lab microfluidics setup and linking to relevant protocols, etc.
BE Board - homepage for the BE Board
OpenWetWare:Presentations - a presentation for introducing new labs to Openwetware.
ICampus Application for OWW - application for an MIT iCampus grant for OpenWetWare (and a good desciption of the site and future goals)
Science 2.0 - some musings by the OWW community about the internet (Web 2.0) and science
Community Portal v2 - playing around with Community portal organization.
BE Board:Dinner Discussion/Alternate publishing models - discussion for BE retreat
User:Jasonk/sidebar - my sidebar, this is a great feature!
OpenWetWare:Steering committee/NSF BDI Grant - help us write a grant for OWW.
OpenWetWare:Steering committee/Goals
OpenWetWare:Presentations/SciFoo - walkthough of the site shown at Sci Foo camp
Jason Kelly/sample wikipedia page for OWW - wikipedia entry for OWW
OpenWetWare:Steering Committee v2 - updating SC webpage
edit your sidebar - would be nice to make it easy for users to figure out how to edit their sidebar, though apparently this isn't the best solution.
Postgenomic test page - testing having our content scraped by postgenomic.
List:RegistryOfStandardBiologicalParties - testing the new mailing list function austin implemented
Nerdbook - scientific networking, get your nerd on. (maybe we need a new name)
OpenWetWare:Reviews -- WikiReviews, will they work? help us find out!
OpenWetWare:Mission -- we have a mission, was decided at the retreat awhile back
OpenWetWare:Respond_to_NSF -- some long term planning thoughts.
Science blogs - list of science blogs
Endy:Screening plasmid/Recent changes
Endy:Evolutionary stability project
Glycerols
Sandbox
- Who is on OWW:
- Square bacteria
MIT audio bridge conference calling
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