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

 * 1) Tools for screening and measurement
 * 2) *Standard Measurement kit for promoters/RBSs
 * 3) **Instructions for kit users can be found at the Registry
 * 4) *PoPS device screening plasmid
 * 5) Library-based Construction
 * 6) SortoStat

Communications

 * Thesis Proposal PDF
 * [[Media:JK.SB3.0.Poster.2007.pdf|SB3.0 Poster (2007)]]
 * [[MEdia:JK.BERetreat.Poster.2007.pdf|MIT BE Retreat Poster (2007)]]
 * [[Media:JK.SyntheticBiology2.0.Poster.pdf|Synthetic Biology 2.0 Poster (2006)]]
 * [[Media:JK ICSB 2005.pdf|ICSB Poster (2005)]]

Current Project Pages

 * Sortostat/Notebook
 * Screening plasmid/Notebook
 * Knight:Evolving Reshmaverters
 * Endy:Chemostat
 * Endy:Inverter composition
 * Endy:Measkit draft

Publications

 * 1) Kelly-JBE pmid=19298678


 * 1) Kosuri-BMCBioinfo2007 pmid=18093293


 * 1) Janes-JCompBio-2004 pmid=15579231
 * (MATLAB files available here, scroll down to Modeling Software:Lauffenburger Lab)

Popular press

 * iGEM 2008: Novice Bioengineers Get Their Freak On (SEED Magazine)

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
 * OWW site tour
 * 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
 * Measurement kit for BioBrick promoters and RBSs (video)
 * March 2008, Advanced Technologies for Agrology, Banff, Canada
 * Standards for programming DNA
 * July 2006, Nature/O'Reilly Science Foo Camp, Google, Mountain View, CA
 * OWW site tour

Videos

 * References standards for biological engineers

  
 * Synchronized pipetting

OWW Pages in Progess
Protocols

Special:OWWStats

New visitor blurb

SC coordinator torch

Community

Synthetic Biology:BioBricks/Standardization/Functional composition

User:Jason R. Kelly/Main page copy

User:Jason R. Kelly/RSS test

User:Jason R. Kelly/Interesting plant stuff

User:Jasonk/wibbit table test

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

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!

Steering committee/NSF BDI Grant - help us write a grant for OWW.

Steering committee/Goals

Presentations/SciFoo - walkthough of the site shown at Sci Foo camp

Jason Kelly/sample wikipedia page for OWW - wikipedia entry for OWW

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.

Evolutionary Stability

List:RegistryOfStandardBiologicalParties - testing the new mailing list function austin implemented

Nerdbook - scientific networking, get your nerd on. (maybe we need a new name)

Reviews -- WikiReviews, will they work? help us find out!

Mission -- we have a mission, was decided at the retreat awhile back

Respond_to_NSF -- some long term planning thoughts.

Science blogs - list of science blogs

Endy Lab:Recent changes

Endy:Screening plasmid/Recent changes

Patent goon squad

Endy:Evolutionary stability project

Physcomitrella patens

Glycerols

 * Endy:Screening plasmid 2.0/glycerol box
 * /Glycerol boxes sent to Stanford

Sandbox
MIT audio bridge conference calling  
 * Who is on OWW:
 * Square bacteria
 * User:Kchang17/notes
 * Endy:Measuring Screening Plasmid on MOFLO





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