User:Jason R. Kelly: Difference between revisions

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==Bio==
==Bio==
[[Image:Jkpic.JPG|right|thumb]]
Jason Kelly
Founder at [http://ginkgobioworks.com Ginkgo BioWorks]


Jason Kelly
Co-Founder of OpenWetWare, 2007


3rd Year Biological Engineering Graduate Student @ MIT in the [[Endy Lab]]
PhD in Biological Engineering @ MIT in the [[Endy Lab]], June 2008


S.B. in Biology and Chemical Engineering @ MIT, 2003
S.B. in Biology and Chemical Engineering @ MIT, 2003
==Contact==
jason AT ginkgobioworks DOT com


==Activities==
==Activities==
[[BE Board:Undergraduate curriculum liaison|BE undergrad curriculum representative]]
[[Image:CirEmblemHandwriteLogo2.png|left|thumb|150px|[[OpenWetWare steering committee|OpenWetWare board member]] - please help out!]]
 
[[Image:IGEM-cropped-edited.PNG|none|thumb|300px|Advisor to the [[IGEM:MIT/2006|2006 MIT iGEM team]].  The team won the prize for best system, and got mentioned on [http://science.slashdot.org/article.pl?sid=06/11/06/1913228 slashdot].  Check out our [http://parts.mit.edu/wiki/index.php/MIT_2006 banana and mint-scented bacteria].]]
[[Endy:Lab Fire Marshall|Endy lab fire marshall]]
[[Image:Service lab.png|thumb|left|Organize the [[SynBERC:COG|SynBERC Automated assembly interest group]]]]
 
[[Image:FreeGenes.JPG|thumb|none|[http://blog.openwetware.org/freegenes/ Started a blog]]]
[[OpenWetWare steering committee]] - please help out!
<br style="clear:both" />
[[Image:Ginkgologo.PNG|none|thumb|300px|[http://ginkgobioworks.com Founder at Ginkgo BW] ]]


==Thesis Project==
==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.    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.   
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 [[Endy:Screening plasmid|FACS-based screening system]] to rapidly measure the input/output function of a genetic circuit and a [[The BioBricks Foundation:Standards/Technical/Measurement|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 [[Sortostat|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===
===Specific Aims===
#[[PoPS device screening plasmid]]
#Tools for screening and measurement
#*[[The BioBricks Foundation:Standards/Technical/Measurement|Standard Measurement kit for promoters/RBSs]]
#**Instructions for kit users can be found [http://partsregistry.org/Measurement at the Registry]
#*[[PoPS device screening plasmid]]
#[[Library-based Construction]]
#[[Library-based Construction]]
#[[Evolutionary Stability]]
#[[SortoStat]]
#*[[SortoStat]]


===Communications===
===Communications===
*[http://hdl.handle.net/1721.1/21169 Thesis Proposal PDF]
*[http://hdl.handle.net/1721.1/21169 Thesis Proposal PDF]
*[[:Image:JK ICSB 2005.pdf|ICSB Poster (2005)]]
*[[Media:JK.SB3.0.Poster.2007.pdf|SB3.0 Poster (2007)]]
*[[:Image:JK.SyntheticBiology2.0.Poster.pdf|Synthetic Biology 2.0 Poster (2006)]]
*[[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===
===Current Project Pages===
*[[Endy:Evolutionary stability project]]
*[[Sortostat/Notebook]]
*[[Sortostat/Growth Tests]]
*[[Endy:Screening plasmid/Notebook|Screening plasmid/Notebook]]
*[[Knight:Evolving Reshmaverters]]
*[[Knight:Evolving Reshmaverters]]
*[[Endy:Chemostat]]
*[[Endy:Chemostat]]
*[[Endy:Inverter composition]]
*[[Endy:Measkit draft]]
==Publications==
<biblio>
#Kelly-JBE pmid=19298678
</biblio>
<biblio>
#Kosuri-BMCBioinfo2007 pmid=18093293
</biblio>
<biblio>
#Janes-JCompBio-2004 pmid=15579231
</biblio>
::<small>([http://www.cellmigration.org/resource/modeling/model_resources.shtml MATLAB files available here, scroll down to Modeling Software:Lauffenburger Lab])</small>
====Popular press====
*[http://www.seedmagazine.com/news/2008/12/igem_2008_novice_bioengineers.php iGEM 2008: Novice Bioengineers Get Their Freak On (SEED Magazine)]
==Talks==
===Upcoming===
*October, 2008, [http://sb4.biobricks.org/ Synthetic Biology 4.0], Hong Kong, China
**Reference Standards for Characterizing Biological Parts
===Previous===
*June 2008, [http://ccbw.calit2.net/ New Communication Channels for Biology Workshop], UCSD
**[[OpenWetWare:Presentations/Tour|OWW site tour]]
*April 2008, [http://www.sys-bio.org/sbwWiki/workshops/standardsandspecifications08 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, [http://bbf.openwetware.org/Workshop2.html BioBrick Foundation Technical Standards Workshop], Berkeley, CA
**[http://video.google.com/googleplayer.swf?docId=3783852973289336417&hl=en Measurement kit for BioBrick promoters and RBSs] (video)
*March 2008, [http://www.aiabanffconference.com/banffconference/index.html Advanced Technologies for Agrology], Banff, Canada
**Standards for programming DNA
*July 2006, [http://www.nature.com/nature/meetings/scifoo/index.html Nature/O'Reilly Science Foo Camp], Google, Mountain View, CA
**[[OpenWetWare:Presentations/SciFoo|OWW site tour]]
==Videos==
<html>
<embed style="width:400px; height:326px;" id="VideoPlayback" type="application/x-shockwave-flash" src="http://video.google.com/googleplayer.swf?docId=3783852973289336417&hl=en" flashvars=""> </embed>
</html>
*References standards for biological engineers
<html>
<object width="425" height="355"><param name="movie" value="http://www.youtube.com/v/jX_Z7hzHjrY&hl=en"></param><param name="wmode" value="transparent"></param><embed src="http://www.youtube.com/v/jX_Z7hzHjrY&hl=en" type="application/x-shockwave-flash" wmode="transparent" width="425" height="355"></embed></object>
</html>
*Synchronized pipetting


==OWW Pages in Progess==
==OWW Pages in Progess==
<google>Protocols</google>
[[Special:OWWStats]]
[[OpenWetWare:New visitor blurb]]
[[OpenWetWare:SC coordinator torch]]
[[OpenWetWare: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.   
[[BioBricks construction tutorial]] - a step-by-step tutorial for a single Biobrick assembly.   


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[[OpenWetWare:Steering committee/NSF BDI Grant]] - help us write a grant for OWW.
[[OpenWetWare:Steering committee/NSF BDI Grant]] - help us write a grant for OWW.


==Papers of Interest==
[[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
 
[[Special:Mypage/sidebar|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 [http://postgenomic.com 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)
 
[[OpenWetWare:Reviews]] -- WikiReviews, will they work?  help us find out!
 
[[OpenWetWare:Mission]] -- we have a mission, was decided at the [[OpenWetWare steering committee/SC retreat|retreat]] awhile back
 
[[OpenWetWare:Respond_to_NSF]] -- some long term planning thoughts.
 
[[Science blogs]] - list of science blogs
 
[[Endy Lab:Recent changes]]
 
[[Endy:Screening plasmid/Recent changes]]


===Library-based Construction===
[[Patent goon squad]]


===Evolutionary Stability===
[[Endy:Evolutionary stability project]]


[[Inhibition of Mutation and Combating of the Evolution of Antibiotic Resistance (Cirz et al)]]
[[Physcomitrella patens]]


==Contact==
==Glycerols==
jasonk AT mit DOT edu
*[[Endy:Screening plasmid 2.0/glycerol box]]
==Random==
*[[/Glycerol boxes sent to Stanford]]
[http://ijs.sgmjournals.org/cgi/content/full/54/5/1709 Square bacteria]


==Testing this (thanks barry)==
==Sandbox==
*Who is on OWW:
*[http://ijs.sgmjournals.org/cgi/content/full/54/5/1709 Square bacteria]
*{{Discussion}}
[http://web.mit.edu/is/services/telecommunications/audiobridges.html MIT audio bridge conference calling]
*[[User:Kchang17/notes]]
*[[Endy:Measuring Screening Plasmid on MOFLO]]
<html>
<html>
<a href="http://clustrmaps.com/counter/maps.php?url=http://openwetware.org/wiki/Jason_Kelly" id="clustrMapsLink"><img src="http://clustrmaps.com/counter/index2.php?url=http://openwetware.org/wiki/Jason_Kelly" border=1 alt="Locations of visitors to this page"onError="this.onError=null; this.src='http://www.meetomatic.com/images/clustrmaps-back-soon.jpg'; document.getElementById('clustrMapsLink').href='http://clustrmaps.com/'">
<a href="http://www3.clustrmaps.com/counter/maps.php?url=http://openwetware.org/wiki/User:Jason_R._Kelly" id="clustrMapsLink"><img src="http://www3.clustrmaps.com/counter/index2.php?url=http://openwetware.org/wiki/User:Jason_R._Kelly" style="border:0px;" alt="Locations of visitors to this page" title="Locations of visitors to this page" id="clustrMapsImg" onError="this.onError=null; this.src='http://www2.clustrmaps.com/images/clustrmaps-back-soon.jpg'; document.getElementById('clustrMapsLink').href='http://www2.clustrmaps.com'" />
</a>
</a>
</html>
</html>


<br style="clear:both" />
<br style="clear:both" />
<html>
<a href="http://www.openwetware.org"><img src="http://openwetware.org/images/c/ce/03_JoinOWW.png" border=0/></a>
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[[Category:Biogang_members]]
__NOTOC__
__NOTOC__
[[Category:Steering Committee member]]
[[Category:People at MIT]]
.
<br style="clear:both" />

Latest revision as of 01:05, 5 November 2010

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

OpenWetWare board member - please help out!
Advisor to the 2006 MIT iGEM team. The team won the prize for best system, and got mentioned on slashdot. Check out our banana and mint-scented bacteria.
Organize the SynBERC Automated assembly interest group
Started a blog


Founder at Ginkgo BW

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. Library-based Construction
  3. SortoStat

Communications

Current Project Pages

Publications

  1. 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 | PubMed ID:19298678 | HubMed [Kelly-JBE]
  1. 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 | PubMed ID:18093293 | HubMed [Kosuri-BMCBioinfo2007]
  1. 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 | PubMed ID:15579231 | HubMed [Janes-JCompBio-2004]
(MATLAB files available here, scroll down to Modeling Software:Lauffenburger Lab)


Popular press

Talks

Upcoming

  • October, 2008, Synthetic Biology 4.0, Hong Kong, China
    • Reference Standards for Characterizing Biological Parts

Previous

Videos

<html> <embed style="width:400px; height:326px;" id="VideoPlayback" type="application/x-shockwave-flash" src="http://video.google.com/googleplayer.swf?docId=3783852973289336417&hl=en" flashvars=""> </embed> </html>

  • References standards for biological engineers

<html> <object width="425" height="355"><param name="movie" value="http://www.youtube.com/v/jX_Z7hzHjrY&hl=en"></param><param name="wmode" value="transparent"></param><embed src="http://www.youtube.com/v/jX_Z7hzHjrY&hl=en" type="application/x-shockwave-flash" wmode="transparent" width="425" height="355"></embed></object> </html>

  • Synchronized pipetting

OWW Pages in Progess

<google>Protocols</google>

Special:OWWStats

OpenWetWare:New visitor blurb

OpenWetWare:SC coordinator torch

OpenWetWare: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

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.

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)

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 Lab:Recent changes

Endy:Screening plasmid/Recent changes

Patent goon squad

Endy:Evolutionary stability project

Physcomitrella patens

Glycerols

Sandbox

  • Who is on OWW:
  • Square bacteria
  • This is a discussion area. To post comments, please type *'''~~~~''':

MIT audio bridge conference calling

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