Difference between revisions of "Davidson Missouri W"

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<center>[[Davidson Missouri W| <span style="color:black">Home</span>]] | [[Davidson Missouri W/Background Information| <span style="color:red">Background Information</span>]] | [[Davidson Missouri W/Solving the HPP in vivo| <span style="color:red">Current Project: Solving the Hamiltonian Path Problem ''in vivo''</span>]] | [[Davidson Missouri W/Mathematical Modeling| <span style="color:red">Mathematical Modeling</span>]] | [[Davidson Missouri W/Gene splitting| <span style="color:red"> Gene Splitting </span>]] | [[Davidson Missouri W/Controlling Expression| <span style="color:red"> Controlling Expression </span>]] | [[Davidson Missouri W/Traveling Salesperson Problem| <span style="color:red">Traveling Salesperson Problem</span> ]] | [[Davidson Missouri W/Backwards promotion and read-through transcription| <span style="color:red">Backwards Promotion and Read-Through Transcription</span>]] | [[Davidson Missouri W/Software|<span style="color:red">Software</span>]] | [[Davidson Missouri W/Resources and Citations|<span style="color:red">Resources and Citations</span>]]</center>
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=The Team=
 
=The Team=
 
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{| border="1" cellpadding="5" cellspacing="0" align="center" width="100%"
 
|-
 
|-
 
! style="color: white; background-color: black;"| The Team
 
! style="color: white; background-color: black;"| The Team
 
! style="color: white; background-color: black;" | The Faculty
 
! style="color: white; background-color: black;" | The Faculty
 
! style="color: white; background-color: black;" | Team Logos
 
! style="color: white; background-color: black;" | Team Logos
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! style="color: white; background-color: black;" | Group Photo
 
|-
 
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|style="color: black; background-color: red;" align="center"| '''Davidson'''
 
|style="color: black; background-color: red;" align="center"| '''Davidson'''
 
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[[Oyinade Adefuye|<span style="color:black">Oyinade Adefuye</span>]]
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[[Davidson Missouri W/Oyinade Adefuye|<span style="color:black">Oyinade Adefuye</span>]]
 
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[[Will DeLoache|<span style="color:black">Will DeLoache</span>]]
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[[Davidson Missouri W/Will DeLoache|<span style="color:black">Will DeLoache</span>]]
 
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[[Jim Dickson|<span style="color:black">Jim Dickson</span>]]
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[[Davidson Missouri W/Jim Dickson|<span style="color:black">Jim Dickson</span>]]
 
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[[Andrew Martens|<span style="color:black">Andrew Martens</span>]]
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[[Davidson Missouri W/Andrew Martens|<span style="color:black">Andrew Martens</span>]]
 
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[[ Amber Shoecraft|<span style="color:black">Amber Shoecraft</span>]]
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[[Davidson Missouri W/Amber Shoecraft|<span style="color:black">Amber Shoecraft</span>]]
 
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[[Mike Waters|<span style="color:black">Mike Waters</span>]]
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[[Davidson Missouri W/Mike Waters|<span style="color:black">Mike Waters</span>]]
 
</b>
 
</b>
  
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|style="color: black; background-color: red;" align="center"|
 
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[[A. Malcolm Campbell|<span style="color:black">A. Malcom Campbell</span>]]
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[[Davidson Missouri W/A. Malcolm Campbell|<span style="color:black">A. Malcom Campbell</span>]]
 
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[[Karmella Haynes|<span style="color:black">Karmella Haynes</span>]]
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[[Davidson Missouri W/Karmella Haynes|<span style="color:black">Karmella Haynes</span>]]
 
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[[Laurie Heyer|<span style="color:black">Laurie Heyer</span>]]
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[[Davidson Missouri W/Laurie Heyer|<span style="color:black">Laurie Heyer</span>]]
 
</b>
 
</b>
  
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|style="color: red; background-color: white;" align="center"|
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|style="color: black; background-color: white;" align="center"|
 
[[Image:DavidsonLogo.gif]]
 
[[Image:DavidsonLogo.gif]]
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|style="color: black; background-color: white;" align="center"|
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[[Image:Team1.jpg|thumb|300px]]
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|style="color: black; background-color: yellow;" align="center"|'''Missouri Western'''
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|style="color: black; background-color: gold;" align="center"|'''Missouri Western'''
 
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[[Jordan Baumgardner|<span style="color:black;">Jordan Baumgardner</span>]]
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[[Davidson Missouri W/Jordan Baumgardner|<span style="color:black;">Jordan Baumgardner</span>]]
 
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[[Tom Crowley|<span style="color:black;">Tom Crowley</span>]]
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[[Davidson Missouri W/Tom Crowley|<span style="color:black;">Tom Crowley</span>]]
 
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[[Lane H. Heard|<span style="color:black;">Lane H. Heard</span>]]
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[[Davidson Missouri W/Lane H. Heard|<span style="color:black;">Lane H. Heard</span>]]
 
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[[Nickolaus Morton|<span style="color:black;">Nickolaus Morton</span>]]
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[[Davidson Missouri W/Nickolaus Morton|<span style="color:black;">Nickolaus Morton</span>]]
 
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[[Michelle Ritter|<span style="color:black;">Michelle Ritter</span>]]
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[[Davidson Missouri W/Michelle Ritter|<span style="color:black;">Michelle Ritter</span>]]
 
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[[Jessica Treece|<span style="color:black;">Jessica Treece</span>]]
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[[Davidson Missouri W/Jessica Treece|<span style="color:black;">Jessica Treece</span>]]
 
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[[Matthew Unzicker|<span style="color:black;">Matthew Unzicker</span>]]
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[[Davidson Missouri W/Matthew Unzicker|<span style="color:black;">Matthew Unzicker</span>]]
 
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[[Amanda Valencia|<span style="color:black;">Amanda Valencia</span>]]
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[[Davidson Missouri W/Amanda Valencia|<span style="color:black;">Amanda Valencia</span>]]
 
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</b>
  
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|style="color: black; background-color: gold;" align="center"|
 
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[[Todd Eckdahl|<span style="color:black;">Todd Eckdahl</span>]]
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[[Davidson Missouri W/Todd Eckdahl|<span style="color:black;">Todd Eckdahl</span>]]
 
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[[Jeff Poet|<span style="color:black;">Jeff Poet</span>]]
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[[Davidson Missouri W/Jeff Poet|<span style="color:black;">Jeff Poet</span>]]
 
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|style="color: red; background-color: white;" align="center"|[[Image:MWLogo.gif]]
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|style="color: black; background-color: white;" align="center"|[[Image:MWLogo.gif]]
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|-
 
|-
  
 
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[[Image:Team_graph.jpg|center|thumb|500px|A Human Representation of Adleman's Graph (see below)]]
 
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=The Problem=
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=Our Project=
 
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{| border="1" cellpadding="5" cellspacing="0" align="center" width="90%"
 
|-
 
|-
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! style="color: black; background-color: red;" width="20%"| In Depth
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! style="color: black; background-color: red;" width="20%"| <font size="+1">In Depth</font>
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! colspan="3" style="color: black; background-color: red;" width="60%"| Overview
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! colspan="3" style="color: black; background-color: red;" width="60%"| <font size="+1">Overview</font>
 
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[[Background Information|<span style="color:red">Background Information</span>]]
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[[Davidson Missouri W/Background Information|<span style="color:red">Background Information</span>]]
 
<br><br><br>
 
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[[Solving the HPP in vivo|<span style="color:red">Current Project: Solving the Hamiltonian Path Problem ''in vivo''</span>]]
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[[Davidson Missouri W/Solving the HPP in vivo|<span style="color:red">Current Project: Solving the Hamiltonian Path Problem ''in vivo''</span>]]
 
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[[Probability and Statistics|<span style="color:red">Probability and Statistics</span>]]
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[[Davidson Missouri W/Mathematical Modeling|<span style="color:red">Mathematical Modeling</span>]]
 
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[[Gene splitting|<span style="color:red">Gene Splitting</span>]]
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[[Davidson Missouri W/Gene splitting|<span style="color:red">Gene Splitting</span>]]
 
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[[Controlling Expression|<span style="color:red">Controlling Expression</span>]]
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[[Davidson Missouri W/Controlling Expression|<span style="color:red">Controlling Expression</span>]]
 
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[[Traveling Salesperson Problem|<span style="color:red">Traveling Salesperson Problem</span>]]
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[[Davidson Missouri W/Traveling Salesperson Problem|<span style="color:red">Traveling Salesperson Problem</span>]]
 
<br><br><br>
 
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[[Backwards promotion and read-through transcription|<span style="color:red">Backwards promotion and Read-Through Transcription</span>]]
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[[Davidson Missouri W/Backwards Promotion and read-through transcription|<span style="color:red">Backwards Promotion and Read-Through Transcription</span>]]
 
<br><br><br>
 
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[[Davidson Missouri W/Resources and Citations|<span style="color:red">Resources and Citations</span>]]
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<br><br><Br>
 
|Hamiltonian Path Problem
 
|Hamiltonian Path Problem
 
As a part of iGEM2006, a combined team from Davidson College and Missouri Western State University reconstituted a hin/hix DNA recombination mechanism which exists in nature in Salmonella as standard biobricks for use in ''E. coli''. The purpose of the 2006 combined team was to provide a proof of concept for a bacterial computer in using this mechanism to solve a variation of The Pancake Problem from Computer Science. This task utilized both biology and mathematics students and faculty from the two institutions.
 
As a part of iGEM2006, a combined team from Davidson College and Missouri Western State University reconstituted a hin/hix DNA recombination mechanism which exists in nature in Salmonella as standard biobricks for use in ''E. coli''. The purpose of the 2006 combined team was to provide a proof of concept for a bacterial computer in using this mechanism to solve a variation of The Pancake Problem from Computer Science. This task utilized both biology and mathematics students and faculty from the two institutions.
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[[Image:AdelmanGraph.JPG|thumb|300px|center| ]]   
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[[Image:AdelmanGraph.JPG|thumb|300px|center|The Adleman graph.]]   
 
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[[Image:HamiltonianGraph.PNG|thumb|700px|center|]]
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[[Image:HamiltonianGraph.PNG|thumb|700px|center|A graph implemented on a plasmid.]]
  
 
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= '''Resources / Citations''' =
 
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[http://parts.mit.edu/wiki/index.php/The_What%27s_and_How%27s Davidson's Wet Lab Protocols]
 
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[http://parts.mit.edu/igem07/index.php/Davidson_Missouri_W/MWSU_protocols Missouri Western's Wet Lab Protocols]
 
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[http://gcat.davidson.edu/iGEM07/genesplitter.html Spliting Genes Web Tool]
 
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[http://www.bio.davidson.edu/courses/Molbio/Protocols/ORIs.html '''Compatibility of Plasmids''']
 
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[http://tools.wikimedia.de/~tangotango/nubio/ A Site with an FAQ on Wikis]
 
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#'''DMW Part Numbers for 2007 are BBa_I715000 to BBa_I715999.'''
 
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#[http://parts.mit.edu/registry/index.php/Help:BioBrick_Part_Names How to Name a New Part]
 
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#[http://parts.mit.edu/registry/index.php/Add_a_Part_to_the_Registry Entering the Part to the Registry]
 
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#[http://parts.mit.edu/registry/index.php/Help:Part_Features How to Annotate a Part]
 
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Cool site for Breakfast
 
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[http://www.cut-the-knot.org/SimpleGames/Flipper.shtml]
 
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Karen Acker's paper describing GFP and TetA(c) with Hix insertions
 
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[http://www.bio.davidson.edu/Courses/Immunology/Students/spring2006/Acker/Acker_finalpaperGFP.doc]
 
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Bruce Henschen's paper describing one-time flippable Hix sites
 
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[http://www.bio.davidson.edu/Courses/genomics/2006/henschen/Bruce_Finalpaper.doc]
 
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Intro to Hamiltonian Path Problem and DNA
 
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[http://www.ams.org/featurecolumn/archive/dna-abc2.html]
 
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Adleman, LM. Molecular Computation of Solutions To Combinatorial Problems. Science.  11 November 1994. Vol. 266. no. 5187, pp. 1021 - 1024
 
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Sambrook and Russell. 2001. Molecular Cloning A Laboratory Manual. Cold Spring Harbor Laboratry Press. Cold Spring Harbor, New York pg. 1.145. 2007 June.
 

Latest revision as of 15:22, 9 August 2007

Home | Background Information | Current Project: Solving the Hamiltonian Path Problem in vivo | Mathematical Modeling | Gene Splitting | Controlling Expression | Traveling Salesperson Problem | Backwards Promotion and Read-Through Transcription | Software | Resources and Citations


DMW-1.jpg

The Team

The Team The Faculty Team Logos Group Photo
Davidson

Oyinade Adefuye
Will DeLoache
Jim Dickson
Andrew Martens
Amber Shoecraft
Mike Waters

A. Malcom Campbell
Karmella Haynes
Laurie Heyer

DavidsonLogo.gif

Team1.jpg
Missouri Western

Jordan Baumgardner
Tom Crowley
Lane H. Heard
Nickolaus Morton
Michelle Ritter
Jessica Treece
Matthew Unzicker
Amanda Valencia

Todd Eckdahl
Jeff Poet

MWLogo.gif


A Human Representation of Adleman's Graph (see below)



Our Project

In Depth Overview

Background Information


Current Project: Solving the Hamiltonian Path Problem in vivo


Mathematical Modeling


Gene Splitting


Controlling Expression


Traveling Salesperson Problem


Backwards Promotion and Read-Through Transcription


Resources and Citations


Hamiltonian Path Problem

As a part of iGEM2006, a combined team from Davidson College and Missouri Western State University reconstituted a hin/hix DNA recombination mechanism which exists in nature in Salmonella as standard biobricks for use in E. coli. The purpose of the 2006 combined team was to provide a proof of concept for a bacterial computer in using this mechanism to solve a variation of The Pancake Problem from Computer Science. This task utilized both biology and mathematics students and faculty from the two institutions.

For 2007, we continue our collaboration and our efforts to manipulate E. coli into mathematics problem solvers as we refine our efforts with the hin/hix mechanism to explore another mathematics problem, the Hamiltonian Path Problem. This problem was the subject of a groundbreaking paper by Adelman in 1994 (citation below) where a unique Hamiltonian path was found in vitro for a particular directed graph on seven nodes. We propose to make progress toward solving the particular problem in vivo.


The Adleman graph.


A graph implemented on a plasmid.
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