Davidson 2006

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===MATLAB Code===
===MATLAB Code===
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==The Original Flipping Simulators==
[http://gcat.davidson.edu/IGEM06/randompancakeflipper.m User-Friendly Version]<br>
[http://gcat.davidson.edu/IGEM06/randompancakeflipper.m User-Friendly Version]<br>
[http://gcat.davidson.edu/IGEM06/powerflipper.m Power-User Version]<br>
[http://gcat.davidson.edu/IGEM06/powerflipper.m Power-User Version]<br>
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[http://gcat.davidson.edu/IGEM06/findmin.m Findmin]<br>
[http://gcat.davidson.edu/IGEM06/findmin.m Findmin]<br>
[http://gcat.davidson.edu/IGEM06/bigtrial.m Bigtrial]<br>
[http://gcat.davidson.edu/IGEM06/bigtrial.m Bigtrial]<br>
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==Graphing Tools==
[http://gcat.davidson.edu/IGEM06/pancakeplotter.m Pancakeplotter]<br>
[http://gcat.davidson.edu/IGEM06/pancakeplotter.m Pancakeplotter]<br>
[http://gcat.davidson.edu/IGEM06/permplotter.m Permplotter]<br>
[http://gcat.davidson.edu/IGEM06/permplotter.m Permplotter]<br>
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[http://gcat.davidson.edu/IGEM06/bioperms.m Bioperms]<br>
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[http://gcat.davidson.edu/IGEM06/adjmat.m Adjmat - creates adjacency matrices]<br>
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[http://gcat.davidson.edu/IGEM06/signedperms.m Signedperms]<br>
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[http://gcat.davidson.edu/IGEM06/bioadjmat.m Bioadjmat - Adjmat with biological equivalence]<br>
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[http://gcat.davidson.edu/IGEM06/adjmat.m Adjmat]<br>
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[http://gcat.davidson.edu/IGEM06/make_radial.m Make_radial - creates a radially-embedded graph]<br>
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[http://gcat.davidson.edu/IGEM06/make_radial.m Make_radial]<br>
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[http://gcat.davidson.edu/IGEM06/find_diam.m Find_diam - finds the diameter of a pancake graph]<br>
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[http://gcat.davidson.edu/IGEM06/find_diam.m Find_diam]<br>
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==Miscellaneous==
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[http://gcat.davidson.edu/IGEM06/signedperms.m Signedperms - lists all signed permutations for a stack of k pancakes]<br>
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[http://gcat.davidson.edu/IGEM06/bioperms.m Bioperms - Signedperms with biological equivalence]<br>
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[http://gcat.davidson.edu/IGEM06/oligo.m Oligo Cuts Optimization]<br>
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Revision as of 20:40, 4 August 2006

Logo.gif


[http://www.bio.davidson.edu/courses/synthetic/photos/FlapJack_HotCakes.html Official Team Photo (rollover image)]

DC team.JPG Logo
Malcolm, Laurie, Sabriya, Erin, Lance


Contents

Project

Who: The Mammoths, and FlapJack and the Pancakes

What: Our goal is to solve the Pancake problem[http://www.cut-the-knot.org/SimpleGames/Flipper.shtml] in a biological system.

When: Summer and Fall '06

Where: Missouri Western State University and Davidson College

Why: Because we love breakfast... well most of us.

How: Trying to invert antibiotic resistance genes using the Hin/Hix inversion method found in Salmonella typhimurium.


  • Our overall goal was to see if we could use synthetic methods to construct an E. coli computer. If we grew 1015 cells, and each cell was attempting to solve the problem, then even rare events might be solvable by E. coli computers.
  • We decided to tackle the burnt pancake problem since DNA, like burnt pancakes, has a directionality. We needed a way to flip the DNA and chose the Hin/Hix system. We had to isolate RE, HixC from S. typhimurium strain XX (need to insert name), and Hin from S. typhimurium, strain TA100 .
  • We decided to test the size constraints first, so we are building stacks of pancakes only one high at first. We will try to flip the promoter (smaller) in one case, and the coding region (bigger) in another case. The coding region is TetR resistance gene isolated from a plasmid in the Registry. For higher stacks of pancakes, we will also use chloramphenicolR and cycloheximideR.

Students

  • Erin Zwack is a rising junior biology major at Davidson College.
  • Lance Harden is a rising sophomore at Davidson College who will probably major in math.
  • Samantha Simpson is a rising sophomore at Davidson College who might design a major in genomics.

Faculty

  • Laurie J. Heyer [http://www.davidson.edu/math/heyer/ Department of Mathematics]
  • Karmella Haynes [http://www.bio.davidson.edu/ Department of Biology - teaching postdoc and visiting assistant professor]

Papers of Interest

Parts Created

Pancake Parts

Questions

Assembly

Progress

Plasmids and Bacteria     Hix and RE    Hin and Antibiotic Pancakes    Ligations

Pancake Simulators aka The Lancelator

MATLAB Code

The Original Flipping Simulators

[http://gcat.davidson.edu/IGEM06/randompancakeflipper.m User-Friendly Version]
[http://gcat.davidson.edu/IGEM06/powerflipper.m Power-User Version]
[http://gcat.davidson.edu/IGEM06/powerflipperplus.m Power-User Update]
[http://gcat.davidson.edu/IGEM06/findmin.m Findmin]
[http://gcat.davidson.edu/IGEM06/bigtrial.m Bigtrial]

Graphing Tools

[http://gcat.davidson.edu/IGEM06/pancakeplotter.m Pancakeplotter]
[http://gcat.davidson.edu/IGEM06/permplotter.m Permplotter]
[http://gcat.davidson.edu/IGEM06/adjmat.m Adjmat - creates adjacency matrices]
[http://gcat.davidson.edu/IGEM06/bioadjmat.m Bioadjmat - Adjmat with biological equivalence]
[http://gcat.davidson.edu/IGEM06/make_radial.m Make_radial - creates a radially-embedded graph]
[http://gcat.davidson.edu/IGEM06/find_diam.m Find_diam - finds the diameter of a pancake graph]

Miscellaneous

[http://gcat.davidson.edu/IGEM06/signedperms.m Signedperms - lists all signed permutations for a stack of k pancakes]
[http://gcat.davidson.edu/IGEM06/bioperms.m Bioperms - Signedperms with biological equivalence]
[http://gcat.davidson.edu/IGEM06/oligo.m Oligo Cuts Optimization]

Personal tools
Past/present/future years