Davidson 2006

From 2006.igem.org

(Difference between revisions)
Jump to: navigation, search
Line 5: Line 5:
|}
|}
    
    
 +
----
<big>'''PROJECT OVERVIEW'''</big>
<big>'''PROJECT OVERVIEW'''</big>
Line 24: Line 25:
* 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 Tet<sup>R</sup> resistance gene isolated from a plasmid in the Registry. For higher stacks of pancakes, we will also use chloramphenicol<sup>R</sup> and cycloheximide<sup>R</sup>.
* 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 Tet<sup>R</sup> resistance gene isolated from a plasmid in the Registry. For higher stacks of pancakes, we will also use chloramphenicol<sup>R</sup> and cycloheximide<sup>R</sup>.
 +
----
<big>'''TEAM MEMBERS'''</big>
<big>'''TEAM MEMBERS'''</big>
Line 31: Line 33:
* [mailto:erzwack@davidson.edu| Erin Zwack] is a rising junior biology major at Davidson College.
* [mailto:erzwack@davidson.edu| Erin Zwack] is a rising junior biology major at Davidson College.
* [mailto:laharden@davidson.edu| Lance Harden] is a rising sophomore math major at Davidson College.
* [mailto:laharden@davidson.edu| Lance Harden] is a rising sophomore math major at Davidson College.
-
* [mailto:sasimpson@davidson.edu| Samantha Simpson] is a rising sophomore at Davidson College who might design a major in genomics.</font face>
+
* [mailto:sasimpson@davidson.edu| Samantha Simpson] is a rising sophomore at Davidson College who might design a major in genomics.
'''Faculty'''
'''Faculty'''
Line 39: Line 41:
<big>'''TEAM RESOURCES'''</big>
<big>'''TEAM RESOURCES'''</big>
 +
 +
'''iGEM 2006 Jamboree'''
 +
*[[Presentation Outline]]
 +
'''White Board'''
'''White Board'''
* [[General Questions]]  
* [[General Questions]]  
Line 44: Line 50:
* [[Biology Questions]]
* [[Biology Questions]]
-
'''Lab Work'''
+
'''Biology Tools (Wet Bench)'''
*[[Pancake Parts]]</font face>
*[[Pancake Parts]]</font face>
-
 
+
*[[The What's and How's]]: Davidson Protocols
-
'''General'''
+
*[http://gcat.davidson.edu/IGEM06/oligo.html Oligo Cuts Optimization]: by Lance Harden
*[[Papers of Interest]]
*[[Papers of Interest]]
-
*[[Presentation Outline]]
 
-
==<font face="chalkboard"><font color= 'tan'>Assembly</font color></font face><font outline color> ==
+
'''Math Tools'''
 +
*Pancake Simulators, aka <font color='red'>T</font color><font color='blue'>h</font color><font color='orange'>e</font color><font color='silver'> L</font color><font color='sky blue'>a</font color><font color='magenta'>n</font color><font color= 'orange'>c</font color><font color='green'>e</font color><font color=cyan>l</font color><font color='red'>a</font color><font color='brown'>t</font color><font color='blue'>o</font color><font color='violet'>r</font color> (MATLAB Code)
 +
* Other 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]
-
* <font face="chalkboard">[[The What's and How's]]: Davidson Protocols</font face>
+
'''Bio-Math Tools'''
-
* <font face="chalkboard"> [[Assembly powerpoint]]</font face>
+
*[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]
 +
 
 +
'''Assembly Plans'''
 +
*[[Assembly powerpoint]]
*[[Assembly plan]]
*[[Assembly plan]]
-
*<font color='black'>Final Assembly plans:</font color>
+
*[[Western Assembly Plan]]
-
**[[Western Assembly Plan]]
+
*[[Davidson Assembly Plan]]
-
**[[Davidson Assembly Plan]]
+
-
 
+
-
== <font color='cyan'><font face="chalkboard">Progress</font face></font color>==
+
-
 
+
-
 
+
-
<font face="chalkboard">[[Plasmids and Bacteria]] &nbsp;&nbsp;&nbsp;
+
-
[[Hix and RE]]&nbsp;&nbsp;&nbsp;
+
-
[[Hin and Antibiotic Pancakes]]&nbsp;&nbsp;&nbsp;
+
-
[[Ligations]]
+
-
</font face>
+
-
 
+
-
==<font face="chalkboard">Pancake Simulators aka <font color='red'>T</font color><font color='blue'>h</font color><font color='orange'>e</font color><font color='silver'> L</font color><font color='sky blue'>a</font color><font color='magenta'>n</font color><font color= 'orange'>c</font color><font color='green'>e</font color><font color=cyan>l</font color><font color='red'>a</font color><font color='brown'>t</font color><font color='blue'>o</font color><font color='violet'>r</font color> (MATLAB Code)==
+
-
 
+
-
===The Original Flipping Simulators===
+
-
[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/powerflipperplus.m Power-User Update]<br>
+
-
[http://gcat.davidson.edu/IGEM06/findmin.m Findmin]<br>
+
-
[http://gcat.davidson.edu/IGEM06/bigtrial.m Bigtrial]<br>
+
-
 
+
-
===Graphing Tools===
+
-
[http://gcat.davidson.edu/IGEM06/pancakeplotter.m Pancakeplotter]<br>
+
-
[http://gcat.davidson.edu/IGEM06/permplotter.m Permplotter]<br>
+
-
[http://gcat.davidson.edu/IGEM06/adjmat.m Adjmat - creates adjacency matrices]<br>
+
-
[http://gcat.davidson.edu/IGEM06/bioadjmat.m Bioadjmat - Adjmat with biological equivalence]<br>
+
-
[http://gcat.davidson.edu/IGEM06/make_radial.m Make_radial - creates a radially-embedded graph]<br>
+
-
[http://gcat.davidson.edu/IGEM06/find_diam.m Find_diam - finds the diameter of a pancake graph]<br>
+
-
===Miscellaneous===
+
'''Progress'''
-
[http://gcat.davidson.edu/IGEM06/signedperms.m Signedperms - lists all signed permutations for a stack of k pancakes]<br>
+
*[[Plasmids and Bacteria]]
-
[http://gcat.davidson.edu/IGEM06/bioperms.m Bioperms - Signedperms with biological equivalence]<br>
+
*[[Hix and RE]]
-
[http://gcat.davidson.edu/IGEM06/oligo.html Oligo Cuts Optimization]<br>
+
*[[Hin and Antibiotic Pancakes]]
-
</font face>
+
*[[Ligations]]

Revision as of 02:00, 18 October 2006

Logo.gif

Project Overview

Davidson Parts

Team Members

Tools and Resources

Check out our [http://www.bio.davidson.edu/courses/synthetic/photos/FlapJack_HotCakes.html Official Team Photo]
Left to Right: Malcolm, Laurie, Sabriya, Erin and Lance

PROJECT OVERVIEW

Goal
Our goal is to mathematically model and genetically engineer a biological system that can compute the solution to a puzzle called the 'pancake problem'. Our work was done in collaboration with the Missouri Western iGEM Team and an undergraduate research fellow from Hampton University.

Approach

Logo

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


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.

TEAM MEMBERS

Students

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

Faculty

  • A. Malcolm Campbell [http://www.bio.davidson.edu/campbell Department of Biology]
  • 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]

TEAM RESOURCES

iGEM 2006 Jamboree

White Board

Biology Tools (Wet Bench)

Math Tools

  • Pancake Simulators, aka The Lancelator (MATLAB Code)
  • Other 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]

Bio-Math Tools

  • [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]

Assembly Plans

Progress

Retrieved from "http://2006.igem.org/wiki/index.php/Davidson_2006"
Personal tools
Past/present/future years