Difference between revisions of "Missouri Western/Davidson iGEM2009"

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This space will be used starting April, 2009 for brainstorming and a shared whiteboard space.
 
This space will be used starting April, 2009 for brainstorming and a shared whiteboard space.
  
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[http://gcat.davidson.edu/GcatWiki/index.php/Davidson_Missouri_W/Davidson_Protocols Davidson Lab Protocols] <br>
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[[Davidson Protocols]] <br>
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[http://gcat.davidson.edu/GcatWiki/index.php/Davidson_Missouri_W/MWSU_protocols MWSU Lab Protocols] <br>
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[[MWSU_protocols]] <br>
 
[http://gcat.davidson.edu/sybr-u/bmc.html BioMath Connections Page] <br>
 
[http://gcat.davidson.edu/sybr-u/bmc.html BioMath Connections Page] <br>
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[http://gcat.davidson.edu/GCATalog-r2.1/GCATalog.htm GCAT-alog Freezer Stocks]<br>
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[http://gcat.davidson.edu/GCATalog GCAT-alog Freezer Stocks]<br>
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[[Laboratory_Notebooks]]
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<center>
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== MWSU-Davidson 2009 iGEM team photo ==
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[[Image:iGEMTeam2009.png|250px|]]<br>
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== The Davidson College part of the 2009 iGEM Team ==
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[[Image:DavidsonTeam2009.png|429px|]]
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</center>
  
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= [[iGEM 2009 Project]] =
  
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[[Ladder problems]]<br>
 
We need to learn more about these topics:
 
We need to learn more about these topics:
 
<center>'''Biology-based'''</center>
 
<center>'''Biology-based'''</center>
  
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#[[How do signal sequences/peptides work in bacteria, and how can we use them?]]
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#[[Plasmid Creation]]
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#[[What is msDNA?]]
 
#[[How is msDNA normally produced?]] Olivia/Alyndria
 
#[[How is msDNA normally produced?]] Olivia/Alyndria
 
#[[How many copies are carried per cell?]] Alyndria
 
#[[How many copies are carried per cell?]] Alyndria
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#[[What role can physical modeling of protein structure play in our project?]] Romina
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#[[What would we need to do to turn this into a BioBrick device?]] Romina
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#[[ How could we swap out msDNA sequences?]] Shamita
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#[[What role can physical modeling of protein structure play in our project?]]
 
#[[What role can physical modeling of proteins play in our project?  Eric Sawyer]]
 
#[[What role can physical modeling of proteins play in our project?  Eric Sawyer]]
 
#[[What other cool reporters are there?  (Discrete On/Off or Continuous)  Bryce Szczepanik]]
 
#[[What other cool reporters are there?  (Discrete On/Off or Continuous)  Bryce Szczepanik]]
 
#[[Can we use promoter strength/opposite directions to subtract?  Clif Davis]]
 
#[[Can we use promoter strength/opposite directions to subtract?  Clif Davis]]
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#[[What is msDNA?]]
 
 
#[[Can we use suppressor tRNAs to encode logical operators (suppressor suppressor logic, SSL)?]]
 
#[[Can we use suppressor tRNAs to encode logical operators (suppressor suppressor logic, SSL)?]]
 
#[[How is msDNA stored in E. coli?]] Olivia
 
#[[How is msDNA stored in E. coli?]] Olivia
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#[[Can we redesign the normal msDNA pathway to produce new segments of DNA of our choosing?]] All
 
#[[Can we redesign the normal msDNA pathway to produce new segments of DNA of our choosing?]] All
 
#[[What are other available reverse transcriptases?]] Leland
 
#[[What are other available reverse transcriptases?]] Leland
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#[[What other math problems (e.g. NP- complete) are accessible to us?  Siya Sun]]
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#[[What other math problems (e.g. NP- complete) are accessible to us?  Annie Siya Sun]]
 
#[[What is the relationship between 3-SAT and map coloring?  Ashley Schnoor]]
 
#[[What is the relationship between 3-SAT and map coloring?  Ashley Schnoor]]
 
#[[What activators are there that turn on a promoter without any help?]]
 
#[[What activators are there that turn on a promoter without any help?]]
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#[[Could we have/use multiple synthetic organelles in a cell?]]
 
#[[Could we have/use multiple synthetic organelles in a cell?]]
 
#[[What ideas from previous iGEM teams are useful to us?]]
 
#[[What ideas from previous iGEM teams are useful to us?]]
 +
#[[Examples of Metabolic Pathways in E.coli]]
  
  
 
<center>'''Math-based'''</center>
 
<center>'''Math-based'''</center>
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#What interesting challenges or problems does origami offer?
 
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#Can we produce a series of increasingly difficult goals that might be possible to produce in the lab?
 
−
#What has been done before and how can we improve upon that?
 
−
#We can perform some pilot experiments using synthesized DNA and later switch to msDNA (maybe).
 
−
#Can we address the Boolean Satisfiability (SAT) problem with a bacterial computer?
 
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#How has 3SAT been addressed with a DNA computer? Can we use those methods?
 
 
#[[Can we get bacteria to solve a problem large enough to challenge a person?]]
 
#[[Can we get bacteria to solve a problem large enough to challenge a person?]]
 +
#[[What interesting challenges or problems does origami offer?]]
 +
#[[Can we produce a series of increasingly difficult goals that might be possible to produce in the lab?]]
 +
#[[What has been done before and how can we improve upon that?]]
 +
#[[We can perform some pilot experiments using synthesized DNA and later switch to msDNA (maybe).]]
 +
#[[Can we address the Boolean Satisfiability (SAT) problem with a bacterial computer?]]
 +
#[[How has 3SAT been addressed with a DNA computer? Can we use those methods?]]
 +
 
#Can we get bacteria to solve a problem large enough to challenge a computer (probably not, but it is fun to think about)?
 
#Can we get bacteria to solve a problem large enough to challenge a computer (probably not, but it is fun to think about)?
−
#What are some linear algebra applications for DNA origami?
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#[[What are some linear algebra applications for DNA origami?]]
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#How can we use origami to solve 3-SAT problems?
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#[[How can we use origami to solve 3-SAT problems?]]
  
 
<center>'''Behavior-based'''</center>
 
<center>'''Behavior-based'''</center>
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<center>'''Solving The 3SAT Problem Using Suppressor Logic'''</center>
 
<center>'''Solving The 3SAT Problem Using Suppressor Logic'''</center>
 
#[[Can we solve a 3-SAT problem with supressor logic?]]
 
#[[Can we solve a 3-SAT problem with supressor logic?]]
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 +
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<center>'''Hin/Hix System'''</center>
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Here is a link to the animation of the Hin/Hix system created by the "E. HOP living computer project folks.
 +
[http://www.bio.davidson.edu/people/kahaynes/FAMU_talk/Living_computer.swf Hin/Hix Animation] <br>

Latest revision as of 16:38, 30 March 2011

This space will be used starting April, 2009 for brainstorming and a shared whiteboard space.

Davidson Protocols
MWSU_protocols
BioMath Connections Page
GCAT-alog Freezer Stocks
Laboratory_Notebooks

MWSU-Davidson 2009 iGEM team photo

IGEMTeam2009.png

The Davidson College part of the 2009 iGEM Team

DavidsonTeam2009.png

iGEM 2009 Project

Ladder problems
We need to learn more about these topics:

Biology-based
  1. How do signal sequences/peptides work in bacteria, and how can we use them?
  2. Plasmid Creation
  3. What is msDNA?
  4. How is msDNA normally produced? Olivia/Alyndria
  5. How many copies are carried per cell? Alyndria
  6. What would we need to do to turn this into a BioBrick device? Romina
  7. How could we swap out msDNA sequences? Shamita
  8. What role can physical modeling of protein structure play in our project?
  9. What role can physical modeling of proteins play in our project? Eric Sawyer
  10. What other cool reporters are there? (Discrete On/Off or Continuous) Bryce Szczepanik
  11. Can we use promoter strength/opposite directions to subtract? Clif Davis
  12. Can we use suppressor tRNAs to encode logical operators (suppressor suppressor logic, SSL)?
  13. How is msDNA stored in E. coli? Olivia
  14. What is the sequence of bacterial reverse transcriptase and can we clone that gene? Shamita
  15. Can we redesign the normal msDNA pathway to produce new segments of DNA of our choosing? All
  16. What are other available reverse transcriptases? Leland
  17. What other math problems (e.g. NP- complete) are accessible to us? Annie Siya Sun
  18. What is the relationship between 3-SAT and map coloring? Ashley Schnoor
  19. What activators are there that turn on a promoter without any help?
  20. Can we use protein interactions to compute? (Post-translation, proteases, quaternary structure) Will Vernon
  21. Could we do something with clocks/counting?
  22. Could we have/use multiple synthetic organelles in a cell?
  23. What ideas from previous iGEM teams are useful to us?
  24. Examples of Metabolic Pathways in E.coli


Math-based
  1. Can we get bacteria to solve a problem large enough to challenge a person?
  2. What interesting challenges or problems does origami offer?
  3. Can we produce a series of increasingly difficult goals that might be possible to produce in the lab?
  4. What has been done before and how can we improve upon that?
  5. We can perform some pilot experiments using synthesized DNA and later switch to msDNA (maybe).
  6. Can we address the Boolean Satisfiability (SAT) problem with a bacterial computer?
  7. How has 3SAT been addressed with a DNA computer? Can we use those methods?
  1. Can we get bacteria to solve a problem large enough to challenge a computer (probably not, but it is fun to think about)?
  2. What are some linear algebra applications for DNA origami?
  3. How can we use origami to solve 3-SAT problems?
Behavior-based
  1. What constructs are we testing?
  2. What school districts do we have access to?
  3. Where is the Synthetic Biology page we want high school teachers to use after the survey?
  4. Do you need any more input from the veterans before the survey is ready?


Solving The 3SAT Problem Using Suppressor Logic
  1. Can we solve a 3-SAT problem with supressor logic?


Hin/Hix System

Here is a link to the animation of the Hin/Hix system created by the "E. HOP living computer project folks. Hin/Hix Animation

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