View source for Missouri Western/Davidson iGEM2009

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

[http://gcat.davidson.edu/GcatWiki/index.php/Davidson_Missouri_W/Davidson_Protocols Davidson Lab Protocols] <br>
[http://gcat.davidson.edu/GcatWiki/index.php/Davidson_Missouri_W/MWSU_protocols MWSU Lab Protocols] <br>
[http://gcat.davidson.edu/sybr-u/bmc.html BioMath Connections Page] <br>
[http://gcat.davidson.edu/GCATalog-r2.1/GCATalog.htm GCAT-along Freezer Stocks]<br>


We need to learn more about these topics:
<center>'''Biology-based'''</center>
#[[What is msDNA?]]
#[[How is msDNA normally produced?]]
#[[How is msDNA stored in E. coli?]] 
#[[How many copies are carried per cell?]] 
#[[What is the sequence of bacterial reverse transcriptase and can we clone that gene?]]
#[[Can we redesign the normal msDNA pathway to produce new segments of DNA of our choosing?]]
#[[Can we use suppressor tRNAs to encode logical operators (suppressor suppressor logic, SSL)?]]
#[[Can we solve a 3-SAT problem with supressor logic?]]
#[[What role can physical modeling of protein structure play in our project?]]



<center>'''Math-based'''</center>
#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 person?]]
#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?
#How can we use origami to solve 3-SAT problems?

<center>'''Behavior-based'''</center>
#[[What constructs are we testing?]]
#[[What school districts do we have access to?]]
#[[Where is the Synthetic Biology page we want high school teachers to use after the survey?]]
#[[Do you need any more input from the veterans before the survey is ready?]]


<center>'''Questions from Missouri Western BMC  4/17/09'''</center>

(In no particular order)

Could we have/use multiple synthetic organelles in a cell?
What ideas from previous iGEM teams are useful to us?
What other math problems (e.g. NP- complete) are accessible to us?  Siya Sun
What is the relationship between 3-SAT and map coloring?  Ashley Schnoor
Could we do something with clocks/counting?
What role can physical modeling of proteins play in our project?  Eric Sawyer
What activators are there that turn on a promoter without any help?
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 protein interactions to compute?  (Post-translation, proteases, quaternary structure)  Will Vernon