From 2006.igem.org

We're the iGEM team from the [http://www.umich.edu/ University of Michigan].

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Contents 1 News 2 Organization 2.1 Mailing Address 2.2 People 2.2.1 Students 2.2.2 Advisors 3 Our Project 3.1 From Design to Manufacturing 4 Links 5 Miscellani

News

• 2006.03.15 We opened our wiki page!

Organization

Mailing Address

Peter Woolf
Department of Chemical Engineering
2300 Hayward St.
3074 H.H. Dow Building
Ann Arbor, MI 48109-2136

People

Students

Aaron Williams	Chris Bauman	Huan (Mike) Li	Sandy Yu
Greg Boggy	Grace Song	Steve Selinsky	Aaron Reifler
Paul Rogero	Brian Harber	Andrew Hodges	Nicolas Perry
Abhik Shah	Patrick Harrington

Not pictured here:

• Yuan Ma
• http://www-personal.umich.edu/~engel/arvind.htm Arvind Rao
• Alyssa Delke

Advisors

http://www.engin.umich.edu/dept/cheme/people/woolf.html Peter Woolf	http://www.biochem.med.umich.edu/biochem/research/profiles/ninfa.html Alex Ninfa	Avi Mayo	Stephen Atkins
http://www.eecs.umich.edu/eecs/etc/fac/facsearchform.cgi?ddv+ Domitilla del Vecchio	http://www.math.lsa.umich.edu/people/facultyDetail.php?id=458 Daniel Forger	http://www.contrib.andrew.cmu.edu/~rp3h Richard Pell	http://www-personal.umich.edu/~emeryc Emery Conrad

Our Project

From Design to Manufacturing

1. Plasmene 

    Plasmene is the first integrated development environment designed specifically for synthetic
    biology.  Plasmene is designed to be a central component in the development process of synthetic
    genetic networks.  Plasmene hopes to integrate the three major components of synthetic genetic
    network development, typology design, modeling results, and fabrication information, into a 
    common environment.  Plasmene will also provide connections to major databases in order to make 
    it easier for users to pull information from the Internet into their projects. The Plasmene 
    project's goal is to increase the productivity of synthetic biologists by freeing the user from 
    the hassle of simple, time-consuming tasks and allowing the researcher to spend more time 
    performing useful research.

Download Proof of Principle Prototype: [http://synthbio.engin.umich.edu/wiki/InformaticsNotes?action=AttachFile&do=get&target=Plasmine0.1.zip Plasmine]

2. Recursive Landing Pads 

    A super-duper-awesomely innovative method for inserting genes and DNA sequences onto E. coli's chromosome 
     (that Steve can explain much better than I can, and hopefully he will as soon as he gets back from class).

3. Modeling Oscillatory Behavior of Clocks 

    A look at the parameter space of clocks and genetic oscillating devices, 
    primarily examining the ideal conditions for generating oscillations.

4. Experimental Manipulation of Lac Operon Kinetic Order 

    
    Experimental assays of strains and plasmids with Op sinks were performed.
    Strains were created by inserting sinks on chromosome. 
    Landing pads included rbs, glnK and trp regions.
    Results showed the following:
     - Sinks on plasmid raise basal level of lacZ expression;
     - Sinks on chromosome raise kinetic order;
     - One strain in particular was of significant interest.
    Findings can be used for "tuning" genetic systems (clocks, oscillators, etc).

Links

[http://synthbio.engin.umich.edu/wiki/ University of Michigan Team Wiki]

Miscellani