University of Michigan 2006

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= News =
= News =
* '''2006.03.15''' We opened our wiki page!
* '''2006.03.15''' We opened our wiki page!
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= Organisation =
+
= Organization =
== Mailing Address ==
== Mailing Address ==
Peter Woolf <br>
Peter Woolf <br>
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Image:Abhik.Shah.jpg|[[abhik|Abhik Shah]]
Image:Abhik.Shah.jpg|[[abhik|Abhik Shah]]
Image:Patrick.Harrington.jpg|[[plhjr|Patrick Harrington]]
Image:Patrick.Harrington.jpg|[[plhjr|Patrick Harrington]]
 +
Image:Alyssa.Delke.jpeg|[[alyssade|Alyssa Delke]]
 +
Image:Hat.jpg|[http://www-personal.umich.edu/~asharad/first.html Asha Radhamohan]
 +
Image:Facebook.jpg|[[sheleung|Shelly Leung]]
</gallery>
</gallery>
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* [[yuanma|Yuan Ma]]
* [[yuanma|Yuan Ma]]
* [[http://www-personal.umich.edu/~engel/arvind.htm Arvind Rao]]
* [[http://www-personal.umich.edu/~engel/arvind.htm Arvind Rao]]
 +
* [[Winardi Kusumaatmaja]]
=== Advisors ===
=== Advisors ===
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Image:Danny.Forger.jpg|[[http://www.math.lsa.umich.edu/people/facultyDetail.php?id=458 Daniel Forger]]
Image:Danny.Forger.jpg|[[http://www.math.lsa.umich.edu/people/facultyDetail.php?id=458 Daniel Forger]]
Image:RichPell.jpg|[[http://www.contrib.andrew.cmu.edu/~rp3h Richard Pell]]
Image:RichPell.jpg|[[http://www.contrib.andrew.cmu.edu/~rp3h Richard Pell]]
 +
Image:EmeryConrad.jpg|[[http://www-personal.umich.edu/~emeryc Emery Conrad]]
</gallery>
</gallery>
-
 
-
==timeline==
 
-
 
-
==tasks==
 
-
* Update Wiki
 
-
 
=Our Project=
=Our Project=
==From Design to Manufacturing==
==From Design to Manufacturing==
-
  '''1. Paul-Tron 2k '''<br>
+
  '''1. Plasmene '''<br>
-
     An integrative prgramming environment for designing and testing genetic systems.
+
     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''' <br>
  '''2. Recursive Landing Pads''' <br>
-
     An innovative method for inserting genes and DNA sequences onto E. coli's chromosome.
+
     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 '''<br>
  '''3. Modeling Oscillatory Behavior of Clocks '''<br>
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     primarily examining the ideal conditions for generating oscillations.
     primarily examining the ideal conditions for generating oscillations.
-
  '''4. Increasing Kinetic Order Through the Use of Sinks '''<br>
+
  '''4. Experimental Manipulation of Lac Operon Kinetic Order '''<br>
-
     A promising method for raising kinetic order in genetic systems to increase chances for oscillations.
+
     [[Image:XsomesOp.gif]]
 +
    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=
=Links=
-
[http://synthbio.engin.umich.edu/wiki/ University of Michigan Team Wiki]
+
*[http://synthbio.engin.umich.edu/wiki/ University of Michigan Team Wiki]
 +
*[http://synthbio.engin.umich.edu/wiki/index.php/Algal_Bloom Algal Bloom Project]
=Miscellani=
=Miscellani=
<center>[[Image:UMlogo.gif]]</center>
<center>[[Image:UMlogo.gif]]</center>

Latest revision as of 00:04, 22 March 2007

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

Contents

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

Alyssa Delke

[http://www-personal.umich.edu/~asharad/first.html Asha Radhamohan]

Shelly Leung

Not pictured here:

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 

    XsomesOp.gif
    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]
  • [http://synthbio.engin.umich.edu/wiki/index.php/Algal_Bloom Algal Bloom Project]

Miscellani

UMlogo.gif
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