University of Michigan 2006

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We're the iGEM team from the [http://www.umich.edu/ University of Michigan].
We're the iGEM team from the [http://www.umich.edu/ University of Michigan].
-
We haven't yet started using the wiki, so for right now, have a look at our [http://synthbio.engin.umich.edu/ homepage].
 
----
----
= News =
= News =
* '''2006.03.15''' We opened our wiki page!
* '''2006.03.15''' We opened our wiki page!
-
= Organisation =
+
= Organization =
== Mailing Address ==
== Mailing Address ==
Peter Woolf <br>
Peter Woolf <br>
Line 16: Line 15:
=== Students ===
=== Students ===
<gallery>
<gallery>
-
Image:Aaron.Williams.jpg|alwill|Aaron Williams
+
Image:Aaron.Williams.jpg|[[alwill|Aaron Williams]]
-
Image:Aaron.Williams.jpg|Aaron Williams
+
Image:Chris.Bauman.jpg|[[cebauman|Chris Bauman]]
-
 
+
Image:mikeLi.jpg|[[mikesongli|Huan (Mike) Li]]
 +
Image:Sandy.Yu.jpg|[[sandyyu|Sandy Yu]]
 +
Image:Greg.Boggyjpg.jpg|[[gboggy|Greg Boggy]]
 +
Image:GraceSong.jpg|[[gracesong|Grace Song]]
 +
Image:Steve.Selinsky.jpg|[[slink|Steve Selinsky]]
 +
Image:AaronReifler.jpg|[[reiflera|Aaron Reifler]]
 +
Image:Paul.Rogerojpg.jpg|[[rogero|Paul Rogero]]
 +
Image:Brian.Harber.jpg|[[bharber|Brian Harber]]
 +
Image:AndrewHodges.jpg|[[aphodges|Andrew Hodges]]
 +
Image:NicolasPerry.jpg|[[nperry|Nicolas Perry]]
 +
Image:Abhik.Shah.jpg|[[abhik|Abhik Shah]]
 +
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>
-
* [[alwill|Aaron Williams]]
+
 
-
* [[cebauman|Chris Bauman]]
+
Not pictured here:
-
* [[mikesongli|Huan Li]]
+
-
* [[sandyyu|Sandy Yu]]
+
* [[yuanma|Yuan Ma]]
* [[yuanma|Yuan Ma]]
-
 
+
* [[http://www-personal.umich.edu/~engel/arvind.htm Arvind Rao]]
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* [[gboggy|Greg Boggy]]
+
* [[Winardi Kusumaatmaja]]
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* [[ukarvind|Arvind Rao]]
+
=== Advisors ===
=== Advisors ===
-
* [[pwoolf|Peter Woolf]]
+
<gallery>
-
* [[avimayo|Avi Mayo]]
+
Image:Peter.Woolf.jpg|[[http://www.engin.umich.edu/dept/cheme/people/woolf.html Peter Woolf]]
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* [[aninfa|Alex Ninfa]]
+
Image:Alex.Ninfa.jpg|[[http://www.biochem.med.umich.edu/biochem/research/profiles/ninfa.html Alex Ninfa]]
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* [[ddv|Domitilla del Veccio]]
+
Image:Avi.Mayo.jpg|[[avimayo|Avi Mayo]]
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* [[forger|Danny Forger]]
+
Image:Stephan.jpg|[[stephen|Stephen Atkins]]
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* [[pell|Richard Pell]]
+
Image:Domitilla.del.jpg|[[http://www.eecs.umich.edu/eecs/etc/fac/facsearchform.cgi?ddv+ Domitilla del Vecchio]]
 +
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:EmeryConrad.jpg|[[http://www-personal.umich.edu/~emeryc Emery Conrad]]
 +
</gallery>
 +
=Our Project=
 +
==From Design to Manufacturing==
 +
'''1. Plasmene '''<br>
 +
    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]
-
==timeline==
+
'''2. Recursive Landing Pads''' <br>
 +
    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).
-
==tasks==
+
'''3. Modeling Oscillatory Behavior of Clocks '''<br>
-
* Edit the wiki!
+
    A look at the parameter space of clocks and genetic oscillating devices,
 +
    primarily examining the ideal conditions for generating oscillations.
-
=Our Project=
+
'''4. Experimental Manipulation of Lac Operon Kinetic Order '''<br>
-
==Ideas==
+
    [[Image:XsomesOp.gif]]
-
1. <br>
+
    Experimental assays of strains and plasmids with Op sinks were performed.
-
2. Holy War <br>
+
    Strains were created by inserting sinks on chromosome.
-
3. Landing Pad <br>
+
    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]
-
=Misc=
+
=Miscellani=
-
Go Blue!
+
<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

Not pictured here:

Advisors

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
Personal tools
Past/present/future years