Freiburg University 2006

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This term was invented by Martin Schneider on the Rule 110 Winter Workshop in 2004 [http://www.rule110.org/amhso/index.html]. We play without rules. We discover the rules that govern life, the universe and everything to exploit these rules and to create Artificial Life. Our short-time aim is the trip to Boston in November 2006 to take a prize in the iGEM.
This term was invented by Martin Schneider on the Rule 110 Winter Workshop in 2004 [http://www.rule110.org/amhso/index.html]. We play without rules. We discover the rules that govern life, the universe and everything to exploit these rules and to create Artificial Life. Our short-time aim is the trip to Boston in November 2006 to take a prize in the iGEM.
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<center>[[Image:Freiburg_Team_06.JPG]]</center>
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<center>[[Image:Freiburg Team 06.jpg]]</center>
The Freiburg Team (well, at least half of it...) from left to right: Irina Petrova, Andrei Kouznetsov, Daniel Hautzinger.
The Freiburg Team (well, at least half of it...) from left to right: Irina Petrova, Andrei Kouznetsov, Daniel Hautzinger.
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== The Team ==
== The Team ==
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====Students====
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==== Students ====
*[[User:Daniel_Hautzinger|Daniel Hautzinger]]
*[[User:Daniel_Hautzinger|Daniel Hautzinger]]
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*[[User:Marc_Wilnauer|Marc Wilnauer]]
 
*[[User:Olga_Soboleva|Olga Soboleva]]
*[[User:Olga_Soboleva|Olga Soboleva]]
*[[User:Irina_Petrova|Irina Petrova]]
*[[User:Irina_Petrova|Irina Petrova]]
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*[[User:Mona_Klein|Mona Klein]]
*[[User:Mona_Klein|Mona Klein]]
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====iGEM instructor====
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==== iGEM instructor ====
*[[User:Andrei_Kouznetsov|Andrei Kouznetsov]]
*[[User:Andrei_Kouznetsov|Andrei Kouznetsov]]
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====Faculty/staff====
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==== Faculty/staff ====
*[[User:Svetlana_Santer|Svetlana Santer]]
*[[User:Svetlana_Santer|Svetlana Santer]]
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== The project: DNA Folding==
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== The project: DNA Folding ==
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===Basic Idea===
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=== Basic Idea ===
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====Abstract====
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==== Abstract ====
The idea is to design a strand of DNA such that it wraps into some meaningful shape. There are three different stages for this project: First, the DNA should fold into a two-dimensional rectangular sheet. Secondly, this sheet should wrap itself up into the shape of a short pipe. And last, these little pipes should hook themselves up to each other such that they form one single long pipe.
The idea is to design a strand of DNA such that it wraps into some meaningful shape. There are three different stages for this project: First, the DNA should fold into a two-dimensional rectangular sheet. Secondly, this sheet should wrap itself up into the shape of a short pipe. And last, these little pipes should hook themselves up to each other such that they form one single long pipe.
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====Scetches - Pipes ====
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==== Scetches - Pipes ====
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[[image:Pipes1.jpg|left|thumb|200px|Pipes - Stage 1]]
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[[image:Pipes1.jpg|left|thumb|200px|Pipes - Step 1]]
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[[image:Pipes2.jpg|left|thumb|150px|Pipes - Stage 2]]  
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[[image:Pipes2.jpg|left|thumb|150px|Pipes - Step 2]]  
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[[image:Pipes3.jpg|left|thumb|150px|Pipes - Stage 3]]  
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[[image:Pipes3.jpg|left|thumb|150px|Pipes - Step 3]]  
<br style="clear:both;"/>
<br style="clear:both;"/>
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The DNA sequence for the Pipes design can be found [http://omnibus.uni-freiburg.de/~kouznet/Tube-M13mp18-NEB-d.txt here].
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The DNA sequence for the Pipes design can be found [http://omnibus.uni-freiburg.de/~kouznet/pipe/Tube-M13mp18-NEB-d.txt here].
===Application: Barbie Nanoatelier===
===Application: Barbie Nanoatelier===
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====Scetches - TShirt ====
====Scetches - TShirt ====
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[[image:TShirt1.jpg|left|thumb|150px|TShirt - Stage 1]]  
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[[image:TShirt1.jpg|left|thumb|150px|TShirt - Step 1]]  
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[[image:TShirt2.jpg|left|thumb|150px|TShirt - Stage 2]]  
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[[image:TShirt2.jpg|left|thumb|150px|TShirt - Step 2]]  
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[[image:TShirt3.JPG|left|thumb|150px|TShirt - Stage 3]]  
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[[image:TShirt3.JPG|left|thumb|150px|TShirt - Step 3]]  
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[[image:TShirt4.JPG|left|thumb|150px|TShirt - Stage 4]]  
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[[image:TShirt4.JPG|left|thumb|150px|TShirt - Step 4]]  
<br style="clear:both;"/>
<br style="clear:both;"/>
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====Scetches - Bluse ====
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==== Scetches - Bluse ====
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[[image:Bluse1.jpg|left|thumb|150px|Bluse - Stage 1]]  
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[[image:Bluse1.jpg|left|thumb|150px|Bluse - Step 1]]  
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[[image:Bluse2.jpg|left|thumb|150px|Bluse - Stage 2]]  
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[[image:Bluse2.jpg|left|thumb|150px|Bluse - Step 2]]  
<br style="clear:both;"/>
<br style="clear:both;"/>
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The DNA sequence for the Bluse design can be found [http://omnibus.uni-freiburg.de/~kouznet/nike-oligos.txt here].
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The DNA sequence for the Bluse design can be found [http://omnibus.uni-freiburg.de/~kouznet/bluse/nike-oligos.txt here].
== GEM Freiburg ==
== GEM Freiburg ==
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An Analysis of Synthetic Biology Research in Europe and North America [http://www2.spi.pt/synbiology/]
An Analysis of Synthetic Biology Research in Europe and North America [http://www2.spi.pt/synbiology/]
DNA synthesis: ATG-Biosynthetics [http://www.atg-biosynthetics.com/]
DNA synthesis: ATG-Biosynthetics [http://www.atg-biosynthetics.com/]
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'''Bold text'''
 

Revision as of 17:05, 7 September 2006

Welcome! We are Alife Mutants.

Uf101.jpg

This term was invented by Martin Schneider on the Rule 110 Winter Workshop in 2004 [http://www.rule110.org/amhso/index.html]. We play without rules. We discover the rules that govern life, the universe and everything to exploit these rules and to create Artificial Life. Our short-time aim is the trip to Boston in November 2006 to take a prize in the iGEM.

Freiburg Team 06.jpg

The Freiburg Team (well, at least half of it...) from left to right: Irina Petrova, Andrei Kouznetsov, Daniel Hautzinger.

Contents

The Team

Students

iGEM instructor

Faculty/staff

The project: DNA Folding

Basic Idea

Abstract

The idea is to design a strand of DNA such that it wraps into some meaningful shape. There are three different stages for this project: First, the DNA should fold into a two-dimensional rectangular sheet. Secondly, this sheet should wrap itself up into the shape of a short pipe. And last, these little pipes should hook themselves up to each other such that they form one single long pipe.

Scetches - Pipes

Pipes - Step 1
Pipes - Step 2
Pipes - Step 3


The DNA sequence for the Pipes design can be found [http://omnibus.uni-freiburg.de/~kouznet/pipe/Tube-M13mp18-NEB-d.txt here].

Application: Barbie Nanoatelier

Once the process of DNA folding into 3D-structures is understood, shapes can be chosen arbitrarily. The idea of the Barbie Nanoatelier is that the DNA should wrap into a 3D-TShirt, 3D-Pants, etc.

Scetches - TShirt

TShirt - Step 1
TShirt - Step 2
TShirt - Step 3
TShirt - Step 4


Scetches - Bluse

Bluse - Step 1
Bluse - Step 2


The DNA sequence for the Bluse design can be found [http://omnibus.uni-freiburg.de/~kouznet/bluse/nike-oligos.txt here].

GEM Freiburg

Club

  • [http://omnibus.uni-freiburg.de/~kouznet/iGEM.htm Manifesto, Self-education program]
  • [http://omnibus.uni-freiburg.de/~kouznet/Fellow06.htm GEM Freiburg Fellow 2006]
  • [http://omnibus.uni-freiburg.de/~kouznet/GEMnews.htm News]

SB Preliminary

  • DNA plug-and-play platform [http://omnibus.uni-freiburg.de/~kouznet/DNAplatform6.pdf 24.05.06] [http://omnibus.uni-freiburg.de/~kouznet/DNAplatform6-1.pdf 27.06.06]
  • [http://omnibus.uni-freiburg.de/~kouznet/BioVLSI.pdf Very Large-Scale Integration design in Biology]
  • [http://omnibus.uni-freiburg.de/~kouznet/GS-design.pdf Genetic systems design from the DNA modules]

Old project ideas

Hey Mutant, have a look!

The easy and serious way

  • [http://www.edge.org/documents/archive/edge187.html#church George Church CONSTRUCTIVE BIOLOGY] - a nice paper about the challenges of modern biology
  • [http://webcast.berkeley.edu/events/details.php?webcastid=15766 The webcast from SB2.0]

These people do great things

Albert Libchaber [http://www.rockefeller.edu/research/abstract.php?id=93] Carlos Bustamante's lab [http://alice.berkeley.edu/] David Deamer [http://www.chemistry.ucsc.edu/deamer_d.html] Eric Kool’s group [http://www.stanford.edu/group/kool/] Erik Winfree [http://www.dna.caltech.edu/~winfree/] Fred Menger’s group [http://www.chemistry.emory.edu/faculty/menger/index.html] Jack Szostak’s lab [http://genetics.mgh.harvard.edu/szostakweb/] Norman Packard’s Protolife [http://www.protolife.net/] Pier Luigi Luisi’s group [http://www.plluisi.org/index.html] Radhika Nagpal [http://www.eecs.harvard.edu/~rad/] Steven Benner’s group [http://www.chem.ufl.edu/groups/benner/]

Local

An Analysis of Synthetic Biology Research in Europe and North America [http://www2.spi.pt/synbiology/]

DNA synthesis: ATG-Biosynthetics [http://www.atg-biosynthetics.com/]

Personal tools
Past/present/future years