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. | ||
| - | <center>[[Image: | + | <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. | ||
| - | |||
== The Team == | == The Team == | ||
| - | ====Students==== | + | ==== Students ==== |
*[[User:Daniel_Hautzinger|Daniel Hautzinger]] | *[[User:Daniel_Hautzinger|Daniel Hautzinger]] | ||
| - | |||
*[[User:Olga_Soboleva|Olga Soboleva]] | *[[User:Olga_Soboleva|Olga Soboleva]] | ||
*[[User:Irina_Petrova|Irina Petrova]] | *[[User:Irina_Petrova|Irina Petrova]] | ||
| Line 21: | Line 19: | ||
*[[User:Mona_Klein|Mona Klein]] | *[[User:Mona_Klein|Mona Klein]] | ||
| - | ====iGEM instructor==== | + | ==== iGEM instructor ==== |
*[[User:Andrei_Kouznetsov|Andrei Kouznetsov]] | *[[User:Andrei_Kouznetsov|Andrei Kouznetsov]] | ||
| - | ====Faculty/staff==== | + | ==== Faculty/staff ==== |
*[[User:Svetlana_Santer|Svetlana Santer]] | *[[User:Svetlana_Santer|Svetlana Santer]] | ||
| - | == The project: DNA Folding== | + | == The project: DNA Folding == |
| - | ===Basic Idea=== | + | === Basic Idea === |
| - | ====Abstract==== | + | ==== 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. | ||
| - | ====Scetches - Pipes ==== | + | ==== Scetches - Pipes ==== |
| - | [[image:Pipes1.jpg|left|thumb|200px|Pipes - | + | [[image:Pipes1.jpg|left|thumb|200px|Pipes - Step 1]] |
| - | [[image:Pipes2.jpg|left|thumb|150px|Pipes - | + | [[image:Pipes2.jpg|left|thumb|150px|Pipes - Step 2]] |
| - | [[image:Pipes3.jpg|left|thumb|150px|Pipes - | + | [[image:Pipes3.jpg|left|thumb|150px|Pipes - Step 3]] |
<br style="clear:both;"/> | <br style="clear:both;"/> | ||
| - | The DNA sequence for the Pipes design can be found [http://omnibus.uni-freiburg.de/~kouznet/Tube-M13mp18-NEB-d.txt here]. | + | 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=== | ||
| Line 50: | Line 48: | ||
====Scetches - TShirt ==== | ====Scetches - TShirt ==== | ||
| - | [[image:TShirt1.jpg|left|thumb|150px|TShirt - | + | [[image:TShirt1.jpg|left|thumb|150px|TShirt - Step 1]] |
| - | [[image:TShirt2.jpg|left|thumb|150px|TShirt - | + | [[image:TShirt2.jpg|left|thumb|150px|TShirt - Step 2]] |
| - | [[image:TShirt3.JPG|left|thumb|150px|TShirt - | + | [[image:TShirt3.JPG|left|thumb|150px|TShirt - Step 3]] |
| - | [[image:TShirt4.JPG|left|thumb|150px|TShirt - | + | [[image:TShirt4.JPG|left|thumb|150px|TShirt - Step 4]] |
<br style="clear:both;"/> | <br style="clear:both;"/> | ||
| - | ====Scetches - Bluse ==== | + | ==== Scetches - Bluse ==== |
| - | [[image:Bluse1.jpg|left|thumb|150px|Bluse - | + | [[image:Bluse1.jpg|left|thumb|150px|Bluse - Step 1]] |
| - | [[image:Bluse2.jpg|left|thumb|150px|Bluse - | + | [[image:Bluse2.jpg|left|thumb|150px|Bluse - Step 2]] |
<br style="clear:both;"/> | <br style="clear:both;"/> | ||
| - | The DNA sequence for the Bluse design can be found [http://omnibus.uni-freiburg.de/~kouznet/nike-oligos.txt here]. | + | 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/] | ||
| - | |||
Revision as of 17:05, 7 September 2006
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.
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
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
Scetches - Bluse
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/]