ETH Zurich 2006

From 2006.igem.org

Revision as of 09:24, 12 August 2005 (view source) Dominic (Talk | contribs) m (→Ballot) ← Older edit		Revision as of 09:32, 12 August 2005 (view source) RealUACM (Talk | contribs) (→Ballot) Newer edit →
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		+	====Additional Comments:====
		+	'''Urs:'''
		+	I think if the whole thing works this project is astonishing. But I'm in doubt about it. The fact
		+	that you could model each step seperatly is of course a big advantage of this project. The
		+	probability that at least a few of the steps work is quite high and so you will see some results at
		+	the end. I'm not so sure about the usefulness. To encapsulate some bacterias which produce a certein
		+	substance could be usefull but I'm not an expert in this stuff.
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		+
		+	====Additional Comments:====
		+	'''Urs:'''
		+	From the engineer's point of few a counter like this is of course a crucial brick. As you can take
		+	the concentration of any substance you like (by transforming it to our input S) and also add for
		+	every single counter step a specific gene needed for an application this counter can be used
		+	whereever you want. The big disadvantage is of course that if the counter doesn't work there will be
		+	no result you can see.
	== External Information ==		== External Information ==

---

Revision as of 09:32, 12 August 2005

Contents 1 Introduction 2 People 2.1 Students 2.2 Supervisors 2.3 Advisors 3 Events & Timeline 4 Project Ideas 4.1 Individual Phenomena 4.2 Oscillator-based Phenomena 4.3 Collaborative Phenomena 5 Development Groups 5.1 Quorum Sensing based (Dominic, Giorgia, Herve) 5.2 Oscillator based (Urs, Christophe, Jonas) 5.3 Generation based (-) 5.4 Other projects (Jonas, Simon, Dominic) 6 Merged Projects 6.1 Ballot 6.1.1 Additional Comments: 6.1.2 Additional Comments: 7 External Information 7.1 Links 7.2 Papers

Introduction

• About us

People

Students

Simon Barkow	Christophe Dessimoz	Zlatko Franjcic
Dominic Frutiger	Robin Künzler	Urs A. Müller
Jonas Nart	Kristian Nolde	Alexander Roth
Tamara Ulrich	Giorgia Valsesia	Herve Vanderschuren

Supervisors

Jörg Stelling

Sven Panke

Eckart Zitzler

Advisors

Uwe Sauer	Martin Fussenegger	Andreas Hierlemann
Kay-Uwe Kirstein	Ruedi Aebersold

Events & Timeline

• Upcoming Talks

• Meetings

• Timeline

Project Ideas

This is the brainstorming section. In this section you will find random ideas and comments without too much consideration of feasability etc. Crazy ideas and wild dreams are welcome!

Individual Phenomena

Designing and tweaking so that the individual behaves in a desired way.

• Buffer Bacteria
• Random Number Generator
• Linear Amplifier

Oscillator-based Phenomena

Some clocking behaviors, such as counters and integrators etc.

• Generation Counter
• Oscillation Counter
• Swiss Watch

Collaborative Phenomena

Some of us have a great interest in some form of emergent phenomena and group dynamics based on simple local rules and external stimulae. Examples would be behaviors like sorting, pattern detections, flocking etc.

• Edge Detection
• Constructor Bacteria
• Sorting Bacteria
• Predator-Prey Behavior
• Pulser

Development Groups

We decided to cluster related projects and to form groups which will dedicate their time to this cluster. The goal is to converge to some single preferred solution based on these project ideas while keeping an eye on feasability, coolness, usefulness, and modular architecture on the way.

If you are in no group yet, please choose one.

Quorum Sensing based (Dominic, Giorgia, Herve)

• Sorting Bacteria
• Pulser
• Constructor Bacteria
• Controlled Cell Division
• Predator-Prey Behavior

Oscillator based (Urs, Christophe, Jonas)

• Generation Counter
• Oscillation Counter
• Swiss Watch

Generation based (-)

• Generation Counter
• Changing Generation Colors

Other projects (Jonas, Simon, Dominic)

• Edge Detection
• Buffer Bacteria

Merged Projects

The two projects below are the outcome of the work of our two remaining development groups. They both have their pros and cons and the discussion continues until at least Monday evening.

• Project X aka "SO-Constructor" by the development group for the Quorum_Sensing_based projects.
• Counter aka "The Thing" by the corresponding development group for Oscillator_based projects.

Ballot

Please everybody make your vote (1 means "forget it" and 10 means "definitely a Nature paper") on the four criteria.

CONSTRUCTOR	Urs	Tamara	Jonas	Zlatko	Giorgia	Simon	Kristian	Herve	Dominic	Alexander	Christophe	Robin
Usefulness	6	-	-	-	-	6	-	-	-	-	-	-
Feasability	4	-	-	-	-	5	-	-	-	-	-	-
Modularity	10	-	-	-	-	9	-	-	-	-	-	-
Coolness	9	-	-	-	-	9	-	-	-	-	-	-

Additional Comments:

Urs:
I think if the whole thing works this project is astonishing. But I'm in doubt about it. The fact
that you could model each step seperatly is of course a big advantage of this project. The 
probability that at least a few of the steps work is quite high and so you will see some results at 
the end. I'm not so sure about the usefulness. To encapsulate some bacterias which produce a certein
substance could be usefull but I'm not an expert in this stuff.

COUNTER	Urs	Tamara	Jonas	Zlatko	Giorgia	Simon	Kristian	Herve	Dominic	Alexander	Christophe	Robin
Usefulness	10	-	-	-	-	8	-	-	-	-	-	-
Feasability	6	-	-	-	-	7	-	-	-	-	-	-
Modularity	7	-	-	-	-	8	-	-	-	-	-	-
Coolness	8	-	-	-	-	9	-	-	-	-	-	-

Additional Comments:

Urs:
From the engineer's point of few a counter like this is of course a crucial brick. As you can take 
the concentration of any substance you like (by transforming it to our input S) and also add for 
every single counter step a specific gene needed for an application this counter can be used 
whereever you want. The big disadvantage is of course that if the counter doesn't work there will be
no result you can see.

External Information

Links

• Modeling and illustration tools

Papers

bulter04, atkinson03, bates05, keiler01, suetsugu03, sudesh00, römling02, ross91, sutherland01, Lai04, zogaj01, miller01, basu05,

goryachev05