ETH Zurich 2006

From 2006.igem.org

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 7 Selected Project 7.1 Input-module 7.2 NOR-module 7.3 Modeling and overall design 7.4 Output Extension 8 External Information 8.1 Links 8.2 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.

We had a couple of discussions about which project we should choose and even a ballot. Some of the overall comments have been written down.

Selected Project

Both projects were found interesting and people would have been willing to contribute to both. However, we voted that the Counter-approach would be the more suitable in the context of iGEM. Thus we will further develop the Counter-project and possibly merge it with one or two modules from the SO-Constructor as output modules.

The project has been split in submodules and corresponding groups:

Input-module

Module description: in a nutshell, this module has 2 system boundaries, both of which are characterized by PoPS. Its purpose is to take a single input PoPS and output 2 different PoPS. One of the outputs should be high and the other low when S is high and vice versa when S is low. Check here for more details.

• Group Members: Christophe, Dominic (coordinator), Giorgia, Herve, Kristian, Zlatko

Next Input-group Session:
2005-08-23: Tuesday, 08:30 (fixed) @ cafeteria polyterrasse. Biological implementation/modeling.

NOR-module

A NOR-module works as follows: There are two inputs and one output. The output is high if and only if the two inputs are low. In other words: The output is low whenever either one (or both) of the inputs are high.

• Group Members: Alex (coordinator), Jonas, Robin, Simon, Tamara, Urs

Next Group Session:
2005.08.25, Thursday 15:00 @ CAB F62

Modeling and overall design

This group is focused on mathematical modeling, illustration, simulations and overall design. There are no permanent members for this group. Anyone can join and leave the group anytime he/she wants. A group coordinator will be assigned at the first meeting.

Next Meeting(Modeling, draw and explain our concept in a pretty layout)
2005-08-17, Wednesday: 09.45 somewhere around Dominic's Office (CLA H 14.1/2)

Output Extension

External Information

Links

• Modeling and illustration tools

Papers

bulter04, atkinson03, bates05, keiler01, suetsugu03, sudesh00, römling02, ross91, sutherland01, Lai04, zogaj01, miller01, basu05, goryachev05, you04, Isalan01, Beerli02, Mani05, Beerli00, Beerli98, Dreier01, Dreier05, Klug05, Yang95, Segal99, Segal03,