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 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	4	-	-	-	6	-	-	-	-	-	-
Feasability	4	8	-	-	-	5	-	-	-	-	-	-
Modularity	10	8	-	-	-	9	-	-	-	-	-	-
Coolness	9	7	-	-	-	9	-	-	-	-	-	-

Additional Comments:

Tamara:

As an engineer, I think the counter is completely useful and totally cool as well. I'm really excited at the prospect that it might actually work (which I frankly still doubt a little bit at the moment). The SO-Constructor definitely is cool as well, but I don't see it's usefulness yet, but as I'm no bilogist, it is not mine to judge.

Talking about modularity, I see that the SO-Constructor has a lot of modules, but they are not 'parallel' modules, but 'serial' modules, i.e. if one module fails, the overlaying modules won't work as well. They strongly depend on each other. I also see the problem of tunig, because there is a real lot of tuning to do and nearly everything needs to be tuned. For me, some questions arise like: Can you simply change the threshold for a certain protein in quorum sensing? Anyway, the probability that we have some results to present in the end is still relatively high.

I don't think the counter is really modular, altough it is a combination of one basic part (the 'thing'). The point is, if that basic part works, the whole counter probably works as well. If it doesn't, then we don't have anything at all. But shouldn't we just take the risk and try it? No risk, no fun :-)

Conclusion: The SO-Constructor is in my opinion the 'safer' option, meaning that we are much more probable to get something that actually works. Whereas the Counter is much more useful and revolutionary, at least when we get to work it somehow.

PS: Can please someone help me to put my text in the nasty little box?

Dominic:
As I already have said during the meeting, I am a little bit concerned about the effects of the 
different presentation styles and levels of detail: it is hard to judge the feasability of one or
the other, since for the SO-Constructor I can see a clear stepwise approach with controllable
biological units to implement, but I am doubtful about the tuning and proper interplay of all these
components - although I am confident that to some degree this can be achieved. 
As for the Counter I am also not sure about the basic biological assumptions, e.g. whether the
toggle switch units are available and will work as well as the symmetric repression/activation
that is necessary, although the modeling part suggests everything is straightforward - but this
might be deceiving.
It is hard for me to judge the biological unpredictabilites and risks, but from an engineering
point of view the Counter building block is of the more useful thing to do, since it has a broad 
application range thanks to the clear interfaces. 
Last but not least such a technical unit seems more suitable in the context of Synthetic Biology.

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 
certain 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	10	-	-	-	8	-	-	-	-	-	-
Feasability	6	7	-	-	-	7	-	-	-	-	-	-
Modularity	7	5	-	-	-	8	-	-	-	-	-	-
Coolness	8	10	-	-	-	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,

you04,