ETH Zurich 2006
From 2006.igem.org
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As I already have said during the meeting, I am a little bit concerned about the effects of the | 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 | 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 | + | 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 | 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. | components - although I am confident that to some degree this can be achieved. | ||
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that is necessary, although the modeling part suggests everything is straightforward - but this | that is necessary, although the modeling part suggests everything is straightforward - but this | ||
might be deceiving. | 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:''' | '''Urs:''' | ||
Revision as of 11:47, 12 August 2005
Contents |
Introduction
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
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.
Oscillator-based Phenomena
Some clocking behaviors, such as counters and integrators etc.
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.
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)
Oscillator based (Urs, Christophe, Jonas)
Generation based (-)
Other projects (Jonas, Simon, Dominic)
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:
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 | - | - | - | - | 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
Papers
bulter04, atkinson03, bates05, keiler01, suetsugu03, sudesh00, römling02, ross91, sutherland01, Lai04, zogaj01, miller01, basu05, goryachev05,
you04,