ETH Zurich 2006
From 2006.igem.org
Revision as of 13:54, 12 August 2005 by Christophe (Talk | contribs)
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 (aka Project X)
| 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 tuning, 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.
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 (aka The Thing)
| 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.
Christophe: About feasibility: i don't agree with much of what has been said here. The counter is made of two toggle switches. These switches exist in the nature (lambda repressor) and have also been synthetized (Gardner et al., partly also on MIT registry). Now, the only things we need to come up with are A) a way of having 4 different types of road blocks, which is, as Sven said, possible using zinc-fingers that target different dna seqs, and B) a way to have S working as an inducer and as a repressor, in a roughly symmetrical manner. And that's all. I am not saying that it is trivial, but seriously, it is really doable. And even if we don't manage it to do it for the jamboree, finishing it later could still be academically very rewarding. Bottom line: The difference between the two projects, i guess, is that most of the work in the QS project would be at the assembling/tuning of existing parts for a very cool final effect, while in the the counter, we would focus the energy of the whole group into realizing a little module that is reliable and reusable. Both projects are cool, both teams have done an increadible amount of preparatory work until now and so at this point, i would be very excited working on either projects.
External Information
Links
Papers
bulter04, atkinson03, bates05, keiler01, suetsugu03, sudesh00, römling02, ross91, sutherland01, Lai04, zogaj01, miller01, basu05, goryachev05,
you04,