Quorum Sensing based
From 2006.igem.org
m (→) |
(→Discussion Meetings) |
||
| (56 intermediate revisions not shown) | |||
| Line 1: | Line 1: | ||
Back to [[ETH Zurich]] main page. | Back to [[ETH Zurich]] main page. | ||
| + | ---- | ||
=Design Group= | =Design Group= | ||
| - | + | This is the subpage of the temporary design group defined during the team meeting on Thu. 2005.08.04 | |
| + | |||
==Purpose== | ==Purpose== | ||
| - | * | + | * To discuss those projects assigned to us (detailed below under "Initial Project Variants") and develop them further, both conceptually (modularity, coolness, usefulness) and implementation-wise (feasability, availability of components). |
| - | * Agree on some favored existing solution or merge current concepts into a new one. | + | * Agree on some favored existing solution or merge current concepts into a new one, [[Project X]]. |
| - | == | + | ==Permanent Members== |
* [[Dominic Frutiger]] | * [[Dominic Frutiger]] | ||
* [[Giorgia Valsesia]] | * [[Giorgia Valsesia]] | ||
* [[Herve Vanderschuren]] | * [[Herve Vanderschuren]] | ||
| - | |||
==Discussion Meetings== | ==Discussion Meetings== | ||
| - | Everybody is more | + | Everybody is more than welcome to join in! |
'''2005.08.05, Friday, 15:30, Discussion/development of group topics, Giorgia & Dominic''' | '''2005.08.05, Friday, 15:30, Discussion/development of group topics, Giorgia & Dominic''' | ||
| - | '''2005.08.07, Sunday, | + | '''2005.08.07, Sunday, 16:00, Discussion/development of group topics, Herve & Dominic''' |
| + | '''2005.08.08, Monday, 10:00, Discussion/development of group topics, all (visitors welcome)''' | ||
| + | '''2005.08.09, Tuesday, 16:00, Discussion of feasability/implementation regarding modules''' | ||
| + | '''2005.08.10, Wednesday, 09:00, Discussion of concept (Dominic, Simon)''' | ||
| + | '''2005.08.10, Wednesday, 17:00, Introduction of current status to Alex (by Dominic)''' | ||
| + | '''2005.08.10, Wednesday, 17:30, Discussion of modules (Giorgia, Dominic) @polyterrasse''' | ||
| + | '''2005.08.11, Thursday, 09:00, Discussion of presentation preps (all)''' | ||
| + | '''2005.08.11, Thursday, 11:15, Discussion of presentation preps and story line (all)''' | ||
| + | '''2005.08.11, Thursday, 14:30, Assigning tasks for presentation, @polyterrasse''' | ||
| + | '''2005.08.11, Thursday, 16:00, Finalizing presentation, @polyterrasse''' | ||
| + | |||
| + | ==Progress History== | ||
| + | During the first two meetings we mainly developed the existing concepts (see "Initial Project Variants" below) further or added variants. | ||
| + | |||
| + | ===Initial Project Variants=== | ||
| + | Here you find a list of the initial projects that were assigned to this group. These projects have their own page. We developed them a little further at first, but now we are merging some of them into [[Project X]]. Thus those projects are no longer maintained by our development group members. | ||
| + | |||
| + | *[[Sorting Bacteria]] (outdated -> [[Project_X]]) | ||
| + | *[[Pulser]] (outdated -> [[Project_X]]) | ||
| + | *[[Constructor Bacteria]] (outdated -> [[Project_X]]) | ||
| + | *[[Controlled Cell Division]] (outdated -> [[Project_X]]) | ||
| + | *[[Predator-Prey Behavior]] (outdated -> see section below "Problems with Pred-Prey") | ||
| + | |||
| + | ===Behavior States=== | ||
| + | On monday we tried to find useful categories to identify what makes the projects similar and what makes them different - in order to reduce the number of true variants and merge interesting functions into a new project idea. We started to divide the existing project ideas further into certain behavior states and their possible expression: | ||
| + | |||
| + | * pattern formation | ||
| + | ** oscillation behavior and/or dynamic equilibria | ||
| + | ** convergence to specific end states with distinct intermediate states | ||
| + | |||
| + | * pattern display | ||
| + | ** fluorescence | ||
| + | ** physical structures | ||
| + | |||
| + | The first step would always be pattern formation. The difficulty with approaches aiming at oscillation behavior and/or dynamic equilibria (such as the [[Pulser]] or the [[Predator-Prey_Behavior]]) is that we can not break them down to intermediate stages and thus there is no step-wise increase of risk: either all aspects work at once and the interplay is balanced leading to some dynamic stability or the whole concept miserably fails. Also, it is more difficult to prove success. | ||
| + | |||
| + | As a result our discussions more and more converged towards approaches with specific static end states and intermediate layers. | ||
| + | |||
| + | ===Modules=== | ||
| + | Also, we tried to break down the existing variants into modules fulfilling a specific function: | ||
| + | |||
| + | {| width=700 | ||
| + | |quorum sensing | ||
| + | |aggregation / sticking | ||
| + | |killer behavior | ||
| + | |- | ||
| + | |cell division sensing | ||
| + | |cell division control | ||
| + | |induced apoptosis | ||
| + | |- | ||
| + | |chemotaxis (+/-) | ||
| + | |nutrition production | ||
| + | |nutrition dependence | ||
| + | |} | ||
| + | |||
| + | Then we discussed the estimated (!) feasability and general usefulness of these modules to get a better feeling of what should be used and what will prove difficult to implement. | ||
| + | |||
| + | ===Problems with Pred-Prey=== | ||
| + | We quickly found that the implementation of true Predator-Prey behavior would be very interesting, but that there are serious drawbacks: | ||
| + | |||
| + | * there are no layers: all functions would have to be successfully implemented at the same time (e.g. production of nutrients in pop A, dependence on nutrients of pop B, balancing the killing behavior of B vs. A) otherwise the whole project would fail. | ||
| + | * the resulting population dynamics would be interesting, but neither very useful nor extendable. | ||
| + | |||
| + | ===Convergence=== | ||
| + | The remaining project ideas, however, seem to share many modules and can be merged into the following new project variant [[Project_X]]. | ||
| + | |||
| + | ==Current Development Stage== | ||
| + | Please see [[Project_X]]. | ||
| + | |||
| + | |||
| + | ---- | ||
Back to [[ETH Zurich]] main page. | Back to [[ETH Zurich]] main page. | ||
Latest revision as of 13:19, 11 August 2005
Back to ETH Zurich main page.
Contents |
Design Group
This is the subpage of the temporary design group defined during the team meeting on Thu. 2005.08.04
Purpose
- To discuss those projects assigned to us (detailed below under "Initial Project Variants") and develop them further, both conceptually (modularity, coolness, usefulness) and implementation-wise (feasability, availability of components).
- Agree on some favored existing solution or merge current concepts into a new one, Project X.
Permanent Members
Discussion Meetings
Everybody is more than welcome to join in!
2005.08.05, Friday, 15:30, Discussion/development of group topics, Giorgia & Dominic 2005.08.07, Sunday, 16:00, Discussion/development of group topics, Herve & Dominic 2005.08.08, Monday, 10:00, Discussion/development of group topics, all (visitors welcome) 2005.08.09, Tuesday, 16:00, Discussion of feasability/implementation regarding modules 2005.08.10, Wednesday, 09:00, Discussion of concept (Dominic, Simon) 2005.08.10, Wednesday, 17:00, Introduction of current status to Alex (by Dominic) 2005.08.10, Wednesday, 17:30, Discussion of modules (Giorgia, Dominic) @polyterrasse 2005.08.11, Thursday, 09:00, Discussion of presentation preps (all) 2005.08.11, Thursday, 11:15, Discussion of presentation preps and story line (all) 2005.08.11, Thursday, 14:30, Assigning tasks for presentation, @polyterrasse 2005.08.11, Thursday, 16:00, Finalizing presentation, @polyterrasse
Progress History
During the first two meetings we mainly developed the existing concepts (see "Initial Project Variants" below) further or added variants.
Initial Project Variants
Here you find a list of the initial projects that were assigned to this group. These projects have their own page. We developed them a little further at first, but now we are merging some of them into Project X. Thus those projects are no longer maintained by our development group members.
- Sorting Bacteria (outdated -> Project_X)
- Pulser (outdated -> Project_X)
- Constructor Bacteria (outdated -> Project_X)
- Controlled Cell Division (outdated -> Project_X)
- Predator-Prey Behavior (outdated -> see section below "Problems with Pred-Prey")
Behavior States
On monday we tried to find useful categories to identify what makes the projects similar and what makes them different - in order to reduce the number of true variants and merge interesting functions into a new project idea. We started to divide the existing project ideas further into certain behavior states and their possible expression:
- pattern formation
- oscillation behavior and/or dynamic equilibria
- convergence to specific end states with distinct intermediate states
- pattern display
- fluorescence
- physical structures
The first step would always be pattern formation. The difficulty with approaches aiming at oscillation behavior and/or dynamic equilibria (such as the Pulser or the Predator-Prey_Behavior) is that we can not break them down to intermediate stages and thus there is no step-wise increase of risk: either all aspects work at once and the interplay is balanced leading to some dynamic stability or the whole concept miserably fails. Also, it is more difficult to prove success.
As a result our discussions more and more converged towards approaches with specific static end states and intermediate layers.
Modules
Also, we tried to break down the existing variants into modules fulfilling a specific function:
| quorum sensing | aggregation / sticking | killer behavior |
| cell division sensing | cell division control | induced apoptosis |
| chemotaxis (+/-) | nutrition production | nutrition dependence |
Then we discussed the estimated (!) feasability and general usefulness of these modules to get a better feeling of what should be used and what will prove difficult to implement.
Problems with Pred-Prey
We quickly found that the implementation of true Predator-Prey behavior would be very interesting, but that there are serious drawbacks:
- there are no layers: all functions would have to be successfully implemented at the same time (e.g. production of nutrients in pop A, dependence on nutrients of pop B, balancing the killing behavior of B vs. A) otherwise the whole project would fail.
- the resulting population dynamics would be interesting, but neither very useful nor extendable.
Convergence
The remaining project ideas, however, seem to share many modules and can be merged into the following new project variant Project_X.
Current Development Stage
Please see Project_X.
Back to ETH Zurich main page.
