Team:ETHZ Basel/Modeling

From 2010.igem.org

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Besides the ''in vivo'' setup allowing the steering of a single ''Escherichia coli'' cell, the whole setup will be modeled. This allows us the testing of the cell detection & tracking as well as the design of the control algorithm in order to start verifying the different biological constructs and to record the successful control of bacterial movement.
Besides the ''in vivo'' setup allowing the steering of a single ''Escherichia coli'' cell, the whole setup will be modeled. This allows us the testing of the cell detection & tracking as well as the design of the control algorithm in order to start verifying the different biological constructs and to record the successful control of bacterial movement.
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== Timetable ==
 
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A rough overview about the timetable
 
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[[Image:timetable.png|center|600px|Timetable of the modeling subgroup.]]
 
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will be accompanied with status updates from the project responsibles:
 
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[[Image:status_explained.png|center|600px|Status update scheme.]]
 
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The individual signs are saved in our wiki space and can be accessed as images with the following name scheme: <br>
 
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percentagecolour.png <br> <br>
 
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percentage: 25, 50, 75, 100 <br>
 
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colour: '''g'''reen, '''o'''range, '''r'''ed <br>
 
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e.g. 50% in red -> filename 50r.png <br>
 
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Please embed it with Image:75g.png|none
 
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[[Image:75g.png|none|50% completed and ok.]]
 
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== Responsibilities ==
 
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The responsibilities of the ongoing tasks and their documentation on this page are as follows: <br> <br>
 
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• receptor models: George <br>
 
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• cell detection & tracking: Thanuja <br>
 
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• microscope setup: Moritz <br>
 
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• movement model: Simona <br>
 
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• coordination and troubleshooting: Christoph <br>
 
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== Questions ==
 
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[[Team:ETHZ_Basel/Modeling/Questions]]
 

Revision as of 18:17, 19 September 2010

Modeling & Information Processing Overview

ETHZ’s project, E-Lemming, aims to modify the chemotaxis property of E.coli such that, instead of response to a chemical attractant/repellent, the bacterium responds to a light stimulus (phototaxis). Furthermore, this light sensitivity is used to control E.coli’s movement by deciding, at any given time, which type of motion will our ‘Lemming – in – disguise’ adopt (tumbling or straight run). This leads to a controllable E.coli, which can follow any pre – defined spatial path/maze/game, as a result of the combination of tumbling and going straight. The bacterium colony is imaged and, by image processing, the position of a single tracked cell is inferred. By activating a light switch, the user decides whether the bacterium should continue running or should change direction.

In the theory world, the steps we are following in mindlessly driving E.coli to our pre - defined target are the following:

• deterministic (ODE) & stochastic models of the chemotaxis pathway (documented from the literature)
• model of the movement of E.coli (built on the information of the pathway derived from the molecular models)
• control algorithms ( built on the user’s desire to play around with E.coli)
• image tracking & image processing algorithms
• java applications/movies of the E.Lemming (the fun part)

Model coupling

Coupled models for the simulation of the whole process and their interfaces.

Besides the in vivo setup allowing the steering of a single Escherichia coli cell, the whole setup will be modeled. This allows us the testing of the cell detection & tracking as well as the design of the control algorithm in order to start verifying the different biological constructs and to record the successful control of bacterial movement.

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