Team:ETHZ Basel/Achievements

From 2010.igem.org

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[[Image:lemmingToolbox.jpg|thumb|350px|'''MATLAB Toolbox''' Screenshot of the Simulink blocks available in the toolbox. Please note that these blocks can be visually assembled with the Simulink blocks of other Toolboxes (e.g. blocks for nearly any mathematical function), and that the algorithms we developed can be accessed directly through Matlab code, too.]]
[[Image:lemmingToolbox.jpg|thumb|350px|'''MATLAB Toolbox''' Screenshot of the Simulink blocks available in the toolbox. Please note that these blocks can be visually assembled with the Simulink blocks of other Toolboxes (e.g. blocks for nearly any mathematical function), and that the algorithms we developed can be accessed directly through Matlab code, too.]]
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As a result of our efforts to make all our computer based tools & algorithms modular and re-usable, we have assembled the entire in-silico setup of the E. Lemming into a MATLAB toolbox. This includes the following Simulink modules that encapsulate the algorithms we used.
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As a result of our efforts to make all our computer based tools & algorithms modular and re-usable, we have assembled the entire ''in silico'' setup of the E. Lemming into a [https://2010.igem.org/Team:ETHZ_Basel/Achievements/Matlab_Toolbox MATLAB Toolbox] that includes 18 Simulink blocks that encapsulate the algorithms we developed/implemented.
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* Image aquisition - to receive images either from a microscope (live image stream) or to work with saved images in a storage device
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The complete toolbox can be [http://sourceforge.net/projects/ethzigem10/files/LemmingToolbox_Setup.zip/download downloaded here].
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* [https://2010.igem.org/Team:ETHZ_Basel/InformationProcessing/CellDetection Cell Detection & Tracking] - to detect cells in the image streams and keep track of their trajectories through out the image stream
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* [https://2010.igem.org/Team:ETHZ_Basel/InformationProcessing/Microscope Microscope control] - to adjust the position of the stage to capture the cells properly, to shine red/far-red light on the cells to influence their movement
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* Input devices - to capture inputs from a joystick or a keyboard
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* [https://2010.igem.org/Team:ETHZ_Basel/InformationProcessing/Controller Controller] - to select a cell & to drive it to a target
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* [https://2010.igem.org/Team:ETHZ_Basel/Modeling Models] (for simulations)
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** [https://2010.igem.org/Team:ETHZ_Basel/Modeling/Combined Molecular Model] - capturing & integrating the biological pathways ([https://2010.igem.org/Team:ETHZ_Basel/Modeling/Chemotaxis chemotaxis pathway] & the [https://2010.igem.org/Team:ETHZ_Basel/Modeling/Light_Switch light switch]) into the simulations
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** [https://2010.igem.org/Team:ETHZ_Basel/Modeling/Movement Movement Model] - simulates the motion of the E .lemming
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** Image generator - to generate a realistic look & feel for the simulations
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* [https://2010.igem.org/Team:ETHZ_Basel/InformationProcessing/Visualization Visualization]
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** Cell Visualization - outputs the visuals combining the microscope images and the outputs of above Simulink blocks
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** [https://2010.igem.org/Team:ETHZ_Basel/InformationProcessing/Game E. lemming 2D] - the game
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The complete toolbox can be [http://sourceforge.net/projects/ethzigem10/files/LemmingToolbox_Setup.zip/download downloaded here]. Please visit the [https://2010.igem.org/Team:ETHZ_Basel/Achievements/Matlab_Toolbox MATLAB Toolbox page] for further information
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== Interworking: Engineering & Biology ==
== Interworking: Engineering & Biology ==
== Simulation ==
== Simulation ==
== Medal Criteria ==
== Medal Criteria ==

Revision as of 13:57, 26 October 2010

Achievements Overview

Short movie of an E. coli cell switching between the tumbling and the straight swimming modes..

BioBrick Toolbox

Being now BBF RFC28 (cloning strategy for combinatorial multip-part assembly [http://dspace.mit.edu/handle/1721.1/46721] ) experts, we highly recommend you to check out our BrickBox collection comprising of proteins used for chemotaxis, cellular anchoring, light sensing and fluorescent reporting. We also gave a lot of thoughts how to make BBF RFC28 (method for combinatorial multi-part assembly based on the Type II restriction enzyme AarI) compatible with Tom Knight's OAS standard.

Also about the characterization of our parts you will find more information on this page.

Don't forget our favourite parts including the light sensing couple PhyB-Pif3 and the Archaeal light receptor!

MATLAB Toolbox (Lemming Toolbox)

MATLAB Toolbox Screenshot of the Simulink blocks available in the toolbox. Please note that these blocks can be visually assembled with the Simulink blocks of other Toolboxes (e.g. blocks for nearly any mathematical function), and that the algorithms we developed can be accessed directly through Matlab code, too.

As a result of our efforts to make all our computer based tools & algorithms modular and re-usable, we have assembled the entire in silico setup of the E. Lemming into a MATLAB Toolbox that includes 18 Simulink blocks that encapsulate the algorithms we developed/implemented.

The complete toolbox can be [http://sourceforge.net/projects/ethzigem10/files/LemmingToolbox_Setup.zip/download downloaded here].

Interworking: Engineering & Biology

Simulation

Medal Criteria

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