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Team:ETHZ Basel/Achievements
From 2010.igem.org
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* '''MATLAB Toolbox (Lemming Toolbox):''' [[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.]] | * '''MATLAB Toolbox (Lemming Toolbox):''' [[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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We managed to develop all our computer based tools & algorithms as re-usable, publicly available modules and we assembled the entire ''in silico'' setup of the E. Lemming into a [https://2010.igem.org/Team:ETHZ_Basel/Achievements/Matlab_Toolbox '''MATLAB Toolbox''']! Our Toolbox includes 18 Simulink blocks encapsulating the algorithms we developed/implemented. We want to share our work with the iGEM community and interested persons and made it freely available for [http://sourceforge.net/projects/ethzigem10/files/LemmingToolbox_Setup.zip/download downloading]. | We managed to develop all our computer based tools & algorithms as re-usable, publicly available modules and we assembled the entire ''in silico'' setup of the E. Lemming into a [https://2010.igem.org/Team:ETHZ_Basel/Achievements/Matlab_Toolbox '''MATLAB Toolbox''']! Our Toolbox includes 18 Simulink blocks encapsulating the algorithms we developed/implemented. We want to share our work with the iGEM community and interested persons and made it freely available for [http://sourceforge.net/projects/ethzigem10/files/LemmingToolbox_Setup.zip/download downloading]. | ||
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* '''New Technical Standard:''' After weeks of applying the cloning strategy [http://dspace.mit.edu/handle/1721.1/46721 BBF RFC28], we came up with our own [https://2010.igem.org/Team:ETHZ_Basel/Achievements/Technical_Standard '''strategy'''] on how BFF RFC28 could be made compatible with Tom Knight`s original assembly standard. | * '''New Technical Standard:''' After weeks of applying the cloning strategy [http://dspace.mit.edu/handle/1721.1/46721 BBF RFC28], we came up with our own [https://2010.igem.org/Team:ETHZ_Basel/Achievements/Technical_Standard '''strategy'''] on how BFF RFC28 could be made compatible with Tom Knight`s original assembly standard. | ||
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* '''Model of light-inducible chemotaxis pathway:''' We worked out a [https://2010.igem.org/Team:ETHZ_Basel/Modeling/Combined '''model to control chemotaxis by light''']. The idea was to instrumentalize light sensitive proteins (LSPs) in order to manipulate the concentrations of the chemotaxis proteins (eg CheY), through an intracellular anchoring reaction. As a consequence, we can take control on this pathway-and direct the E.lemming's movement! | * '''Model of light-inducible chemotaxis pathway:''' We worked out a [https://2010.igem.org/Team:ETHZ_Basel/Modeling/Combined '''model to control chemotaxis by light''']. The idea was to instrumentalize light sensitive proteins (LSPs) in order to manipulate the concentrations of the chemotaxis proteins (eg CheY), through an intracellular anchoring reaction. As a consequence, we can take control on this pathway-and direct the E.lemming's movement! | ||
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* '''Movement Model:''' We made a [https://2010.igem.org/Team:ETHZ_Basel/Modeling/Movement '''stochastic model to realistically simulate the chemotaxis motion'''] of the cell ''in silico'', which responds to the light input that is converted into changes in the chemotaxis pathway, that influence the motion of the E. lemming. | * '''Movement Model:''' We made a [https://2010.igem.org/Team:ETHZ_Basel/Modeling/Movement '''stochastic model to realistically simulate the chemotaxis motion'''] of the cell ''in silico'', which responds to the light input that is converted into changes in the chemotaxis pathway, that influence the motion of the E. lemming. | ||
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* '''μPlateImager - software for the microscope:''' We developed [https://2010.igem.org/Team:ETHZ_Basel/InformationProcessing/InformationFlow '''μPlateImager'''], a platform independent software which enables the parallel acquisition of images and the remote control of light input signals. As a result, we achieved to control our E. lemmings with light, LIVE, while having them under the lens! Watch our short movie on this page! | * '''μPlateImager - software for the microscope:''' We developed [https://2010.igem.org/Team:ETHZ_Basel/InformationProcessing/InformationFlow '''μPlateImager'''], a platform independent software which enables the parallel acquisition of images and the remote control of light input signals. As a result, we achieved to control our E. lemmings with light, LIVE, while having them under the lens! Watch our short movie on this page! | ||
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* '''E. lemming 2D - The Game:''' We invented a [https://2010.igem.org/Team:ETHZ_Basel/InformationProcessing/Game '''synthetic biology shooting game'''] featuring our very own E. lemming! Give it a try and play with our E. lemming! | * '''E. lemming 2D - The Game:''' We invented a [https://2010.igem.org/Team:ETHZ_Basel/InformationProcessing/Game '''synthetic biology shooting game'''] featuring our very own E. lemming! Give it a try and play with our E. lemming! | ||
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* '''Controller: ''' We developed [https://2010.igem.org/Team:ETHZ_Basel/InformationProcessing/Controller '''five novel controllers'''] for directing the E. lemming to the desired target. As stimuli for altering the bacterial movement, we use light inputs. | * '''Controller: ''' We developed [https://2010.igem.org/Team:ETHZ_Basel/InformationProcessing/Controller '''five novel controllers'''] for directing the E. lemming to the desired target. As stimuli for altering the bacterial movement, we use light inputs. | ||
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* '''Systems Design:''' See how we managed to use our models to support the wetlab and vice versa when we [https://2010.igem.org/Team:ETHZ_Basel/Achievements/Systems_Design '''designed the system''']. | * '''Systems Design:''' See how we managed to use our models to support the wetlab and vice versa when we [https://2010.igem.org/Team:ETHZ_Basel/Achievements/Systems_Design '''designed the system''']. | ||
Revision as of 15:04, 27 October 2010
Achievements Overview
The unprocessed microscope images are available here.
- The E. lemming: Watch the smallest remotely controlled robot in action at ETH Zurich! The implementation using a chimeric fusion of Archeal Receptor to Bacterial chemotactic transducer enabled us to generate the first E. lemming. You find here recorded videos of live images of the light controlled E. coli - The E. lemming is alive!
- BioBrick Toolbox: Get a glimpse of our collection of BioBricks that showcases the proteins we made not only for E. lemming's chemotaxis signaling network and cellular anchoring, but also for its light sensing & fluorescence reporting pathway, including our favorites: the light-sensitive couple PhyB-Pif3 and the Archeal light receptor-an intra-species fusion protein! You also find here the characterization of our parts.
- 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.
We managed to develop all our computer based tools & algorithms as re-usable, publicly available modules and we assembled the entire in silico setup of the E. Lemming into a MATLAB Toolbox! Our Toolbox includes 18 Simulink blocks encapsulating the algorithms we developed/implemented. We want to share our work with the iGEM community and interested persons and made it freely available for [http://sourceforge.net/projects/ethzigem10/files/LemmingToolbox_Setup.zip/download downloading].
- New Technical Standard: After weeks of applying the cloning strategy [http://dspace.mit.edu/handle/1721.1/46721 BBF RFC28], we came up with our own strategy on how BFF RFC28 could be made compatible with Tom Knight`s original assembly standard.
- Model of light-inducible chemotaxis pathway: We worked out a model to control chemotaxis by light. The idea was to instrumentalize light sensitive proteins (LSPs) in order to manipulate the concentrations of the chemotaxis proteins (eg CheY), through an intracellular anchoring reaction. As a consequence, we can take control on this pathway-and direct the E.lemming's movement!
- Movement Model: We made a stochastic model to realistically simulate the chemotaxis motion of the cell in silico, which responds to the light input that is converted into changes in the chemotaxis pathway, that influence the motion of the E. lemming.
- μPlateImager - software for the microscope: We developed μPlateImager, a platform independent software which enables the parallel acquisition of images and the remote control of light input signals. As a result, we achieved to control our E. lemmings with light, LIVE, while having them under the lens! Watch our short movie on this page!
- E. lemming 2D - The Game: We invented a synthetic biology shooting game featuring our very own E. lemming! Give it a try and play with our E. lemming!
- Controller: We developed five novel controllers for directing the E. lemming to the desired target. As stimuli for altering the bacterial movement, we use light inputs.
- Systems Design: See how we managed to use our models to support the wetlab and vice versa when we designed the system.
