From 2010.igem.org

Revision as of 12:54, 27 October 2010

Achievements Overview

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

BioBrick Toolbox

Get a glimpse of our collection of BioBricks that showcases the proteins we made for E. lemming's chemotaxis, cellular anchoring, light sensing & fluorescence reporting including our favorites: the light sensing couple PhyB-Pif3 and the Archaeal light receptor. You find here also 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.

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. This is available for [http://sourceforge.net/projects/ethzigem10/files/LemmingToolbox_Setup.zip/download downloading].

New Technical Standard

After weeks of cloning with [http://dspace.mit.edu/handle/1721.1/46721 BBF RFC28] we came up with a strategy for this to be easily be made compatible to Tom Knight`s original assembly standard.

Model of light-inducible chemotaxis pathway

We made a model to control the chemotaxis by using light. The idea was to use Light Receptive Proteins to change the concentrations of the proteins responsible for chemotaxis, in such a way that the motion of the cell can be controlled the way we want.

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 to control our E. lemmings with light, while having them under the lens.

E. lemming - The Game

We have made a synthetic biology shooting game featuring our very own E. lemming!

Controller

We developed five different controllers that can be used to guide the E. lemming to a desired target, using the light inputs that influence the motion of E. lemming

Systems Design

See how we managed to use modeling to support the wetlab and vice versa when we designed the system.

Systems Implementation

Have a look at how we simulated the whole setup in silico.