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Revision as of 13:44, 25 October 2010

Achievements Overview

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

BioBrick Toolbox

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. This includes the following Simulink modules that encapsulate the algorithms we used.

• Image aquisition - to receive images either from a microscope (live image stream) or to work with saved images in a storage device
• Cell Detection & Tracking - to detect cells in the image streams and keep track of their trajectories through out the image stream
• 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
• Input devices - to capture inputs from a joystick or a keyboard
• Controller - to select a cell & to drive it to a target
• Models (for simulations)
  • Molecular Model - capturing & integrating the biological pathways into the simulations
  • Movement Model - simulates the motion of the E .lemming
  • Image generator - to generate a realistic look & feel for the simulations
• Visualization
  • Cell Visualization - outputs the visuals combining the microscope images and the outputs of above Simulink blocks
  • E. lemming 2D - the game

The complete toolbox can be downloaded here [add link]. Please visit the [MATLAB Toolbox page] for further information

Interworking: Engineering & Biology

Simulation

Medal Criteria