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From 2010.igem.org

Lemming Toolbox (Matlab/Simulink)

Background

During the iGem competition we developed several fast algorithms (e.g. for cell detection and tracking), complex models, as well as novel visualization, user input and microscope control approaches. Already during their development we took serious efforts to construct all parts in a modular and interchangeable way to deal with the combinatorial diversity of the questions our models as well as the information processing had to answer. Besides the various modules which can easily be reused by people experienced in programming, we also developed a graphical block representation of the various modules based on Simulink. This graphical user interface (GUI) can also be used by people with no or only little programming knowledge to solve complex tasks. These tasks do not have to be necessarily related to our iGem project, but can e.g. include the simulation of wild type chemotaxis, the detection of various cell types or the transfer of image data between a microscope and Matlab. We bundled all for other people useful Matlab and Simulink files into an easy to use Matlab Toolbox, which we named the Lemming Toolbox. This Lemming Toolbox was also used extensively during our project and speeded up the in-silico part significantly due to its modular design, which allowed for fast reassembly of program parts to solve urgent last-minute questions.

Since science is based on the open availability of information and approaches, we decided to give something back to the Systems and Synthetic Biology community by cleaning and documenting the Lemming Toolkit and making it available as Open Source under the GNU General Public License (see [1]). In the following we give a short overview about the abilities and requirements of the software, as well as providing free download possibilities. Finally we shortly present the various systems (Simulink models) build with the help of the Lemming Toolkit, for which we also provide download possibilities. We hope that the Lemming Toolkit can help other researches as well as future iGem participants to faster solve their tasks.