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The blue brain, a Swiss national brain initiative, aims to create a digital brain reconstruction by reverse-engineering mammalian brain circuits. The mission of the project, founded in May 2005 by the Brain and Mental Institute of the Federal Polytechnic School of Lausanne (EPFL) in Switzerland, is to use biologically detailed reconstructions and digital simulations of the mammalian brain to identify the fundamental principles of the brain Structure And function in health and illness. The project is headed by founding director Henry Markram, who also directs the European Human Brain Project, and co-directed by Felix Schürmann and Sean Hill. Using a Blue Gene supercomputer running Michael Hines's NEURON software, the simulation is not simply an artificial neural network, but involves a biologically realistic model of neurons. It is expected to eventually shed light on the nature of consciousness.

There are several sub projects, including the Cajal Blue Brain, coordinated by the Super computing and Visualization Center of Madrid (CeSViMa), and others run by universities and independent laboratories. Supercomputer-based reconstructions and simulations built by the project offer a radically new approach to understanding multilevel structure and brain function. The new research strategy exploits the inter-dependencies in experimental data to obtain dense maps of the brain, without measuring every detail of its multiple levels of organization (molecules, cells, microcircuits, brain regions, whole brain). This strategy allows the project to build digital reconstructions (computer models) of the brain to an unprecedented level of biological detail. Supercomputer-based simulation of their behavior makes understanding the brain a manageable problem, providing a new tool for studying the complex interactions within the different levels of organization of the brain and for investigating the links between levels leading from genes to Cognition.