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Neuro Informatics Software Released to Open Source



10 January 2018. A collection of software from the Blue Brain Project for reconstructing models of mammal brain circuitry is being made freely available to the research community. The Blue Brain Project is an undertaking of Ecole polytechnique fédérale de Lausanne, or EPFL, in Switzerland.

The Blue Brain Project, located in Geneva, is building detailed three-dimensional digital reconstructions and simulations of rodent brain circuitry, which the initiative plans to eventually expand to the human brain. Teams working on this initiative are creating computer models and simulations of neuron circuits, from data reported in experimental studies, with the aim of better understanding the multi-level complexities of those circuits in fine biological detail.

The project began in 2005, with the help of IBM, that installed a supercomputer on the EPFL campus for carrying out the large-scale computational tasks. Researchers on the project so far reproduced detailed maps of the cellular anatomy, connectivity, and electrical behavior of a small part of the neocortex of young rats, the section of the cerebral cortex supporting hearing and vision.

Part of the project, called Blue Brain Nexus, collects and catalogs the software for developing data models. Blue Brain Nexus, say the project managers, was created to help organize, store, and process exceptionally large volumes of data for use by Blue Brain community. The software provides data modeling for experimental data, single-cell models, circuits, and simulations, as well as for validations. Blue Brain Nexus is being evaluated for use with the neuroinformatics platform of the Human Brain Project, Europe-wide initiative funded by the EU.

The Blue Brain Nexus may have applications beyond neuroscience, says the project team. Blue Brain Nexus acts as both a repository and data catalog, and is designed to capture and index data from any scientific domain. Blue Brain Nexus users, for example, can organize their own domains in the repository and catalog, allowing the software to act as a platform in other disciplines.

In addition, Blue Brain Nexus enables greater transparency in its data. Users can track the origin of the data, says the project team, as well as see ways the data are being employed. As a result, users can assess the quality and build trust in the data.

Blue Brain Nexus is available for download through GitHub. The software makes it possible for users to register their data schema and taxonomies, submit data to the platform, and discover related data for examination. Blue Brain Nexus is distributed under a version 2.0 open-source license of the Apache Software Foundation.

The following video tells more about the Blue Brain Project.

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