Software

Blue Brain’s reconstruction and related simulations are made possible by a comprehensive software ecosystem for each step in the reconstruction and simulation process. Blue Brain systematically releases open source software.

Data Management

Neuroinformatics is an essential aspect of Blue Brain’s methodology and provides a fundamental data management structure and set of activities by which Blue Brain operates. Neuroinformatics is concerned with organizing neuroscience data and providing tools to facilitate the analysis of this data. Blue Brain Nexus has been built by the Blue Brain Project to organize, store and process exceptionally large volumes of data and support usage by a broad number of users.

Building

Blue Brain building tools aim to build comprehensive digital reconstructions of brain structures at different levels of organization that are compatible with the available experimental data. The strategy of these tools is to identify interdependencies in the experimental data and use them to constrain the reconstruction process. Blue Brain software applications are customizable to be reusable for various brain regions for the benefit of the community.

Analysis

Within Blue Brain’s workflow is the analysis of simulation results. The analysis stage is initially for model validation and then subsequently for simulation-based investigations of brain function and dysfunction, diagnostic tools and possible treatments.  The analysis step of Blue Brain’s workflow is supported by two open source software tools – the Electrophysiology Feature Extraction Library (eFEL) and NeuroM.

Exploration

Exploration relies on building software that combines data integration, analysis and interactive visualization to build, modify and navigate through large scientific datasets. Blue Brain BioExplorer is a tool for scientists to extract and analyze scientific data from interactive exploration.

Text Mining and Knowledge Engineering

Blue Brain has built an open source two component framework – Blue Brain Search and Blue Graph, for Knowledge Graph guided literature review using its Machine Learning and Data and Knowledge Engineering expertise

In silico Experiment

In order to improve performance and benefit from new computing architectures, the core functionalities of the widely used NEURON simulator have been isolated and optimized into a new simulator CoreNEURON. This software tool helps existing NEURON users to simulate their models faster, better utilizes computing resources and helps to deliver science early. This software tool is developed in collaboration with Michael Hines at Yale University.

Visualization

Blue Brain has developed a state-of-the-art modular visualization architecture for large data visualization over a wide range of use cases to deliver an unprecedented capability of viewing, analyzing, validating, troubleshooting and communicating neuroscientific structures and functions.