Blue Brain Software Suites

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.

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.

Atlas Suite

A suite to build and analyze volumetric brain atlases.

Deep Atlas Suite

Deep Atlas is a suite of tools created by the Blue Brain Project to manipulate brain atlas images.

Morphology Suite

A suite to build, analyze and visualize morphologies.

Vasculature Suite

Vasculature Suite is a set of tools created by the Blue Brain Project to process and visualize large-scale morphological reconstructions of the brain vasculature.

Single Cell E-Model Suite

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.

Circuit Model Suite

A suite to build, analyze and visualize circuits.


The Blue Brain BioExplorer (BBBE) is a tool for scientists to extract and analyze scientific data from visualization and interactive exploration.