79 projects
bluepyefe
Blue Brain Python E-feature extraction
efel
Electrophys Feature Extract Library (eFEL)
brainbuilder
BrainBuilder is a tool to define the cells that will compose a circuit.
dir-content-diff
Simple tool to compare directory contents.
bluecellulab
Biologically detailed neural network simulations and analysis.
libsonata
SONATA files reader
brain-indexer
A spatial index implementation for spheres, morphologies and synapses
Connectome-Utilities
Complex network representation and analysis layer
bluepyemodel
Blue Brain Python Electrical Modeling Pipeline
bluepysnap
Simulation and Neural network Analysis Productivity layer
neurodamus
A BBP Simulation Control application for NEURON
bluepyopt
Blue Brain Python Optimisation Library (bluepyopt)
connectome-manipulator
A connectome manipulation framework for SONATA circuits
currentscape
Module to easily plot currentscape.
synthesis-workflow
Workflow used for synthesis and its validation.
region-grower
Synthesize cells in a given spatial context.
NMODL-nightly
NEURON Modeling Language Source-to-Source Compiler Framework
axon-synthesis
A package to synthesize artificial axons
blue-brain-atlas-pipeline
Package defining a SnakeMake pipeline to create the Blue Brain Atlas datasetsand push them into Nexus.
scholarag
Pipelines for RAG on scientific papers
blueetl
Multiple simulations analysis tool
blueetl-core
Core transformations for BlueETL
NeuroTS
Synthesis of artificial neurons using their topological profiles package.
brayns
Brayns Python API
neurocollage
A tool to create 2D morphology collage plots based on matplotlib.
blue-brain-data-push
Package creating resource payloads from atlas datasets and push them along with the corresponding dataset files into Nexus.
diameter-synthesis
Diametrize cells.
data-validation-framework
Simple framework to create data validation workflows.
bba-pipeline
Package defining a SnakeMake pipeline to create the Blue Brain Atlas datasetsand push them into Nexus.
blue-brain-token-fetch
Package to perform fetching and automatic refreshing of the Nexus access token using Keycloak. Using the CLI you can choose to either have its value periodically written in the file whose path is given in input or either have it periodically printed on the console output.
bluepymm
Model Management Python Library (bluepymm)
neuroagent
Search agent for neuroscience.
scholaretl
ETL for parsing scientific papers.
axon-projection
A code that analyses long-range axons provided as input, and classify them based on the brain regions they project to.
emodel-generalisation
Generalisation of neuronal electrical models with MCMC
bbp-workflow
Automated pipelines of batch jobs using python and the luigi framework
neurom
NeuroM: a light-weight neuron morphology analysis package
morphio
A neuron morphology IO library
ngv-ctools
NGV Architecture c++ modules
knowledge-graph-inference
Tools for performing knowledge inference.
atlas-densities
Library containing command lines and tools to compute volumetric cell densities in the rodent brain
bbp-atlas-pipeline-validator
A pipeline validator for Blue Brain Project
EModelRunner
Runs cells from Blue Brain Project cell packages, such as sscx, synapse plasticity, etc.
entity-management
Access to production entity management
morphology-workflows
Workflows used for morphology processing.
cgal-pybind
Python bindings for some CGAL classes
fz-td-recipe
Read and modify parameters used in neuroscientific in silico circuit building.
AstroVascPy
Simulating blood flow in vasculature
morph-tool
A collection of CLIs and python function related to morphology handling
multiscale-run
MultiscaleRun is a Python package to run brain cells simulation at different scales. It orchestrates the coupling between several brain simulators like Neuron and STEPS but also solvers like AstroVascPy for the cerebral blood flow. The package also embeds a Julia solver to simulate the astrocytes activity.
atlas-placement-hints
Library containing command lines and tools to compute placement hints
functionalizer
A PySpark implementation of the Blue Brain Project Functionalizer
blue-cwl
Common Workflow Language inspired workflow definitions.
psp-validation
PSP analysis tools
neuroc
NeuroC: a collection of tools for morphology cloning applications
nexusforge
Building and Using Knowledge Graphs made easy.
ArchNGV
NGV architecture modules
NeuroR
A morphology repair tool
plotly-helper
Package that makes plotly easy
vascpy
Vasculature API
TMD
A python package for the topological analysis of neurons.
voxcell
Voxcell is a small library to handle probability distributions that have a spatial component and to use them to build collection of cells in space.
atlas-splitter
CLI to split atlas regions and modify annotations accordingly
BluePyParallel
Provides an embarrassingly parallel tool with sql backend.
sphinx-bluebrain-theme
Blue Brain Project theme for Sphinx
atlas-direction-vectors
Commands to compute direction vectors in volumetric brain regions. Direction vectors are 3D unit vectors associated to voxels of a brain region. They represent the directions of the fiber tracts.
bioexplorer
Python API for the Blue Brain BioExplorer
atlas-commons
Library containing common functions to build atlases
nrn-modeldb-ci
NEURON ModelDB CI tools
brion
BlueBrain I/O Library
luigi-tools
Tools to work with luigi.
NMODL
NEURON Modeling Language Source-to-Source Compiler Framework
bluepyentity
NEXUS Productivity Layer
MVDTool
Python bindings to the MVD3 neuroscience file format
bluegraph
Knowledge Graphs analytics.
rockets
Rockets python client
basalt
Graph API powered by RocksDB persistent key-value store for fast storage
flake8-oist-steps
Check usage STEPS subcellular simulator
hpcbench
Specify and run your benchmarks
