HBP researchers have developed digital tools that facilitate the study and integration of insights from different scales of the brain. The HBP book “An extensive guide to the tools developed” provides a comprehensive snapshot of a set of these tools. Within the book, you will find descriptions of each tool sorted in chapters according to the spatial scale of the brain that they are typically applied to.
To accompany the book, we here provide a list of up-to-date links to access each of these tools. These include links that provide further documentation about the individual tool or set of tools as well as direct access to the digital tools themselves.
Filter tools:
AngoraPy
Access tool on GithubAccess tool in EBRAINS Collaboratory
AnonyMl
Access tool on GithubArbor
View tool website
Access tool in EBRAINS Collaboratory
Arbor GUI
Access tool on GithubBIDS Extension Proposal Computational Model Specifications
Access tool on Github
View tool documentation
BioBB
View tool website
Access tool in EBRAINS Collaboratory
BioExcel-CV19
View tool website
Access tool in EBRAINS Collaboratory
BioNAR
View tool website
BlueNaaS-SingleCell
Access tool on Github
View tool website
BlueNaaS-Subcellular
View tool website
Access tool in EBRAINS Collaboratory
BluePyEfe
Access tool on Github
BluePyMM
Access tool on Github
BluePyOpt
Access tool on Github
Brain Cockpit
Access tool on Github
Access tool in EBRAINS Collaboratory
BrainScaleS
View tool website
Brayns
Access tool on Github
Brion
Access tool on Github
BSB
View tool website
Access tool on EBRAINS
bsp-usecase-wizard
Access tool on EBRAINS
Access tool in EBRAINS Collaboratory
BVEP
Access tool on Github
Access tool in EBRAINS Collaboratory
CGMD Platform
View tool website
CLSI Service Account
Access tool on Github
CNS-ligands
View tool website
Access tool in EBRAINS Collaboratory
Cobrawap
View tool website
Access tool in EBRAINS Collaboratory
Collaboratory Bucket service
Access tool in EBRAINS Collaboratory
Collaboratory Drive
Access tool in EBRAINS Collaboratory
Collaboratory IAM
Access tool in EBRAINS Collaboratory
Collaboratory Lab
Access tool in EBRAINS Collaboratory
Collaboratory Office
Access tool in EBRAINS Collaboratory
Collaboratory Wiki
Access tool in EBRAINS Collaboratory
CoreNEURON
View tool website
CxSystem2
Access tool on Github
DeepSlice
View tool website
EBRAINS Ethics & Society Toolkit
Access tool on EBRAINS
View tool documentation
EBRAINS Image Service
Access tool in EBRAINS Collaboratory
EBRAINS Knowledge Graph
View tool website
EDI Toolkit
View tool website
eFEL
Access tool on Github
Elephant
View tool website
View tool tutorial
FAConstructor
Access tool on Github
fairgraph
Access tool on Github
Fast sampling with neuromorphic hardware
Access tool on Github (Quantum)
Access tool on Github (Electronic Visions)
fastPLl
Access tool on Github
Feed-forward LFP-MEG estimator from mean-field models
Access tool in EBRAINS Collaboratory
FIL
Access tool on Github
Download tool
FMRALIGN
Access tool on Github
Foa3D
Access tool on Github
Frites
Access tool on Github
gridspeccer
Access tool on Github
Hai-Cgp
Access tool on Github
Health Data Cloud
View tool website
Access tool in EBRAINS Collaboratory
Hodgkin-Huxley Neuron Builder
View tool websiteHPC Job Proxy
Access tool in EBRAINS Collaboratory
HPC Status Monitor
Access tool on EBRAINSHuman Intracerebral EEG Platform
View tool website
Access tool on EBRAINS
Hybrid MM/CG Webserver
View tool website
Access tool in EBRAINS Collaboratory
Insite
Access tool on Github
Interactive Brain Atlas Viewer
View tool website
View tool in EBRAINS Knowledge Graph
JuGEx
View tool website
Access tool on Github
KnowledgeSpace
View tool website
Access tool in EBRAINS Collaboratory
L2L
Access tool in EBRAINS Collaboratory
Leveltlab/SpectralSegmentation
Access tool on GithubLFPy
View tool website
Access tool in EBRAINS Collaboratory
libsonata
Access tool on Github
Live Papers
Access tool on Ebrains
View tool website
Livre
Access tool on Github
View tool in EBRAINS Knowledge Graph
LocaliZoom
Access tool on Github
Access tool in EBRAINS Collaboratory
MD-IFP
Access tool on Github
Access tool in EBRAINS Collaboratory
MEDUSA
View tool website
MeshView
Access tool on Github
Access tool in EBRAINS Collaboratory
MIP
View tool website
Access tool on EBRAINS
Model Validation Service
Access tool on Github
Access tool in EBRAINS Collaboratory
Model Validation Test Suites
Access tool in EBRAINS CollaboratoryMoDEL-CNS
View tool website
Access tool in EBRAINS Collaboratory
Modular Science
Access tool on Github
Access tool in EBRAINS Collaboratory
Monsteer
Access tool on Github
MorphlO
Access tool on Github
Morphology alignment tool
View tool website
View HBP Webpage of tool
MorphTool
Access tool on Github
Multi-Brain
Access tool on Github
Multi-lmage-OSD
Access tool on Github
MUSIC
Access tool on Github
Access tool in EBRAINS Collaboratory
NEAT
View tool website
Neo
View tool website
Neo Viewer
View tool website
NEST Desktop
View tool website
Access tool in EBRAINS Collaboratory
NEST Simulator
View tool website
NESTML
View tool website
NetPyNE
View tool website
Access tool on Github
NEURO-CONNECT
View tool website
NeuroFeatureExtract
View tool websiteNeurogenPy
Access tool on Github
Access tool in EBRAINS Collaboratory
NeuroM
Access tool on Github
Neuromorphic Computing Job Queue
Access tool on Github
Neuronize v2
View tool website
View tool in EBRAINS Knowledge Graph
NeuroR
Access tool on Github
Neurorobotics Platform
View tool website
Neurorobotics Platform Robot Designer
Access tool on Github
NeuroScheme
View tool website
NeuroScOPeS
Access tool on Github
NeuroSuites
View tool website
NeuroTessMesh
View tool website
NMODL Framework
Access tool on Github
NSuite
Access tool on EBRAINSNutil
Access tool on Github
Document Webpage
ODE-toolbox
View tool website
openMlNDS
Access tool on Github
Access tool in EBRAINS Collaboratory
openMlNDS metadata for TVB-ready data
View tool in EBRAINS Knowledge Graph
Download tool
PCI
Access tool on Github
PIPSA
View tool website
Access tool in EBRAINS Collaboratory
PoSCE
Access tool on Github
Provenance API
View tool website
Access tool in EBRAINS Collaboratory
PyNN
View tool website
Access tool in EBRAINS Collaboratory
Pyramidal Explorer
View tool website
QCAlign software
View tool website
Access tool on Github
QuickNll
Access tool on Github
Quota Manager
Access tool in EBRAINS Collaboratory
RateML
View tool websiteRegion-wise CBPP using the Julich Brain Atlas
View tool publication
RRI Capacity Development Resources
View tool website
rsHRF
View tool website (1)
View tool website (2)
RTNeuron
Access tool on Github
View tool in EBRAINS Knowledge Graph
sbs: Spike-based Sampling
View tool website
Access tool on Github
SDA 7
View tool website (1)
View tool website (2)
Shape & Appearance Modelling
Access tool on Github
siibra-api
Access tool on Github
siibra-explorer
Access tool on Github
siibra-python
Access tool on Github
Single Cell Model (Re)builder Notebook
Access tool on Github
Slurm Plugin for Co-allocation of Compute and Data Resources
Access tool on Github
Access tool in EBRAINS Collaboratory
Snudda
Access tool on GithubSomaSegmenter
Access tool on Github
SpiNNaker
Access tool on Github
Access tool in EBRAINS Collaboratory
SSB toolkit
Access tool on Github (1)
Access tool on Github (2)
Subcellular model building and calibration tool set
Access tool on EBRAINS
Access tool in EBRAINS Collaboratory
Synaptic Events Fitting
Access tool on Github
Synaptic Plasticity Explorer
View tool websiteSynaptic proteome database in SQLite
View tool in EBRAINS Knowledge Graph
Synaptome.db
View tool website
Tide
Access tool on Github
TVB EBRAINS
View tool website
Access tool in EBRAINS Collaboratory
TVB Image Processing Pipeline
Access tool on Github
View tool in EBRAINS Knowledge Graph
TVB Inversion
Access tool on Github
Access tool in EBRAINS Collaboratory
TVB Web App
Access tool on EBRAINS
View tool website
TVB Widgets
Access tool on Github (Widgets)
Access tool on Github (Bucket)
TVB-Multiscale
Access tool on Github
Access tool in EBRAINS Collaboratory
VIOLA
Access tool on Github
Vishnu 1.0
View tool website
Access tool on Github
ViSimpl
View tool website
VisuAlign
Access tool on Github
VMetaFlow
View tool website
Access tool on Github
voluba
View tool website (1)
View tool website (2)
voluba-mriwarp
View tool website Access tool on GithubWebAlign
Access tool on Github
Access tool in EBRAINS Collaboratory
webilastik
View tool website
Access tool in EBRAINS Collaboratory
WebWarp
Access tool on Github
Access tool in EBRAINS Collaboratory
ZetaStitcher
Access tool on Github
TRAMD
Access tool on Github
Access tool in EBRAINS Collaboratory
