Filter tools:
AngoraPy Read more
https://github.com/ccnmaastricht/angorapy https://wiki.ebrains.eu/bin/view/Collabs/angorapy/AnonvMl
https://github.com/iTCf/anonymi
Arbor
https://arbor-sim.org
https://wiki.ebrains.eu/bin/view/Collabs/technical-coordination/EBRAINS%20components/Arbor/
Arbor GUI
BIDS Extension Proposal Computational Model Specifications
https://github.com/bids-standard/bids-specification/pull/967
https://docs.google.com/document/d/1NT1ERdL41oz3NibIFRyVQ2iR8xH-dKY-lRCB4eyVeRo/edit#heading=h.mqkmyp254xh6
BioBB
https://mmb.irbbarcelona.org/biobb/
https://wiki.ebrains.eu/bin/view/Collabs/biobb
BioExcel-CV19
https://bioexcel-cv19.bsc.es/#/
https://wiki.ebrains.eu/bin/view/Collabs/molecular-tools-bioexcel-covid19
BioNAR
https://bioconductor.org/packages/release/bioc/html/BioNAR.html
BlueNaaS-SingleCell
https://github.com/BlueBrain/BlueNaaS-SingleCell
https://blue-naas-bsp-epfl.apps.hbp.eu/
BlueNaaS-Subcellular
https://subcellular-bsp-epfl.apps.hbp.eu/home
https://wiki.ebrains.eu/bin/view/Collabs/subcellular-modeling-and-simulation/
BluePyEfe
https://github.com/BlueBrain/BluePyEfe
BluePyMM
https://github.com/BlueBrain/BluePyMM
BluePyOpt
https://github.com/BlueBrain/BluePyOpt
Brain Cockpit
https://alexisthual.github.io/brain-cockpit/
https://wiki.ebrains.eu/bin/view/Collabs/documentation/tools-and-services-documentation/
BrainScaleS
https://ebrains.eu/service/neuromorphic-computing
Brayns
https://github.com/BlueBrain/Brayns/
Brion
https://github.com/BlueBrain/Brion/
BSB
https://bsb.readthedocs.io/en/latest/
https://ebrains.eu/service/brain-scaffold-builder/
bsp-usecase-wizard
https://ebrains-cls-interactive.github.io/online-use-cases.html
https://wiki.ebrains.eu/bin/view/Collabs/technical-coordination/EBRAINS%20components/bsp-usecase-wizard/?srid=pRTH2UKb
BVEP
https://github.com/ins-amu/BVEP
https://wiki.ebrains.eu/bin/view/Collabs/bayesian-virtual-epileptic-patient
CGMD Platform
https://molsim.sci.univr.it/mermaid/begin.php
CLSI Service Account
https://humanbrainproject.github.io/hbp-bsp-service-account/
CNS-ligands
https://mmb.irbbarcelona.org/webdev/slim/CNS/public/
https://wiki.ebrains.eu/bin/view/Collabs/molecular-tools-central-nervous-system
Cobrawap
https://cobrawap.readthedocs.io
https://wiki.ebrains.eu/bin/view/Collabs/slow-wave-analysis-pipeline
Collaboratory Bucket service
https://wiki.ebrains.eu/bin/view/Collabs/the-collaboratory/Documentation%20Bucket/
https://wiki.ebrains.eu/bin/view/Collabs/the-collaboratory/Documentation%20Bucket/
Collaboratory Drive
https://wiki.ebrains.eu/bin/view/Collabs/the-collaboratory/Documentation%20Drive/
https://wiki.ebrains.eu/bin/view/Collabs/the-collaboratory/Documentation%20Drive/
Collaboratory IAM
https://wiki.ebrains.eu/bin/view/Collabs/the-collaboratory/Documentation%20IAM/
https://wiki.ebrains.eu/bin/view/Collabs/the-collaboratory/Documentation%20IAM/
Collaboratory Lab
https://wiki.ebrains.eu/bin/view/Collabs/the-collaboratory/Documentation%20Lab/
https://wiki.ebrains.eu/bin/view/Collabs/the-collaboratory/Documentation%20Lab/
Collaboratory Office
https://wiki.ebrains.eu/bin/view/Collabs/the-collaboratory/Documentation%20Office/
https://wiki.ebrains.eu/bin/view/Collabs/the-collaboratory/Documentation%20Office/
Collaboratory Wiki
https://wiki.ebrains.eu/bin/view/Collabs/the-collaboratory/Documentation%20Wiki/
https://wiki.ebrains.eu/bin/view/Collabs/the-collaboratory/Documentation%20Wiki/
CoreNEURON
https://nrn.readthedocs.io/en/8.2.2/coreneuron/index.html
CxSvstem2
https://github.com/VisualNeuroscience-UH/CxSystem2
DeepSlice
www.deepslice.org
EBRAINS Ethics & Society Toolkit
https://ebrainsethicsandsociety.tekno.dk/
https://drive.ebrains.eu/library/dc1cf9e7-575e-4522-bd40-e95b38fed5a2/SGA3%20WP9/T9.2%20RRI/Sub-Task%209.2.3%20Long-term%20implications%20-%20foresight
EBRAINS Image Service
https://wiki.ebrains.eu/bin/view/Collabs/hbp-image-service-user-guide
https://wiki.ebrains.eu/bin/view/Collabs/hbp-image-service-user-guide
EBRAINS Knowledge Graph
https://kg.ebrains.eu
EDI Toolkit
www.edi-toolkit.org
eFEL
https://github.com/BlueBrain/eFEL/
Elephant
https://python-elephant.org
https://tutorials.python-elephant.org
FAConstructor
https://github.com/3d-pli/FAConstructor
fairgraph
https://github.com/HumanBrainProject/fairgraph
Fast sampling with neuromorphic hardware
https://github.com/unibe-cns/variational-quantum-ground-states
https://github.com/electronicvisions/
fastPLl
https://github.com/3d-pli/fastpli
Feed-forward LFP-MEG estimator from mean-field models
https://wiki.ebrains.eu/bin/view/Collabs/estimation-of-lfp-and-meg-signals-from-m/
https://wiki.ebrains.eu/bin/view/Collabs/estimation-of-lfp-and-meg-signals-from-m/
FIL
https://github.com/WCHN/Label-Training
https://figshare.com/ndownloader/files/31699187
FMRALIGN
https://github.com/Parietal-INRIA/fmralign
Foa3D
https://github.com/lens-biophotonics/Foa3D
Frites
https://github.com/brainets/frites
https://github.com/brainets/frites/
gridspeccer
https://github.com/gridspeccer/gridspeccer
Hai-Cgp
https://github.com/Happy-Algorithms-League/hal-cgp
Health Data Cloud
https://www.healthdatacloud.eu/
https://wiki.ebrains.eu/bin/view/Collabs/health-data-cloud/
Hodgkin-Huxley Neuron Builder
HPC Job Proxy
https://wiki.ebrains.eu/bin/view/Collabs/ebrains-hpc-job-proxy
https://wiki.ebrains.eu/bin/view/Collabs/ebrains-hpc-job-proxy
HPC Status Monitor
Human Intracerebral EEG Platform
https://www.humanbrainproject.eu/en/science-development/focus-areas/medical-data-analytics/
ebrains.eu
Hybrid MM/CG Webserver
https://mmcg.grs.kfa-juelich.de/
https://wiki.ebrains.eu/bin/view/Collabs/hybrid-mmcg-webserver/Webserver
Insite
https://github.com/VRGroupRWTH/insite
Interactive Brain Atlas Viewer
https://www.brainsimulation.org/atlasweb/
https://search.kg.ebrains.eu/instances/21091719-b4a3-4d0b-815f-1bd0c51b0126
JuGEx
https://www.fz-juelich.de/en/inm/inm-1/expertise/tools-services-and-research-data/jugex
https://github.com/INM-1-FZJ-Cytoarchitecture/jugex
KnowledgeSpace
https://knowledge-space.org/
https://wiki.ebrains.eu/bin/view/Collabs/technical-coordination/EBRAINS%20components/KnowledgeSpace/
L2L
https://wiki.ebrains.eu/bin/view/Collabs/l2l-hyper-parameter-optimization/
Leveltlab/SpectralSegmentation
LFPy
https://lfpy.readthedocs.io/
https://wiki.ebrains.eu/bin/view/Collabs/technical-coordination/EBRAINS%20components/LFPy/
libsonata
https://github.com/BlueBrain/libsonata
Live Papers
https://ebrains.eu/service/live-papers
https://live-papers.brainsimulation.eu
Livre
https://github.com/BlueBrain/Livre/
https://search.kg.ebrains.eu/instances/01eec0a0-ba2c-4e3a-b394-2c44f02464d1
LocaliZoom
https://github.com/Neural-Systems-at-UIO/LocaliZoom
https://wiki.ebrains.eu/bin/view/Collabs/quint-demo
MD-IFP
https://github.com/HITS-MCM/MD-IFP
https://wiki.ebrains.eu/bin/view/Collabs/protein-ligand-unbinding-rates/
MEDUSA
https://framagit.org/cpoupon/gkg
MeshView
https://github.com/Neural-Systems-at-UIO/MeshView-for-Brain-Atlases
https://wiki.ebrains.eu/bin/view/Collabs/quint-demo
MIP
https://ebrains.eu/service/medical-informatics-platform
ebrains.eu
Model Validation Service
https://github.com/HumanBrainProject/hbp-validation-framework
https://wiki.ebrains.eu/bin/view/Collabs/model-validation
Model Validation Test Suites
MoDEL-CNS
https://mmb.irbbarcelona.org/MoDEL-CNS/#/
https://wiki.ebrains.eu/bin/view/Collabs/molecular-tools-model-cns
Modular Science
https://github.com/multiscale-cosim/EBRAINS-cosim
https://wiki.ebrains.eu/bin/view/Collabs/technical-coordination/EBRAINS%20components/Multiscale%20co-simulation%20framework/
Monsteer
https://github.com/BlueBrain/Monsteer/
MorphlO
https://github.com/BlueBrain/MorphIO/
Morphology alignment tool
https://slice-aligner.apps.hbp.eu/
https://neuroinformatics.nl/HBP/slice-aligner/
MorphTool
https://github.com/BlueBrain/morph-tool
Multi-Brain
https://github.com/WTCN-computational-anatomy-group/mb
Multi-lmage-OSD
https://github.com/Neural-Systems-at-UIO/Multi-Image-OSd
MUSIC
https://github.com/INCF/MUSIC/wiki
https://wiki.ebrains.eu/bin/view/Collabs/technical-coordination/EBRAINS%20components/MUSIC/
NEAT
https://neatdend.readthedocs.io/en/latest/
Neo
https://neuralensemble.org/neo
Neo Viewer
https://neo-viewer.brainsimulation.eu
NEST Desktop
https://nest-desktop.readthedocs.io
https://wiki.ebrains.eu/bin/view/Collabs/nest-desktop/
NEST Simulator
https://nest-simulator.org
NESTML
https://nestml.readthedocs.org/
NetPyNE
http://netpyne.org
https://ebrains-cls-interactive.github.io/online-use-cases.html#/small_circuit_insilico_experiments
NEURO-CONNECT
https://ssl.biomax.de/NeuroCONNECT/
NeuroFeatureExtract
NeurogenPy
https://github.com/javiegal/neurogenpy
https://wiki.ebrains.eu/bin/view/Collabs/technical-coordination/EBRAINS%20components/Neurogenpy/
NeuroM
https://github.com/BlueBrain/neurom
Neuromorphic Computing Job Queue
https://github.com/HumanBrainProject/hbp_neuromorphic_platform
Neuronize v2
https://vg-lab.es/neuronizev2/
https://search.kg.ebrains.eu/?category=Software&q=neuronize#a485ec6a-f0ac-418b-8175-2c0415511c8d
NeuroR
https://github.com/BlueBrain/NeuroR/
Neurorobotics Platform
https://neurorobotics.net
Neurorobotics Platform Robot Designer
https://github.com/HBPNeurorobotics/BlenderRobotDesigner
NeuroScheme
https://vg-lab/neuroscheme
NeuroScOPeS
https://gitlab.rrze.fau.de/ProModell/neuroscopes_sim-pipeline.git
NeuroSuites
https://neurosuites.com/
NeuroTessMesh
https://vg-lab.es/neurotessmesh
NMODL Framework
https://github.com/BlueBrain/nmodl
NSuite
Nutil
https://github.com/Neural-Systems-at-UIO/nutil
https://nutil.readthedocs.io
ODE-toolbox
https://ode-toolbox.readthedocs.org/
openMlNDS
https://github.com/HumanBrainProject/openMINDS
https://wiki.ebrains.eu/bin/view/Collabs/openminds/
openMlNDS metadata for TVB-ready data
https://search.kg.ebrains.eu/instances/4edef2ff-e653-40a5-a222-0a5759fdaaaf
https://drive.ebrains.eu/f/6ac926e0e2ba4f22ae12/
PCI
https://github.com/thierrynieus/PerturbationalComplexityIndex
PIPSA
https://pipsa.h-its.org
https://wiki.ebrains.eu/bin/view/Collabs/computation-of-protein-association-rates
PoSCE
https://github.com/mrahim/posce
Provenance API
https://prov.brainsimulation.eu/docs
https://wiki.ebrains.eu/bin/view/Collabs/migration-faq/Requirements/Provenance
PyNN
https://neuralensemble.org/PyNN
https://wiki.ebrains.eu/bin/view/Collabs/pynn-resources
Pyramidal Explorer
https://vg-lab.es/pyramidalexplorer
QCAlign software
https://www.nitrc.org/projects/qcalign
https://github.com/Neural-Systems-at-UIO/QCAlign
QuickNll
https://github.com/Neural-Systems-at-UIO/QuickNII
Quota Manager
https://wiki.ebrains.eu/bin/view/Collabs/quota-management
https://wiki.ebrains.eu/bin/view/Collabs/quota-management
RateML
Region-wise CBPP using the Julich Brain Atlas
https://doi.org/10.25493/D4HH-VJJ
RRI Capacity Development Resources
https://www.humanbrainproject.eu/en/science-development/ethics-and-society/ethics-society-training-resources/
rsHRF
http://bids-apps.neuroimaging.io/rsHRF/
https://www.nitrc.org/projects/rshrf
RTNeuron
https://github.com/BlueBrain/RTNeuron/
https://search.kg.ebrains.eu/instances/9cf09bbc-5daa-4063-a834-02ef7ec4c16b
sbs: Spike-based Sampling
https://zenodo.org/record/3686015#.ZEahrexBxyq
https://github.com/electronicvisions/spike-based-sampling/tree/v1.8.2
SDA 7
https://mcm.h-its.org/sda7/
https://websda.h-its.org
Shape & Appearance Modelling
https://github.com/WTCN-computational-anatomy-group/Shape-Appearance-Model
siibra-api
https://github.com/fzj-inm1-bda/siibra-api
siibra-explorer
https://github.com/fzj-inm1-bda/siibra-explorer
siibra-python
https://github.com/fzj-inm1-bda/siibra-python/
Single Cell Model (Re)builder Notebook
https://ebrains-cls-interactive.github.io/online-use-cases.html#/single_cell_modeling
Slurm Plugin for Co-allocation of Compute and Data Resources
https://github.com/HumanBrainProject/coallocation-slurm-plugin
https://wiki.ebrains.eu/bin/view/Collabs/technical-coordination/EBRAINS%20components/SLURM/
Snudda
SomaSegmenter
https://github.com/lens-biophotonics/SomaSegmenter
SpiNNaker
https://spinnakermanchester.github.io/
https://wiki.ebrains.eu/bin/view/Collabs/neuromorphic
SSB toolkit
https://github.com/rribeiro-sci/SSBtoolkit
https://gitlab.ebrains.eu/rribeiro/SSBtoolkit
Subcellular model building and calibration tool set
https://www.ebrains.eu/tools/subcellular-model-building-and-calibration-tool-set
https://wiki.ebrains.eu/bin/view/Collabs/subcellular-modeling-and-simulation/
Synaptic Events Fitting
https://ebrains-cls-interactive.github.io/online-use-cases.html
Synaptic Plasticity Explorer
Synaptic proteome database in SQLite
https://search.kg.ebrains.eu/instances/Dataset/f9590f64-b8f9-4d70-a966-7af3b60ea2ae
Synaptome.db
http://bioconductor.org/packages/release/data/annotation/html/synaptome.db.html
Tide
https://github.com/BlueBrain/Tide/
TVB EBRAINS
https://www.thevirtualbrain.org/
https://wiki.ebrains.eu/bin/view/Collabs/user-story-tvb/
TVB Image Processing Pipeline
https://github.com/BrainModes/tvb-pipeline
https://search.kg.ebrains.eu/instances/399d3689-d359-4268-ab4b-c8f764512cf5
TVB Inversion
https://github.com/the-virtual-brain/tvb-inversion
https://wiki.ebrains.eu/bin/view/Collabs/tvb-inversion/
TVB Web App
https://ebrains.eu/service/the-virtual-brain/
https://thevirtualbrain.apps.hbp.eu/user/profile
TVB Widgets
https://github.com/the-virtual-brain/tvb-widgets
https://github.com/the-virtual-brain/tvb-ext-bucket
TVB-Multiscale
https://github.com/the-virtual-brain/tvb-multiscale
https://wiki.ebrains.eu/bin/view/Collabs/the-virtual-brain-multiscale/
VIOLA
http://hbpvis.github.io/VIOLA/
http://hbpvis.github.io/VIOLA/
Vishnu 1.0
https://www.vg-lab.es/vishnu
https://github.com/gmrvvis/Vishnu
ViSimpl
https://vg-lab.es/visimpl
VisuAlign
https://github.com/Neural-Systems-at-UIO/VisuAlign
VMetaFlow
https://www.vg-lab.es/vmetaflow
https://github.com/VMetaFlow/VMetaFlow
voluba
https://voluba.apps.hbp.eu/#/
https://voluba.readthedocs.io/en/latest/
voluba-mriwarp
WebAlign
https://github.com/Neural-Systems-at-UIO/WebAlign
https://wiki.ebrains.eu/bin/view/Collabs/quint-demo
webilastik
https://app.ilastik.org
https://wiki.ebrains.eu/bin/view/Collabs/quint-demo/webilastik
WebWarp
https://github.com/Neural-Systems-at-UIO/WebWarp
https://wiki.ebrains.eu/bin/view/Collabs/quint-demo
ZetaStitcher
https://github.com/lens-biophotonics/ZetaStitcher/
TRAMD
https://github.com/HITS-MCM/tauRAMD
https://wiki.ebrains.eu/bin/view/Collabs/protein-ligand-unbinding-rates/
