Last modified by graber on 2023/09/28 09:25
From version 9.1
edited by sarakonradi
on 2021/04/27 10:27
Change comment: There is no comment for this version
To version 1.3
edited by graber
on 2021/04/22 09:24
Change comment: There is no comment for this version

Summary

Details

Page properties
Title
... ... @@ -1,1 +1,1 @@
1 -Tools and services documentation 2
1 +Tools and services documentation
Author
... ... @@ -1,1 +1,1 @@
1 -XWiki.sarakonradi
1 +XWiki.graber
Content
... ... @@ -1,28 +1,56 @@
1 -(% style="text-align: center;" %)
2 -== Findable. Accessible. User-facing. ==
3 -
4 -(% style="text-align: center;" %)
5 -=== Welcome to the single entry point to user-level documentation for EBRAINS tools and services. Here you can find a list of EBRAINS offerings sorted by Service Category (SC) and their documentation links. ===
6 -
7 -
8 -| [[fairgraph>>url:https://fairgraph.readthedocs.io/en/latest/]] | [[Arbor>>url:https://arbor.readthedocs.io/en/v0.5/]] |
9 -| [[Bids Manager & Pipeline>>url:https://github.com/Dynamap/BIDS_Manager]] | [[BluePyMM>>url:https://bluepymm.readthedocs.io/en/latest/index.html]] | [[BluePyOpt>>url:https://bluepyopt.readthedocs.io/en/latest/]] |
10 -| [[BrainScaleS>>url:https://flagship.kip.uni-heidelberg.de/jss/FileExchange/D9.7.1_Neuromorphic_Platform_Specification_-_public_version.pdf?fID=1887&s=qqdXDg6HuX3&uID=65]] | [[CoreNeuron>>url:https://github.com/BlueBrain/CoreNeuron]] | [[Elephant>>url:https://elephant.readthedocs.io/en/latest/index.html]] |
11 -| [[Fenix>>url:https://fenix-ri.eu/about-fenix/documentation]] | [[HBP Validation Framework - Python Client>>url:http://hbp-validation-client.readthedocs.io/]] | [[HiBoP>>url:https://collab.humanbrainproject.eu/#/collab/78584/nav/531987?state=uuid%3Df72e40d9-a0bf-4ab7-8a27-462911107c5f]] |
12 -| [[Hodgkin Huxley Neuron Builder>>url:https://humanbrainproject.github.io/hbp-sp6-guidebook/online_usecases/single_cell_building/hippocampus/p1_hh_neuron_builder/p1_hh_neuron_builder.html]] | [[Insite beta>>url:https://vrgrouprwth.github.io/insite/]] | [[Interactive Atlas Viewer>>url:https://interactive-viewer.readthedocs.io/en/latest/]] |
13 -| [[JuGEx>>url:https://www.fz-juelich.de/inm/inm-1/DE/Forschung/_docs/JuGex/JuGex_node.html]] | [[KnowledgeSpace>>url:https://knowledge-space.org/documentation]] | [[Multi-scale brain simulation with TVB-NEST>>url:https://github.com/the-virtual-brain/tvb-multiscale/tree/master/docs]] |
14 -| [[NEST Desktop>>url:https://nest-desktop.readthedocs.io]] | [[NEST>>url:https://nest-simulator.readthedocs.io/en/v2.20.0/]] | [[NESTML>>url:https://nestml.readthedocs.io/en/latest/]] |
15 -| [[NEURON>>url:https://www.neuron.yale.edu/neuron/docs]] | [[Neo>>url:https://neo.readthedocs.io/en/stable/]] | [[Neo Viewer>>url:https://neo-viewer.brainsimulation.eu/]] |
16 -| [[NeuroM>>url:https://neurom.readthedocs.io/en/v1.4.17/]] | [[NeuroScheme>>url:https://neuroscheme-documentation.readthedocs.io/en/latest/]] | [[NeuroTessMesh>>url:https://neurotessmesh-documentation.readthedocs.io/en/latest/]] |
17 -| [[Neuromorphic Platform Python client>>url:https://electronicvisions.github.io/hbp-sp9-guidebook/]] | [[Neurorobotics Platform>>url:https://www.neurorobotics.net/Documentation/nrp/user_manual/index.html]] | [[Nutil>>url:https://wiki.ebrains.eu/bin/view/Collabs/quint]] |
18 -| [[ODE-toolbox>>url:https://ode-toolbox.readthedocs.io/en/master/]] | [[PyJuGex>>url:https://www.fz-juelich.de/inm/inm-1/DE/Forschung/_docs/JuGex/JuGex_node.html]] | [[PyNN>>url:http://neuralensemble.org/docs/PyNN/]] |
19 -| [[QuickNII>>url:https://www.nitrc.org/docman/?group_id=1341]] | [[SLURM plugin for the co-allocation of compute and data resources>>url:https://github.com/HumanBrainProject/coallocation-slurm-plugin/blob/master/README.md]] | [[SpiNNaker Jupyter Service>>url:http://spinnakermanchester.github.io/common_pages/5.0.0/How_to_use_Jupyter_notebooks_on_SpiNNaker.pdf]] |
20 -| [[SpiNNaker Local Boards>>url:https://spinnakermanchester.github.io/]] | [[SpiNNaker Machine>>url:https://spinnakermanchester.github.io/]] | [[SpiNNaker Remote Access>>url:https://flagship.kip.uni-heidelberg.de/jss/FileExchange/D9.7.1_Neuromorphic_Platform_Specification_-_public_version.pdf?fID=1887&s=qqdXDg6HuX3&uID=65]] |
21 -| [[SpiNNaker Software>>url:http://spinnakermanchester.github.io/]] | [[SpiNNaker-NRP integration>>url:http://spinnakermanchester.github.io/common_pages/5.0.0/How_to_use_Jupyter_notebooks_on_SpiNNaker.pdf]] | [[TVB Brain Atlas Viewer>>url:#]] |
22 -| [[TVB image processing pipeline>>url:https://drive.google.com/file/d/1VcXf3GX3KoihF4UzJQXzuGL4XWoqj5Jr/view]] | [[TVB-HPC>>url:https://github.com/the-virtual-brain/tvb-hpc/tree/master/docs]] | [[The Virtual Brain>>url:http://docs.thevirtualbrain.org/index.html]] |
23 -| [[The Virtual Brain Web-App>>url:http://docs.thevirtualbrain.org/]] | [[Unicore>>url:https://www.unicore.eu/documentation/]] | [[ViSimpl>>url:https://visimpl-documentation.readthedocs.io/en/latest/]] |
24 -| [[VoluBA>>url:https://voluba-user-doc.apps-dev.hbp.eu/]] |
25 -
26 -=== Support ===
27 -
28 -In SGA3, the High Level Support Team (HLST, T4.13) is responsible for coordinating documentation efforts in EBRAINS. Contact the [[HLST>>https://ebrains.eu/support/]] if you have questions about this page or our tools, services and workflows.
1 +| | | |
2 +| --- | --- | --- |
3 +| [ fairgraph 0.5.1](https://fairgraph.readthedocs.io/en/latest/) | [3D Slicer 4.10.2](https://www.slicer.org/wiki/Documentation/4.10) |
4 +| [3D Structure Tensor Analysis ](https://github.com/lens-biophotonics/st_fibre_analysis_hbp) | [3DSlicer 4.10.1](https://github.com/Slicer/Slicer) | [3DSpineMFE 1.0_RC4](https://github.com/ComputationalIntelligenceGroup/3DSpineMFE/blob/master/README.md) |
5 +| [3DSpineS 0.1](https://github.com/ComputationalIntelligenceGroup/3DSpineS/blob/master/README.Rmd) | [3DSynapsesSA 1.2](https://neurosuites.com/static/neurosuite/docs/3DSynapsesSA/3DSynapsesSA_users_guide_v1.1.pdf) | [Android app for multimodal data acquisition from wearables 1.0](https://c4science.ch/diffusion/9555/browse/master/README.md) |
6 +| [Arbor v0.2.2](https://arbor.readthedocs.io/en/latest/index.html) | [Arbor v0.5](https://arbor.readthedocs.io/en/v0.5/) | [BasalUnit 1.0.4](#) |
7 +| [Bids Manager & Pipeline 0.2.5](https://github.com/Dynamap/BIDS_Manager) | [BluePyMM 0.6.65](https://bluepymm.readthedocs.io/en/latest/index.html) | [BluePyOpt 1.9.3](https://bluepyopt.readthedocs.io/en/latest/) |
8 +| [Brain Simulation Platform Service Account 1.0.0](https://humanbrainproject.github.io/hbp-bsp-service-account/) | [Brayns 1.0.0](http://bluebrain.github.io/Brayns-1.0/index.html) | [Brion 3.2.0](#) |
9 +| [Central Nervous System bioactive compounds beta](#) |[ChemBioServer 2](https://chembioserver.vi-seem.eu/Tutorial.php) | [Clint Explorer 0.1](https://gmrv.es/gmrvvis/clintexplorer/) |
10 +| [Connectivity-based Psychometric Prediction Framework 1.1](https://github.com/inm7/cbpp/blob/master/README.md) | [Connectomic Composition Predictor (2020-03-03)](https://github.com/ntimonid/Connectomic-Composition-Predictor-CCP-/blob/master/PrimaryLibrary.ipynb) | [CoreNeuron 0.16](https://github.com/BlueBrain/CoreNeuron) |
11 +| [Cube 4.4.4](https://apps.fz-juelich.de/scalasca/releases/cube/4.4/docs/guide/html/) | [CxSystem2 1.0](https://cxsystem2.readthedocs.io/en/latest/) | [DC Explorer 1.0](#) |
12 +| [Data Catalogue 1.6.0](https://github.com/LREN-CHUV/data-catalog-setup/blob/master/README.md) | [Demics 1.0.0-alpha](https://github.com/FZJ-INM1-BDA/demics/blob/master/README.md) | [EBRAINS Knowledge Graph v2.3 ](https://kg.ebrains.eu/) |
13 +| [Elephant 0.6.4](https://elephant.readthedocs.io/en/v0.6.4/index.html) | [Elephant 0.7.0](https://elephant.readthedocs.io/en/latest/index.html) | [Event-Based Heart Rate Estimation from ECG Signals 1.0](https://c4science.ch/source/Event_based_gQRS/browse/master/README.md) |
14 +| [ExploreASL 1.3.0](https://docs.google.com/document/d/10OpHiXTxDUtNar-FAQQeq9unS9j0zC4y0X86okK0t_U/edit#heading=h.gjdgxs) | [Extra-P 3.0](https://www.scalasca.org/scalasca/software/extra-p/documentation.html) | [Extrae 3.7.1](https://tools.bsc.es/doc/html/extrae/index.html) |
15 +| [FAConstructor 1.7.0](https://iffmd.fz-juelich.de/s/HJTaAO9aN#) | [Factorisation-based Image Labelling 0.1.1](#) | [Feature Extraction Graphical User Interface 1.4](https://humanbrainproject.github.io/hbp-sp6-guidebook/online_usecases/trace_analysis/efel_gui/efel_gui.html) |
16 +| [Frites - Framework for information theoretical analysis of electrophysiological data and statistics 0.3.8](https://brainets.github.io/frites/index.html) | [Gabaclassifier 1.0](https://github.com/ComputationalIntelligenceGroup/gabaclassifier/blob/master/README.md) | [Ginkgo/GlobalTractography](#) |
17 +| [Ginkgo/MEDUSA 1.0](#) |[HBP Validation Framework - Python Client 0.5.28](http://hbp-validation-client.readthedocs.io/) | [HiBoP 2.2.3a](https://collab.humanbrainproject.eu/#/collab/78584/nav/531987?state=uuid%3Df72e40d9-a0bf-4ab7-8a27-462911107c5f) |
18 +| [HippoUnit 1.3.5](https://hippounit.readthedocs.io/) | [Hodgkin Huxley Neuron Builder 1.3.0](https://humanbrainproject.github.io/hbp-sp6-guidebook/online_usecases/single_cell_building/hippocampus/p1_hh_neuron_builder/p1_hh_neuron_builder.html) | [Human Brain Project HPC Status Monitor 1.0.0](https://humanbrainproject.github.io/hbp-sp6-guidebook/hpc_status_monitor/hpc_status_monitor.html#) |
19 +| [ImageJ 2.0.0-rc-71](https://github.com/imagej/imagej) | [ImageJ 2.0.0-rc-72](https://github.com/imagej/imagej/blob/master/README.md) | [InDiProv 2.0](https://github.com/HBPVIS/InDiProv/blob/master/README.md) |
20 +| [Insite beta](https://vrgrouprwth.github.io/insite/) | [Interactive Atlas Viewer 2.2.3](https://interactive-viewer.readthedocs.io/en/latest/) | [JuGEx 1.0](https://www.fz-juelich.de/inm/inm-1/DE/Forschung/_docs/JuGex/JuGex_node.html) |
21 +| [JupyterLab v1.2.4](https://jupyterlab.readthedocs.io/en/stable/index.html) | [KnowledgeSpace v3.0.0](https://knowledge-space.org/documentation) | [LePetitPrince 0.01a](#) |
22 +| [Lempel Ziv Perturbational Complexity Index 1.0](https://github.com/iTCf/PCIcalc) | [Livre 0.8.0](https://bluebrain.github.io/Livre-0.8/index.html) | [LocaliZoom 0.9](https://collab.humanbrainproject.eu/#/collab/5401/nav/42133) |
23 +| [MIP Microservice Infrastructure 4.0.2](https://github.com/HBPMedical/mip-microservices-infrastructure/tree/master/docs) | [MRIcroGL v1.2.20200331](https://www.nitrc.org/plugins/mwiki/index.php/mricrogl:MainPage) | [MRIcron v1.0.20190902](https://people.cas.sc.edu/rorden/mricron/index.html) |
24 +| [MRtrix3 3.0.2](https://mrtrix.readthedocs.io/en/3.0.2/) | [MRtrix3_connectome 0.4.2](https://github.com/BIDS-Apps/MRtrix3_connectome/blob/0.4.2/README.md) | [MSPViz v0.2.6](https://github.com/gmrvvis/MSPViz/blob/master/README.md) |
25 +| [MeLVin 1.0](https://www.youtube.com/watch?v=-gNbR7fnV9Q) | [MeshView 0.9](https://www.nitrc.org/plugins/mwiki/index.php/meshview:MainPage) | [MorphoUnit 1.0.4](#) |
26 +| [Multi-Brain 0.1.0](https://github.com/WTCN-computational-anatomy-group/diffeo-segment/blob/v0.1.0/manual-mb.pdf) | [Multi-scale brain simulation with TVB-NEST 1.0.1](https://github.com/the-virtual-brain/tvb-multiscale/tree/master/docs) | [NEST Desktop 2.4.1](https://nest-desktop.readthedocs.io) |
27 +| [NEST Desktop 2.5.0](https://nest-desktop.readthedocs.io) | [NEST Instrumentation App 0.3](https://github.com/compneuronmbu/NESTInstrumentationApp/blob/master/README.md) | [NEST v2.20.0](https://nest-simulator.readthedocs.io/en/v2.20.0/) |
28 +| [NESTML 3.1](https://nestml.readthedocs.io/en/latest/) | [NEURON 7.7.2](https://www.neuron.yale.edu/neuron/docs) | [NMODL Framework 0.2](https://bluebrain.github.io/nmodl/html/index.html) |
29 +| [NSuite 1.0](https://nsuite.readthedocs.io/en/latest/index.html) | [Nehuba - Online visualization of large volumetric brain images alpha](https://github.com/HumanBrainProject/nehuba) | [Neo 0.8.0](https://neo.readthedocs.io/en/stable/) |
30 +| [Neo Viewer 1.0.0](https://neo-viewer.brainsimulation.eu/) | [NetPyNE 0.9.5](http://www.netpyne.org/index.html) | [NetPyNE GUI 0.5.2](https://github.com/MetaCell/NetPyNE-UI/wiki) |
31 +| [NetworkUnit 0.1.1](https://github.com/INM-6/NetworkUnit) | [NeuroM 1.4.17](https://neurom.readthedocs.io/en/v1.4.17/) | [NeuroSTR 0.1](https://computationalintelligencegroup.github.io/neurostr/doc/) |
32 +| [NeuroScheme 0.3](https://neuroscheme-documentation.readthedocs.io/en/latest/) | [NeuroSuites 1.0](https://gitlab.com/mmichiels/neurosuite/-/tree/master/documentation) | [NeuroTessMesh 0.0.1](https://neurotessmesh-documentation.readthedocs.io/en/latest/) |
33 +| [Neurolucida 2019](#) |[Neurolucida Version 2020.1.3](#) | [Neuromorphic Platform Python client 0.8.2](https://electronicvisions.github.io/hbp-sp9-guidebook/) |
34 +| [Neuron Segmentation Tool](https://github.com/lens-biophotonics/neuron_segmentation_model_hbp/tree/master/tensorflow_2.5D_model) | [Neuronize 2.0.0](https://docs.google.com/document/d/1wgXFyhbiehLDr7nEg-jvb9HlIiybbW7U0OCjRGzgWj0/edit?usp=sharing) | [Neurorobotics Platform 3.0](https://www.neurorobotics.net/Documentation/nrp/user_manual/index.html) |
35 +| [Nilearn 0.5.2](http://nilearn.github.io/user_guide.html) | [Nilearn 0.6.2](http://nilearn.github.io/user_guide.html) | [Nutil 0.33](https://www.nitrc.org/plugins/mwiki/index.php/nutil:MainPage) |
36 +| [Nutil 0.403](https://wiki.ebrains.eu/bin/view/Collabs/quint) | [ODE-toolbox v2.0](https://ode-toolbox.readthedocs.io/en/master/) | [OTF2 2.2](http://perftools.pages.jsc.fz-juelich.de/cicd/otf2/docs/otf2-2.2/html/) |
37 +| [PLIViewer 1.2.0](https://devhub.vr.rwth-aachen.de/VR-Group/pli_vis/blob/master/readme.md) | [ParaView 5.8.0](https://www.paraview.org/documentation/) | [Paraver 4.8.2](https://tools.bsc.es/doc/1364.pdf) |
38 +| [PoSCE 0.1a](#) | [PyJuGex 1.0.1alpha](https://www.fz-juelich.de/inm/inm-1/DE/Forschung/_docs/JuGex/JuGex_node.html) | [PyNN 0.9.5](http://neuralensemble.org/docs/PyNN/) |
39 +| [PyramidalExplorer 0.2.0](https://gmrv.es/pyramidalexplorer/) | [QuickNII v2.2](https://www.nitrc.org/docman/?group_id=1341) | [RTNeuron 3.0](https://bluebrain.github.io/RTNeuron-3.0/index.html) |
40 +| [ReMoToo 0.0.2](https://github.com/vg-lab/ReMoToo/blob/v0.0.2/README.md) | [Remote Connection Manager 1.2](https://wiki.u-gov.it/confluence/pages/viewpage.action?pageId=324275042) | [SCAIView-NEURO-2020](https://www.scaiview.com/en/first-steps.html) |
41 +| [SDA: Simulation of Diffusional Association 7.2.4](https://mcm.h-its.org/sda/doc/doc_sda7/doc.html) | [SLURM plugin for the co-allocation of compute and data resources v1.0](https://github.com/HumanBrainProject/coallocation-slurm-plugin/blob/master/README.md) | [SNT 3.1.105](https://imagej.net/SNT) |
42 +| [Scalasca 2.5](https://apps.fz-juelich.de/scalasca/releases/scalasca/2.5/docs/UserGuide.pdf) | [Score-P 6.0](http://scorepci.pages.jsc.fz-juelich.de/scorep-pipelines/docs/scorep-6.0/html/) | [Single Cell Model Builder Notebook 1.1](https://humanbrainproject.github.io/hbp-sp6-guidebook/online_usecases/single_cell_building/hippocampus/build_scm_hbp/build_scm_hbp.html) |
43 +| [Single Cell Model Rebuilder Notebook 1.1](https://humanbrainproject.github.io/hbp-sp6-guidebook/online_usecases/single_cell_building/hippocampus/rebuild_existing/rebuild_scm.html) | [SpectralSegmentation 1.0](https://github.com/Leveltlab/SpectralSegmentation/blob/master/README.md) | [SpykeViewer 0.4.2](https://spyke-viewer.readthedocs.io/en/latest/index.html) |
44 +| [Surf Ice v1.0.20190902](https://www.nitrc.org/plugins/mwiki/index.php/surfice:MainPage) | [Synaptic events fitting Notebook 1.3](https://humanbrainproject.github.io/hbp-sp6-guidebook/online_usecases/trace_analysis/syn_events_fit/syn_events_fit.html#synaptic-events-fitting) | [Synaptic plasticity 0.1](https://collab.humanbrainproject.eu/#/collab/1655/nav/18580) |
45 +| [TVB Brain Atlas Viewer 1.0](#) |[TVB image processing pipeline 1.0](https://drive.google.com/file/d/1VcXf3GX3KoihF4UzJQXzuGL4XWoqj5Jr/view) | [TVB-HPC v1.0-beta](https://github.com/the-virtual-brain/tvb-hpc/tree/master/docs) |
46 +| [The Jupyter Notebook 6.0.2](https://jupyter-notebook.readthedocs.io/en/stable/) | [The Virtual Brain 1.5.8](http://docs.thevirtualbrain.org/index.html) | [The Virtual Brain Web-App 2.0.6](http://docs.thevirtualbrain.org/) |
47 +| [The fast and parallel Virtual Brain 1.0](https://collab.humanbrainproject.eu/#/collab/65304/nav/444404) | [Threading Building Blocks 2019 Update 9](https://software.intel.com/en-us/tbb/documentation) | [Tide 1.5.0](https://bluebrain.github.io/Tide-1.5/index.html) |
48 +| [UG4 4.3.1](http://ug4.github.io/docs/) | [Unicore 8.0.0](https://www.unicore.eu/documentation/) | [VIOLA 2020-01-31](https://github.com/HBPVIS/VIOLA/wiki/VIOLA-User-Manual) |
49 +| [VTK 8.2.0](https://www.kitware.com/products/books/VTKUsersGuide.pdf) | [VTK-m 1.5.0](http://m.vtk.org/images/c/c9/VTKmUsersGuide-1-5.pdf) | [Vaa3D v3.597](https://github.com/Vaa3D/Vaa3D_Wiki/wiki/Vaa3D-Wiki) |
50 +| [Vaa3D v3.601](https://github.com/Vaa3D/Vaa3D_Wiki/wiki/Vaa3D-Wiki) | [ViSimpl 0.1.3](https://visimpl-documentation.readthedocs.io/en/latest/) | [Vishnu 1.0](https://gmrv.es/gmrvvis/vishnu/) |
51 +| [VoluBA (04.01.2020)](https://voluba-user-doc.apps-dev.hbp.eu/) | [Woken 3.0.2](https://github.com/HBPMedical/woken/blob/master/README.md) | [ZetaStitcher 0.5.0](https://lens-biophotonics.github.io/ZetaStitcher/) |
52 +| [deNEST 1.0.1](https://denest.readthedocs.io/en/latest/) | [eFEL 3.0](https://efel.readthedocs.io/en/latest/installation.html#installing-the-c-standalone-library) | [eFELunit 1.1.5](https://github.com/appukuttan-shailesh/eFELunit) |
53 +| [fMRIPrep 20.1.1](https://fmriprep.org/en/stable/) | [fastPLI 0.9.8](https://github.com/3d-pli/fastpli/wiki) | [fmralign 0.0.1](https://parietal-inria.github.io/fmralign-docs/) |
54 +| [hbp-spatial-backend 0.1.0.dev0](https://hbp-spatial-backend.apps.hbp.eu/redoc) | [ilastik 1.3.3](http://ilastik.org/documentation/index.html) | [multipipsa 4.0.2](#) |
55 +| [neurostr 1.0](https://github.com/ComputationalIntelligenceGroup/neurostrr) | [notebooks_review2019](https://github.com/mb-BCA/notebooks_review2019) | [openMINDS metadata for TVB-ready data 1](#) |
56 +| [pyGAlib 1.1.0](https://github.com/gorkazl/pyGAlib/blob/master/README.md) | [pyJUSBB 0.0.1](https://github.com/shahrzadkh/pyJUSBB/wiki) |