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Last modified by graber on 2023/09/28 09:25
From version 48.1
edited by graber
on 2023/04/06 10:08
Change comment: There is no comment for this version
To version 26.1
edited by sarakonradi
on 2021/04/30 09:11
Change comment: There is no comment for this version

Summary

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1 -XWiki.graber
1 +XWiki.sarakonradi
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1 1  (% style="text-align: center;" %)
2 +== Findable. Accessible. User-facing. ==
3 +
4 +(% style="text-align: center;" %)
2 2  === 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 topic, and their documentation links. ===
3 3  
7 +
4 4  === Collaboratory ===
5 5  
6 6  |**[[Collaboratory>>url:https://wiki.ebrains.eu/bin/view/Collabs/the-collaboratory/]]**
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9 9  === Find data ===
10 10  
11 11  |**[[EBRAINS Knowledge Graph>>url:https://kg.ebrains.eu/]]**
12 -A user-driven, data-sharing and data-management infrastructure accelerating scientific progress by providing access to large collections of curated, heterogeneous neuroscience data.|**[[KnowledgeSpace>>url:https://knowledge-space.org/documentation]]**
13 -Encyclopedia and open data access portal for neuroscience that serves as a framework where large-scale neuroscience projects can expose their data to the neuroscience community-at-large.|**[[fairgraph>>url:https://fairgraph.readthedocs.io/en/latest/]]**
14 -Python API for the Human Brain Project Neural Activity Resource, capable of changing, and working with Metadata|
16 +A user-driven, data-sharing and data-management infrastructure accelerating scientific progress by providing access to large collections of curated, heterogeneous neuroscience data.
15 15  
16 16  === Share data ===
17 17  
18 -|**[[Data curation>>url:https://wiki.ebrains.eu/bin/view/Collabs/data-curation ]]**
19 -The place to share your neuroscience data on the EBRAINS platform.|**[[Data publishing>>url:https://ebrains.eu/services/data-knowledge/share-data/guidelines/]]**
20 -The place to submit your dataset for publication along with a manuscript for a peer-reviewed journal.
20 +|**[[KnowledgeSpace>>url:https://knowledge-space.org/documentation]]**
21 +Encyclopedia and open data access portal for neuroscience that serves as a framework where large-scale neuroscience projects can expose their data to the neuroscience community-at-large.|**[[fairgraph>>url:https://fairgraph.readthedocs.io/en/latest/]]**
22 +Python API for the Human Brain Project Neural Activity Resource, capable of changing, and working with Metadata
21 21  
22 22  === Brain atlases ===
23 23  
24 -|**[[PyJuGEx>>url:https://www.fz-juelich.de/inm/inm-1/DE/Forschung/_docs/JuGex/JuGex_node.html]]**
25 -Find a set of differentially expressed genes between two user defined volumes of interest based on JuBrain maps.|**[[Julich-Brain Gene Expression>>url:https://www.fz-juelich.de/inm/inm-1/DE/Forschung/_docs/JuGex/JuGex_node.html]]**
26 -Decoding the chain from genes to cognition requires detailed insights how areas with specific gene activities and microanatomical architectures contribute to brain function and dysfunction.|**[[QuickNII>>url:https://wiki.ebrains.eu/bin/view/Collabs/quicknii-and-visualign]]**
27 -QuickNII is a tool for user guided affine registration (anchoring) of 2D experimental image data, typically high resolution microscopic images, to 3D atlas reference space, facilitating data integration through standardized coordinate systems.|
28 -|**[[siibra-explorer>>url:https://siibra-explorer.readthedocs.io/en/latest/]]**
29 -siibra-explorer is a browser-based viewer for the visual exploration of the EBRAINS atlases at microscopic detail, as well as the discovery of related multimodal data features. It is tightly integrated with the EBRAINS Knowledge Graph, allowing the seamless querying of semantically and spatially anchored datasets.|**[[siibra-python>>url:https://siibra-python.readthedocs.io/en/latest/]]**
30 -siibra-python is a comprehensive Python client providing access to EBRAINS atlases and offering an easy and well-structured way to include maps, reference templates, region definitions and linked datasets in reproducible programmatic workflows.|**[[VoluBA>>url:https://voluba-user-doc.apps-dev.hbp.eu/]]**
31 -VoluBA (Volumetric Brain Anchoring) is an online service for anchoring of high-resolution volumes of interest from imaging experiments to very large reference volumes.|
26 +|**[[Interactive Atlas Viewer>>url:https://interactive-viewer.readthedocs.io/en/latest/]]**
27 +Interactive Atlas Viewer is a frontend module wrapping around nehuba.It provides additional features, such as metadata integration, data visualisation and a robust plugin system.|**[[JuGEx>>url:https://www.fz-juelich.de/inm/inm-1/DE/Forschung/_docs/JuGex/JuGex_node.html]]**
28 +JuGEx links cytoarchitecture and gene expression to investigate multilevel human brain organization.|**[[Nutil>>url:https://wiki.ebrains.eu/bin/view/Collabs/quint]]**
29 +Nutil aims to both simplify and streamline the mechanism of pre-and-post processing 2D brain image data from mouse and rat.|
30 +|**[[PyJuGex>>url:https://www.fz-juelich.de/inm/inm-1/DE/Forschung/_docs/JuGex/JuGex_node.html]]**
31 +JuGEx is an integrated framework of the AllenBrain and JuBrain atlases for statistical analysis of differential gene expression in the adult human brain.|**[[QuickNII>>url:https://www.nitrc.org/docman/?group_id=1341]]**
32 +QuickNII is a tool for user guided affine registration (anchoring) of 2D experimental image data, typically high resolution microscopic images, to 3D atlas reference space, facilitating data integration through standardized coordinate systems.|**[[VoluBA>>url:https://voluba-user-doc.apps-dev.hbp.eu/]]**
33 +volumetric brain anchoring|
32 32  
33 33  === Data analysis ===
34 34  
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37 37  A Python package for working with the Human Brain Project Model Validation Framework.|**[[Neo>>url:https://neo.readthedocs.io/en/stable/]]**
38 38  an object model for handling electrophysiology data in multiple formats.|
39 39  |**[[Neo Viewer>>url:https://neo-viewer.brainsimulation.eu/]]**
40 -Django/Angular software for graphing neural activity data (analog signals, spike trains etc.) read from Neo files.|**[[NeuroScheme>>url:https://neuroscheme-documentation.readthedocs.io/en/latest/]]**
41 -NeuroScheme is a tool for navigating, exploring, creating and interacting with NeuroScience data using abstract, schematic or expressive representations.|**[[NeuroTessMesh>>url:https://neurotessmesh-documentation.readthedocs.io/en/latest/]]**
42 -A Tool for the Generation and Visualization of Neuron Meshes and Adaptive On-the-Fly Refinement|
43 -|**[[Nutil>>url:https://wiki.ebrains.eu/bin/view/Collabs/quint]]**
44 -Nutil aims to both simplify and streamline the mechanism of pre-and-post processing 2D brain image data from mouse and rat.|**[[ViSimpl>>url:https://visimpl-documentation.readthedocs.io/en/latest/]]**
45 -ViSimpl integrates a set of visualization and interaction tools that provide a multi-view visual analysis of brain simultation data.|**[[ilastik>>url:http://ilastik.org/documentation/index.html]]**
46 -ilastik is a simple, user-friendly tool for interactive image classification, segmentation and analysis.|
42 +Django/Angular software for graphing neural activity data (analog signals, spike trains etc.) read from Neo files.|**[[ViSimpl>>url:https://visimpl-documentation.readthedocs.io/en/latest/]]**
43 +ViSimpl integrates a set of visualization and interaction tools that provide a multi-view visual analysis of brain simultation data.
47 47  
48 48  === Simulation ===
49 49  
50 -|[[**Arbor**>>url:https://docs.arbor-sim.org]]
47 +|**[[Arbor>>url:https://arbor.readthedocs.io/en/v0.5/]]**
51 51  Arbor is a library for implementing performance portable network simulations of multi-compartment neuron models.|**[[BluePyMM>>url:https://bluepymm.readthedocs.io/en/latest/index.html]]**
52 52  Model Management Python Library|**[[BluePyOpt>>url:https://bluepyopt.readthedocs.io/en/latest/]]**
53 53  BluePyOpt is an extensible framework for data-driven model parameter optimisation that wraps and standardizes several existing open-source tools.|
54 -
55 55  |**[[CoreNeuron>>url:https://github.com/BlueBrain/CoreNeuron]]**
56 56  CoreNeuron implements the core functionalities of the NEURON simulator targeting high efficiency when using millions of threads.|**[[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]]**
57 57  The Hodgkin-Huxley Neuron Builder web-application is a use case that allows the user to interactively go through the entire single cell model building pipeline.|**[[Multi-scale brain simulation with TVB-NEST>>url:https://github.com/the-virtual-brain/tvb-multiscale/tree/master/docs]]**
58 58  Simulate multi-scale brain network models with TVB and NEST.|
59 -
60 -|**[[NEST>>url:https://nest-simulator.readthedocs.io]]**
55 +|**[[NEST>>url:https://nest-simulator.readthedocs.io/en/v2.20.0/]]**
61 61  NEST is a simulator for spiking neural network models that focuses on the dynamics, size and structure of neural systems rather than on the exact morphology of individual neurons|**[[NEST Desktop>>url:https://nest-desktop.readthedocs.io]]**
62 62  A web-based GUI application for NEST simulator.|**[[NESTML>>url:https://nestml.readthedocs.io/en/latest/]]**
63 63  A domain specific language to describe neuron models in NEST.|
64 -
65 65  |**[[NEURON>>url:https://www.neuron.yale.edu/neuron/docs]]**
66 66  Simulation enviroment for building and using computational models of neurons and networks of neurons|**[[NeuroM>>url:https://neurom.readthedocs.io/en/v1.4.17/]]**
67 -NeuroM is a Python toolkit for the analysis and processing of neuron morphologies.|**[[PyNN>>url:http://neuralensemble.org/docs/PyNN/]]**
68 -A Python package for simulator-independent specification of neuronal network models.|
69 -
61 +NeuroM is a Python toolkit for the analysis and processing of neuron morphologies.|**[[NeuroScheme>>url:https://neuroscheme-documentation.readthedocs.io/en/latest/]]**
62 +NeuroScheme is a tool for navigating, exploring, creating and interacting with NeuroScience data using abstract, schematic or expressive representations.|
63 +|**[[NeuroTessMesh>>url:https://neurotessmesh-documentation.readthedocs.io/en/latest/]]**
64 +A Tool for the Generation and Visualization of Neuron Meshes and Adaptive On-the-Fly Refinement|**[[PyNN>>url:http://neuralensemble.org/docs/PyNN/]]**
65 +A Python package for simulator-independent specification of neuronal network models.|**[[TVB Brain Atlas Viewer>>url:None]]**
66 +An interactive viewer of human brain function.|
70 70  |**[[TVB image processing pipeline>>url:https://ebrains.eu/]]**
71 71  This pipeline combines the BIDS Apps mrtrix3_connectome, fmriprep and tvb_converter into a neuroimaging pipeline to compute structural and functional connectomes from MRI data.|**[[TVB-HPC>>url:https://github.com/the-virtual-brain/tvb-hpc/tree/master/docs]]**
72 72  This is a Python package for generating code for parameter sweeps and Bayesian inversion.|**[[The Virtual Brain>>url:http://docs.thevirtualbrain.org/index.html]]**
73 73  "The Virtual Brain" Project (TVB Project) has the purpose of offering modern tools to the Neurosciences community, for computing, simulating and analyzing functional and structural data of human brains, brains modeled at the level of population of neurons.|
74 -
75 75  |**[[The Virtual Brain Web-App>>url:http://docs.thevirtualbrain.org/]]**
76 -The Virtual Brain Web App at HBP.|**[[NeuroR>>url:https://elephant.readthedocs.io/en/latest/index.html]]**NeuroR is a collection of tools to repair morphologies.|**[[Local Field Potentials in Python>>url:https://lfpy.readthedocs.io/]]**LFPy is a Python module for the calculation of extracellular potentials and magnetic signals from activity in multicompartment neuron and network models.|
72 +The Virtual Brain Web App at HBP.
77 77  
78 -|**[[Snudda>>url:https://github.com/Hjorthmedh/Snudda/wiki]]**Snudda is a tool that allows the user to place neurons within multiple volumes, then performs touch detection to infer where putative synapses are based on reconstructed neuron morphologies.
79 -
80 -
81 81  === Neurorobotics ===
82 82  
83 83  |**[[Neurorobotics Platform>>url:https://www.neurorobotics.net/Documentation/nrp/user_manual/index.html]]**
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86 86  === Medical data analytics ===
87 87  
88 88  |**[[Bids Manager & Pipeline>>url:https://github.com/Dynamap/BIDS_Manager]]**
89 -Bids Manager is a tool that allows various users to easily import and explore databases in BIDS format. Bids Pipeline, an extension of Bids Manager, allows to launch process on BIDS database.|**[[Brainstorm>>url:https://neuroimage.usc.edu/brainstorm/Introduction]]**Brainstorm is a collaborative, open-source application dedicated to the analysis of brain recordings:
90 -MEG, EEG, fNIRS, ECoG, depth electrodes and multiunit electrophysiology.|**[[HiBoP>>url:https://collab.humanbrainproject.eu/#/collab/78584/nav/531987?state=uuid%3Df72e40d9-a0bf-4ab7-8a27-462911107c5f]]**3D visualization software for intracranial EEG.|
82 +Bids Manager is a tool that allows various users to easily import and explore databases in BIDS format. Bids Pipeline, an extension of Bids Manager, allows to launch process on BIDS database.|**[[HiBoP>>url:https://collab.humanbrainproject.eu/#/collab/78584/nav/531987?state=uuid%3Df72e40d9-a0bf-4ab7-8a27-462911107c5f]]**
83 +3D visualization software for intracranial EEG.
91 91  
92 -|**[[ImaGIN>>url:https://wiki.ebrains.eu/bin/view/Collabs/quicknii-and-visualign]]**SPM-based Matlab toolbox for processing intracranial EEG recordings (SEEG and ECOG).|**[[IntranAt Electrodes>>url:https://intranat.readthedocs.io/]]**A software to visualize electrodes implantation on image data and prepare database for group studies.
93 -
94 94  === Neuromorphic computing ===
95 95  
96 -|**[[BrainScaleS>>url:https://wiki.ebrains.eu/bin/view/Collabs/neuromorphic/BrainScaleS/]]**
87 +|**[[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]]**
97 97  Neural network emulation in 1000x accelerated biological real-time.|**[[Neuromorphic Platform Python client>>url:https://electronicvisions.github.io/hbp-sp9-guidebook/]]**
98 -Client software for the Human Brain Project Neuromorphic Computing Platform.|**[[SpiNNaker Jupyter Service>>url:https://spinnakermanchester.github.io/common_pages/5.0.0/How_to_use_Jupyter_notebooks_on_SpiNNaker.pdf]]**
89 +Client software for the Human Brain Project Neuromorphic Computing Platform.|**[[SpiNNaker Jupyter Service>>url:http://spinnakermanchester.github.io/common_pages/5.0.0/How_to_use_Jupyter_notebooks_on_SpiNNaker.pdf]]**
99 99  Jupyter notebook service running next to the SpiNNaker 1Million machine in Manchester.|
100 100  |**[[SpiNNaker Local Boards>>url:https://spinnakermanchester.github.io/]]**
101 101  Physical SpiNNaker boards that are loaned to or owned by individuals or groups, but not connected to the SpiNNaker 1Million machine in Manchester.|**[[SpiNNaker Machine>>url:https://spinnakermanchester.github.io/]]**
102 102  The SpiNNaker 1Million core machine in Manchester consisting of 1200 SpiNNaker boards.|**[[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]]**
103 103  The SpiNNaker batch execution service allowing Neuromorphic Computing Platform jobs to be run on the SpiNNaker 1Million machine in Manchester.|
104 -|**[[SpiNNaker Software>>url:https://spinnakermanchester.github.io/]]**
105 -The Software used to compile and execute Neural Networks described in PyNN on SpiNNaker hardware.|**[[SpiNNaker-NRP integration>>url:https://spinnakermanchester.github.io/common_pages/5.0.0/How_to_use_Jupyter_notebooks_on_SpiNNaker.pdf]]**
95 +|**[[SpiNNaker Software>>url:http://spinnakermanchester.github.io/]]**
96 +The Software used to compile and execute Neural Networks described in PyNN on SpiNNaker hardware.|**[[SpiNNaker-NRP integration>>url:http://spinnakermanchester.github.io/common_pages/5.0.0/How_to_use_Jupyter_notebooks_on_SpiNNaker.pdf]]**
106 106  Allows the NRP to use SpiNNaker as a brain for robotic simulations.
107 107  
108 108  === High-performance computing ===
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114 114  
115 115  === Support ===
116 116  
117 -Contact the [[EBRAINS High Level Support Team (HLST)>>https://ebrains.eu/support/]] if you have questions about our tools, services and workflows.
108 +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.