Version 62.1 by graber on 2023/06/15 07:14
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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
4 === Collaboratory ===
5
6 |**[[Collaboratory>>url:https://wiki.ebrains.eu/bin/view/Collabs/the-collaboratory/]]**
7 Workspaces in the Cloud for your research, development, documentation, and collaboration.
8
9 === Find data ===
10
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|
15
16 === Share data ===
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.
21
22 === Brain atlases ===
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://quicknii.readthedocs.io]]**
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
29 |**[[siibra-explorer>>url:https://siibra-explorer.readthedocs.io/en/latest/]]**
30 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/]]**
31 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/]]**
32 VoluBA (Volumetric Brain Anchoring) is an online service for anchoring of high-resolution volumes of interest from imaging experiments to very large reference volumes.|
33
34 |**[[VisuAlign>>url:https://visualign.readthedocs.io]]**
35 VisuAlign is a tool for applying user-guided nonlinear refinements (inplane) to an existing, affine 2D-to-3D registration, such as created using QuickNII.| | |
36
37 === Data analysis ===
38
39 |**[[Elephant>>url:https://elephant.readthedocs.io/en/latest/index.html]]**
40 Elephant is an open-source Python library for the analysis of neurophysiology data, using Neo data structures.|**[[HBP Validation Framework - Python Client>>url:http://hbp-validation-client.readthedocs.io/]]**
41 A Python package for working with the Human Brain Project Model Validation Framework.|**[[Neo>>url:https://neo.readthedocs.io/en/stable/]]**
42 an object model for handling electrophysiology data in multiple formats.|
43
44 |**[[Neo Viewer>>url:https://neo-viewer.brainsimulation.eu/]]**
45 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/]]**
46 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/]]**
47 A Tool for the Generation and Visualization of Neuron Meshes and Adaptive On-the-Fly Refinement|
48
49 |**[[Nutil>>url:https://nutil.readthedocs.io/en/latest/]]**
50 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/]]**
51 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]]**
52 ilastik is a simple, user-friendly tool for interactive image classification, segmentation and analysis.|
53
54 |**[[Brain-cockpit>>url:https://alexisthual.github.io/brain-cockpit/]]**
55 Web-based application to explore large fMRI datasets and inter-subject alignments.|**[[Cobrawap>>url:https://cobrawap.readthedocs.io/]]**
56 Cobrawap is a Python-based, adaptable, and reusable pipeline for analyzing cortical wave activity.|**[[Viziphant>>url:https://viziphant.readthedocs.io/en/latest/index.html]]**
57 Viziphant provides an easy way to generate plots and interactive visualizations of neuroscientific data and analysis results|
58
59 |**[[MeshView>>url:https://meshview-for-brain-atlases.readthedocs.io]]**
60 MeshView is a web application for real-time 3D display of surface mesh data representing structural parcellations from volumetric atlases, such as the Waxholm Space Atlas of the Sprague Dawley Rat Brain.|**[[LocaliZoom>>url:https://localizoom.readthedocs.io/en/latest/]]**
61 Web application for viewing of series of high-resolution 2D images that have been anchored to reference atlases.| |
62
63 === Simulation ===
64
65 |[[**Arbor**>>url:https://docs.arbor-sim.org]]
66 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]]**
67 Model Management Python Library|**[[BluePyOpt>>url:https://bluepyopt.readthedocs.io/en/latest/]]**
68 BluePyOpt is an extensible framework for data-driven model parameter optimisation that wraps and standardizes several existing open-source tools.|
69
70 |**[[CoreNeuron>>url:https://github.com/BlueBrain/CoreNeuron]]**
71 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]]**
72 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]]**
73 Simulate multi-scale brain network models with TVB and NEST.|
74
75 |**[[NEST>>url:https://nest-simulator.readthedocs.io]]**
76 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]]**
77 A web-based GUI application for NEST simulator.|**[[NESTML>>url:https://nestml.readthedocs.io/en/latest/]]**
78 A domain specific language to describe neuron models in NEST.|
79
80 |**[[NEURON>>url:https://www.neuron.yale.edu/neuron/docs]]**
81 Simulation enviroment for building and using computational models of neurons and networks of neurons|**[[NeuroM>>url:https://neurom.readthedocs.io/en/v1.4.17/]]**
82 NeuroM is a Python toolkit for the analysis and processing of neuron morphologies.|**[[PyNN>>url:http://neuralensemble.org/docs/PyNN/]]**
83 A Python package for simulator-independent specification of neuronal network models.|
84
85 |**[[TVB image processing pipeline>>url:https://ebrains.eu/]]**
86 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]]**
87 This is a Python package for generating code for parameter sweeps and Bayesian inversion.|**[[The Virtual Brain>>url:http://docs.thevirtualbrain.org/index.html]]**
88 "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.|
89
90 |**[[The Virtual Brain Web-App>>url:http://docs.thevirtualbrain.org/]]**
91 The Virtual Brain Web App at HBP.|**[[NeuroR>>url:https://neuror.readthedocs.io/]]**
92 NeuroR is a collection of tools to repair morphologies.|**[[LFPy>>url:https://lfpy.readthedocs.io/]]**
93 LFPy is a Python module for the calculation of extracellular potentials and magnetic signals from activity in multicompartment neuron and network models.|
94
95 |**[[Snudda>>url:https://github.com/Hjorthmedh/Snudda/wiki]]**
96 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.|**[[BlueNaaS-Subcellular>>url:https://subcellular-bsp-epfl.apps.hbp.eu/static/docs.html]]**
97 BlueNaaS-Subcellular is designed as a web based environment for the creation and simulation of reaction-diffusion models.|**[[libsonata>>url:https://libsonata.readthedocs.io/en/stable/]]**
98 A C++ / Python API for reading SONATA circuit files.|
99
100 === Neurorobotics ===
101
102 |**[[Neurorobotics Platform>>url:https://www.neurorobotics.net/Documentation/nrp/user_manual/index.html]]**
103 The NRP supports closed-loop neuroscience and embodied AI by connecting brains and bodies in simulation.
104
105 === Medical data analytics ===
106
107 |**[[Bids Manager & Pipeline>>url:https://github.com/Dynamap/BIDS_Manager]]**
108 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]]**
109 Brainstorm is a collaborative, open-source application dedicated to the analysis of brain recordings:
110 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]]**
111 3D visualization software for intracranial EEG.|
112
113 |**[[ImaGIN>>url:https://wiki.ebrains.eu/bin/view/Collabs/quicknii-and-visualign]]**
114 SPM-based Matlab toolbox for processing intracranial EEG recordings (SEEG and ECOG).|**[[IntranAt Electrodes>>url:https://intranat.readthedocs.io/]]**
115 A software to visualize electrodes implantation on image data and prepare database for group studies.|**[[Medical Informatics Platform (MIP)>>url:https://github.com/HBPMedical/mip-docs]]**
116 The MIP is an open-source platform enabling federated data analysis in a secure environment for centers interested in initiating or joining disease-oriented federations with the aim of analyzing large-scale distributed clinical datasets.|
117
118 |**[[Human Intracerebral EEG Platform (HIP)>>url:https://hip-infrastructure.github.io/build/html/index.html]]**
119 The HIP is a state-of-the-art open-source platform, offering integrated tools and workflows for optimized collection, storage, sharing, processing and analysis of multiscale Human intracerebral EEG data.
120
121 === Neuromorphic computing ===
122
123 |**[[BrainScaleS>>url:https://wiki.ebrains.eu/bin/view/Collabs/neuromorphic/BrainScaleS/]]**
124 Neural network emulation in 1000x accelerated biological real-time.|**[[Neuromorphic Platform Python client>>url:https://electronicvisions.github.io/hbp-sp9-guidebook/]]**
125 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]]**
126 Jupyter notebook service running next to the SpiNNaker 1Million machine in Manchester.|
127 |**[[SpiNNaker Local Boards>>url:https://spinnakermanchester.github.io/]]**
128 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/]]**
129 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]]**
130 The SpiNNaker batch execution service allowing Neuromorphic Computing Platform jobs to be run on the SpiNNaker 1Million machine in Manchester.|
131 |**[[SpiNNaker Software>>url:https://spinnakermanchester.github.io/]]**
132 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]]**
133 Allows the NRP to use SpiNNaker as a brain for robotic simulations.
134
135 === High-performance computing ===
136
137 |**[[Fenix>>url:https://fenix-ri.eu/about-fenix/documentation]]**
138 Delivering e-infrastructure services federated as the Fenix Infrastructure.|**[[SLURM plugin for the co-allocation of compute and data resources>>url:https://github.com/HumanBrainProject/coallocation-slurm-plugin/blob/master/README.md]]**
139 A plugin for SLURM used for the co-allocation of compute and data resources.|**[[Unicore>>url:https://www.unicore.eu/documentation/]]**
140 A set of software components for federated access to high-performance compute and data resources.|
141
142 === Support ===
143
144 Contact the [[EBRAINS High Level Support Team (HLST)>>https://ebrains.eu/support/]] if you have questions about our tools, services and workflows.