Version 75.1 by graber on 2023/09/01 07:54
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graber 32.1 1 (% style="text-align: center;" %)
annedevismes 43.1 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. ===
sarakonradi 9.1 3
graber 32.1 4 === Collaboratory ===
graber 35.1 5
graber 32.1 6 |**[[Collaboratory>>url:https://wiki.ebrains.eu/bin/view/Collabs/the-collaboratory/]]**
graber 24.1 7 Workspaces in the Cloud for your research, development, documentation, and collaboration.
graber 35.1 8
graber 32.1 9 === Find data ===
graber 35.1 10
graber 75.1 11 |(% style="width:33%" %)**[[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.|(% style="width:33%" %)**[[KnowledgeSpace>>https://knowledge-space.org/documentation/#what_is_ks]]**
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.|(% style="width:33%" %)**[[fairgraph>>url:https://fairgraph.readthedocs.io/en/latest/]]**
graber 36.1 14 Python API for the Human Brain Project Neural Activity Resource, capable of changing, and working with Metadata|
graber 28.2 15
graber 32.1 16 === Share data ===
graber 35.1 17
graber 34.1 18 |**[[Data curation>>url:https://wiki.ebrains.eu/bin/view/Collabs/data-curation ]]**
graber 32.1 19 The place to share your neuroscience data on the EBRAINS platform.|**[[Data publishing>>url:https://ebrains.eu/services/data-knowledge/share-data/guidelines/]]**
graber 28.2 20 The place to submit your dataset for publication along with a manuscript for a peer-reviewed journal.
graber 35.1 21
graber 32.1 22 === Brain atlases ===
graber 35.1 23
graber 47.1 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]]**
graber 60.2 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]]**
graber 48.1 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.|
graber 61.1 28
graber 37.1 29 |**[[siibra-explorer>>url:https://siibra-explorer.readthedocs.io/en/latest/]]**
graber 46.1 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/]]**
graber 48.1 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.|
graber 24.1 33
graber 61.1 34 |**[[VisuAlign>>url:https://visualign.readthedocs.io]]**
graber 64.1 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.|**[[WebAlign>>url:https://webalign.readthedocs.io]]**
36 WebAlign is an online tool for spatial registration of histological section images from rodent brains to reference 3D atlases.|**[[WebWarp>>url:https://webwarp.readthedocs.io/en/latest/index.html]]**
graber 65.1 37 WebWarp is an online tool for nonlinear refinement of spatial registration of histological section images from rodent brains to reference 3D atlases.|
graber 61.1 38
graber 32.1 39 === Data analysis ===
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41 |**[[Elephant>>url:https://elephant.readthedocs.io/en/latest/index.html]]**
graber 32.1 42 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/]]**
graber 35.1 43 A Python package for working with the Human Brain Project Model Validation Framework.|**[[Neo>>url:https://neo.readthedocs.io/en/stable/]]**
graber 36.1 44 an object model for handling electrophysiology data in multiple formats.|
graber 55.1 45
graber 35.1 46 |**[[Neo Viewer>>url:https://neo-viewer.brainsimulation.eu/]]**
graber 32.1 47 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/]]**
graber 35.1 48 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/]]**
graber 36.1 49 A Tool for the Generation and Visualization of Neuron Meshes and Adaptive On-the-Fly Refinement|
graber 55.1 50
graber 60.3 51 |**[[Nutil>>url:https://nutil.readthedocs.io/en/latest/]]**
graber 35.1 52 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/]]**
graber 32.1 53 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]]**
graber 36.1 54 ilastik is a simple, user-friendly tool for interactive image classification, segmentation and analysis.|
graber 55.1 55
graber 53.1 56 |**[[Brain-cockpit>>url:https://alexisthual.github.io/brain-cockpit/]]**
graber 54.2 57 Web-based application to explore large fMRI datasets and inter-subject alignments.|**[[Cobrawap>>url:https://cobrawap.readthedocs.io/]]**
graber 55.1 58 Cobrawap is a Python-based, adaptable, and reusable pipeline for analyzing cortical wave activity.|**[[Viziphant>>url:https://viziphant.readthedocs.io/en/latest/index.html]]**
59 Viziphant provides an easy way to generate plots and interactive visualizations of neuroscientific data and analysis results|
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graber 61.1 61 |**[[MeshView>>url:https://meshview-for-brain-atlases.readthedocs.io]]**
62 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/]]**
graber 69.1 63 Web application for viewing of series of high-resolution 2D images that have been anchored to reference atlases.|**[[BluePyEfe>>url:https://bluepyefe.readthedocs.io/en/latest/]]**
graber 67.1 64 BluePyEfe eases the process of reading and extracting electircal features from experimental recordings.|
graber 61.1 65
graber 74.1 66 |(% style="width:33%" %)**[[eFEL: Electrophys Feature Extraction Library>>url:https://efel.readthedocs.io/en/latest]]**
67 Automatically extract eFeatures from time series data recorded from neurons, both in vitro and in silico.|(% style="width:33%" %) |
graber 72.1 68
graber 32.1 69 === Simulation ===
graber 35.1 70
graber 71.1 71 |**[[Arbor>>url:https://docs.arbor-sim.org]]**
graber 69.1 72 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]]**
graber 35.1 73 Model Management Python Library|**[[BluePyOpt>>url:https://bluepyopt.readthedocs.io/en/latest/]]**
graber 36.1 74 BluePyOpt is an extensible framework for data-driven model parameter optimisation that wraps and standardizes several existing open-source tools.|
graber 46.1 75
graber 35.1 76 |**[[CoreNeuron>>url:https://github.com/BlueBrain/CoreNeuron]]**
graber 32.1 77 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]]**
graber 35.1 78 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]]**
graber 36.1 79 Simulate multi-scale brain network models with TVB and NEST.|
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graber 35.1 81 |**[[NEST>>url:https://nest-simulator.readthedocs.io]]**
graber 32.1 82 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]]**
graber 33.1 83 A web-based GUI application for NEST simulator.|**[[NESTML>>url:https://nestml.readthedocs.io/en/latest/]]**
graber 36.1 84 A domain specific language to describe neuron models in NEST.|
graber 46.1 85
graber 35.1 86 |**[[NEURON>>url:https://www.neuron.yale.edu/neuron/docs]]**
87 Simulation enviroment for building and using computational models of neurons and networks of neurons|**[[NeuroM>>url:https://neurom.readthedocs.io/en/v1.4.17/]]**
graber 33.1 88 NeuroM is a Python toolkit for the analysis and processing of neuron morphologies.|**[[PyNN>>url:http://neuralensemble.org/docs/PyNN/]]**
graber 36.1 89 A Python package for simulator-independent specification of neuronal network models.|
graber 46.1 90
graber 35.1 91 |**[[TVB image processing pipeline>>url:https://ebrains.eu/]]**
92 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]]**
graber 32.1 93 This is a Python package for generating code for parameter sweeps and Bayesian inversion.|**[[The Virtual Brain>>url:http://docs.thevirtualbrain.org/index.html]]**
graber 36.1 94 "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.|
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graber 35.1 96 |**[[The Virtual Brain Web-App>>url:http://docs.thevirtualbrain.org/]]**
graber 58.1 97 The Virtual Brain Web App at HBP.|**[[NeuroR>>url:https://neuror.readthedocs.io/]]**
graber 57.1 98 NeuroR is a collection of tools to repair morphologies.|**[[LFPy>>url:https://lfpy.readthedocs.io/]]**
graber 49.1 99 LFPy is a Python module for the calculation of extracellular potentials and magnetic signals from activity in multicompartment neuron and network models.|
graber 46.1 100
graber 49.1 101 |**[[Snudda>>url:https://github.com/Hjorthmedh/Snudda/wiki]]**
graber 54.1 102 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]]**
graber 60.1 103 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/]]**
graber 60.2 104 A C++ / Python API for reading SONATA circuit files.|
sarakonradi 25.1 105
graber 64.1 106 |**[[Brain Scaffold Builder>>url:https://bsb.readthedocs.io/]]**
graber 65.1 107 The BSB is a framework for reconstructing and simulating multi-paradigm neuronal network models. It removes much of the repetitive work associated with writing the required code and lets you focus on the parts that matter. It helps write organized, well-parametrized and explicit code understandable and reusable by your peers.|**[[InSite>>url:https://vrgrouprwth.github.io/insite/]]**
graber 66.1 108 Insite provides a middleware that enables users to acquire data from NEST, Abror and TVB via the in-transit paradigm.|**[[Subcellular model building and calibration toolset>>url:https://github.com/icpm-kth]]**
109 Tools for data-driven building of subcellular biochemical signaling pathway models, including interoperable modules for model building, calibration, and model analysis.|
graber 64.1 110
graber 32.1 111 === Neurorobotics ===
graber 35.1 112
graber 32.1 113 |**[[Neurorobotics Platform>>url:https://www.neurorobotics.net/Documentation/nrp/user_manual/index.html]]**
graber 33.1 114 The NRP supports closed-loop neuroscience and embodied AI by connecting brains and bodies in simulation.
graber 35.1 115
graber 32.1 116 === Medical data analytics ===
graber 35.1 117
graber 32.1 118 |**[[Bids Manager & Pipeline>>url:https://github.com/Dynamap/BIDS_Manager]]**
graber 49.1 119 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]]**
120 Brainstorm is a collaborative, open-source application dedicated to the analysis of brain recordings:
121 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]]**
122 3D visualization software for intracranial EEG.|
graber 35.1 123
graber 49.1 124 |**[[ImaGIN>>url:https://wiki.ebrains.eu/bin/view/Collabs/quicknii-and-visualign]]**
graber 50.1 125 SPM-based Matlab toolbox for processing intracranial EEG recordings (SEEG and ECOG).|**[[IntranAt Electrodes>>url:https://intranat.readthedocs.io/]]**
graber 54.1 126 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]]**
graber 54.2 127 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.|
graber 45.1 128
graber 54.1 129 |**[[Human Intracerebral EEG Platform (HIP)>>url:https://hip-infrastructure.github.io/build/html/index.html]]**
graber 54.2 130 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.
graber 54.1 131
graber 32.1 132 === Neuromorphic computing ===
graber 35.1 133
graber 32.1 134 |**[[BrainScaleS>>url:https://wiki.ebrains.eu/bin/view/Collabs/neuromorphic/BrainScaleS/]]**
135 Neural network emulation in 1000x accelerated biological real-time.|**[[Neuromorphic Platform Python client>>url:https://electronicvisions.github.io/hbp-sp9-guidebook/]]**
136 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]]**
graber 36.1 137 Jupyter notebook service running next to the SpiNNaker 1Million machine in Manchester.|
graber 32.1 138 |**[[SpiNNaker Local Boards>>url:https://spinnakermanchester.github.io/]]**
139 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/]]**
140 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]]**
graber 36.1 141 The SpiNNaker batch execution service allowing Neuromorphic Computing Platform jobs to be run on the SpiNNaker 1Million machine in Manchester.|
graber 32.1 142 |**[[SpiNNaker Software>>url:https://spinnakermanchester.github.io/]]**
143 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]]**
graber 23.1 144 Allows the NRP to use SpiNNaker as a brain for robotic simulations.
graber 35.1 145
graber 32.1 146 === High-performance computing ===
graber 35.1 147
graber 32.1 148 |**[[Fenix>>url:https://fenix-ri.eu/about-fenix/documentation]]**
149 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]]**
150 A plugin for SLURM used for the co-allocation of compute and data resources.|**[[Unicore>>url:https://www.unicore.eu/documentation/]]**
graber 36.1 151 A set of software components for federated access to high-performance compute and data resources.|
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graber 32.1 153 === Support ===
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graber 32.1 155 Contact the [[EBRAINS High Level Support Team (HLST)>>https://ebrains.eu/support/]] if you have questions about our tools, services and workflows.