Version 26.1 by sarakonradi on 2021/04/30 09:11
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2 == Findable. Accessible. User-facing. ==
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sarakonradi 26.1 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 topic, and their documentation links. ===
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graber 24.1 8 === Collaboratory ===
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graber 24.1 10 |**[[Collaboratory>>url:https://wiki.ebrains.eu/bin/view/Collabs/the-collaboratory/]]**
11 Workspaces in the Cloud for your research, development, documentation, and collaboration.
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graber 24.1 13 === Find data ===
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graber 24.1 15 |**[[EBRAINS Knowledge Graph>>url:https://kg.ebrains.eu/]]**
16 A user-driven, data-sharing and data-management infrastructure accelerating scientific progress by providing access to large collections of curated, heterogeneous neuroscience data.
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graber 24.1 18 === Share data ===
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graber 24.1 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
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graber 20.1 24 === Brain atlases ===
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graber 22.1 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]]**
graber 21.1 28 JuGEx links cytoarchitecture and gene expression to investigate multilevel human brain organization.|**[[Nutil>>url:https://wiki.ebrains.eu/bin/view/Collabs/quint]]**
sarakonradi 25.1 29 Nutil aims to both simplify and streamline the mechanism of pre-and-post processing 2D brain image data from mouse and rat.|
graber 24.1 30 |**[[PyJuGex>>url:https://www.fz-juelich.de/inm/inm-1/DE/Forschung/_docs/JuGex/JuGex_node.html]]**
graber 21.1 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]]**
graber 24.1 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/]]**
sarakonradi 25.1 33 volumetric brain anchoring|
graber 24.1 34
graber 22.1 35 === Data analysis ===
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graber 24.1 37 |**[[Elephant>>url:https://elephant.readthedocs.io/en/latest/index.html]]**
graber 21.1 38 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 24.1 39 A Python package for working with the Human Brain Project Model Validation Framework.|**[[Neo>>url:https://neo.readthedocs.io/en/stable/]]**
sarakonradi 25.1 40 an object model for handling electrophysiology data in multiple formats.|
graber 24.1 41 |**[[Neo Viewer>>url:https://neo-viewer.brainsimulation.eu/]]**
graber 22.1 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/]]**
graber 24.1 43 ViSimpl integrates a set of visualization and interaction tools that provide a multi-view visual analysis of brain simultation data.
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graber 24.1 45 === Simulation ===
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graber 24.1 47 |**[[Arbor>>url:https://arbor.readthedocs.io/en/v0.5/]]**
48 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]]**
49 Model Management Python Library|**[[BluePyOpt>>url:https://bluepyopt.readthedocs.io/en/latest/]]**
sarakonradi 25.1 50 BluePyOpt is an extensible framework for data-driven model parameter optimisation that wraps and standardizes several existing open-source tools.|
graber 24.1 51 |**[[CoreNeuron>>url:https://github.com/BlueBrain/CoreNeuron]]**
52 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]]**
53 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]]**
sarakonradi 25.1 54 Simulate multi-scale brain network models with TVB and NEST.|
graber 24.1 55 |**[[NEST>>url:https://nest-simulator.readthedocs.io/en/v2.20.0/]]**
56 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]]**
57 A web-based GUI application for NEST simulator.|**[[NESTML>>url:https://nestml.readthedocs.io/en/latest/]]**
sarakonradi 25.1 58 A domain specific language to describe neuron models in NEST.|
graber 24.1 59 |**[[NEURON>>url:https://www.neuron.yale.edu/neuron/docs]]**
60 Simulation enviroment for building and using computational models of neurons and networks of neurons|**[[NeuroM>>url:https://neurom.readthedocs.io/en/v1.4.17/]]**
61 NeuroM is a Python toolkit for the analysis and processing of neuron morphologies.|**[[NeuroScheme>>url:https://neuroscheme-documentation.readthedocs.io/en/latest/]]**
sarakonradi 25.1 62 NeuroScheme is a tool for navigating, exploring, creating and interacting with NeuroScience data using abstract, schematic or expressive representations.|
graber 24.1 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]]**
sarakonradi 25.1 66 An interactive viewer of human brain function.|
graber 24.1 67 |**[[TVB image processing pipeline>>url:https://ebrains.eu/]]**
68 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]]**
69 This is a Python package for generating code for parameter sweeps and Bayesian inversion.|**[[The Virtual Brain>>url:http://docs.thevirtualbrain.org/index.html]]**
sarakonradi 25.1 70 "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.|
graber 24.1 71 |**[[The Virtual Brain Web-App>>url:http://docs.thevirtualbrain.org/]]**
72 The Virtual Brain Web App at HBP.
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graber 24.1 74 === Neurorobotics ===
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graber 24.1 76 |**[[Neurorobotics Platform>>url:https://www.neurorobotics.net/Documentation/nrp/user_manual/index.html]]**
77 The NRP supports closed-loop neuroscience and embodied AI by connecting brains and bodies in simulation.
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graber 21.1 79 === Medical data analytics ===
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graber 22.1 81 |**[[Bids Manager & Pipeline>>url:https://github.com/Dynamap/BIDS_Manager]]**
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.
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graber 22.1 85 === Neuromorphic computing ===
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graber 23.1 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]]**
88 Neural network emulation in 1000x accelerated biological real-time.|**[[Neuromorphic Platform Python client>>url:https://electronicvisions.github.io/hbp-sp9-guidebook/]]**
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]]**
sarakonradi 25.1 90 Jupyter notebook service running next to the SpiNNaker 1Million machine in Manchester.|
graber 23.1 91 |**[[SpiNNaker Local Boards>>url:https://spinnakermanchester.github.io/]]**
92 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/]]**
93 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]]**
sarakonradi 25.1 94 The SpiNNaker batch execution service allowing Neuromorphic Computing Platform jobs to be run on the SpiNNaker 1Million machine in Manchester.|
graber 23.1 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]]**
97 Allows the NRP to use SpiNNaker as a brain for robotic simulations.
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graber 24.1 99 === High-performance computing ===
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graber 24.1 101 |**[[Fenix>>url:https://fenix-ri.eu/about-fenix/documentation]]**
102 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]]**
103 A plugin for SLURM used for the co-allocation of compute and data resources.|**[[Unicore>>url:https://www.unicore.eu/documentation/]]**
sarakonradi 25.1 104 A set of software components for federated access to high-performance compute and data resources.|
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sarakonradi 9.1 106 === Support ===
107
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.