Version 28.2 by graber on 2021/06/15 08:47
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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 ===
9 |**[[Collaboratory>>url:https://wiki.ebrains.eu/bin/view/Collabs/the-collaboratory/]]**
10 Workspaces in the Cloud for your research, development, documentation, and collaboration.
11 === Find data ===
12 |**[[EBRAINS Knowledge Graph>>url:https://kg.ebrains.eu/]]**
graber 28.2 13 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]]**
14 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/]]**
15 Python API for the Human Brain Project Neural Activity Resource, capable of changing, and working with Metadata|
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graber 24.1 17 === Share data ===
graber 28.2 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.
graber 20.1 21 === Brain atlases ===
graber 22.1 22 |**[[Interactive Atlas Viewer>>url:https://interactive-viewer.readthedocs.io/en/latest/]]**
graber 28.1 23 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.|**[[QuickNII>>url:https://wiki.ebrains.eu/bin/view/Collabs/quicknii-and-visualign]]**
graber 24.1 24 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/]]**
graber 28.1 25 volumetric brain anchoring|
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graber 22.1 27 === Data analysis ===
graber 24.1 28 |**[[Elephant>>url:https://elephant.readthedocs.io/en/latest/index.html]]**
graber 21.1 29 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 30 A Python package for working with the Human Brain Project Model Validation Framework.|**[[Neo>>url:https://neo.readthedocs.io/en/stable/]]**
graber 28.1 31 an object model for handling electrophysiology data in multiple formats.|
graber 24.1 32 |**[[Neo Viewer>>url:https://neo-viewer.brainsimulation.eu/]]**
graber 28.1 33 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/]]**
34 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/]]**
35 A Tool for the Generation and Visualization of Neuron Meshes and Adaptive On-the-Fly Refinement|
36 |**[[Nutil>>url:https://wiki.ebrains.eu/bin/view/Collabs/quint]]**
37 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/]]**
38 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]]**
39 ilastik is a simple, user-friendly tool for interactive image classification, segmentation and analysis.|
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graber 24.1 41 === Simulation ===
42 |**[[Arbor>>url:https://arbor.readthedocs.io/en/v0.5/]]**
43 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]]**
44 Model Management Python Library|**[[BluePyOpt>>url:https://bluepyopt.readthedocs.io/en/latest/]]**
graber 28.1 45 BluePyOpt is an extensible framework for data-driven model parameter optimisation that wraps and standardizes several existing open-source tools.|
46 |**[[BrainScaleS>>url:https://wiki.ebrains.eu/bin/view/Collabs/neuromorphic/BrainScaleS/]]**
47 Neural network emulation in 1000x accelerated biological real-time.|**[[CoreNeuron>>url:https://github.com/BlueBrain/CoreNeuron]]**
graber 24.1 48 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 28.1 49 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.|
50 |**[[Multi-scale brain simulation with TVB-NEST>>url:https://github.com/the-virtual-brain/tvb-multiscale/tree/master/docs]]**
51 Simulate multi-scale brain network models with TVB and NEST.|**[[NEST>>url:https://nest-simulator.readthedocs.io/en/v2.20.0/]]**
graber 24.1 52 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 28.1 53 A web-based GUI application for NEST simulator.|
54 |**[[NESTML>>url:https://nestml.readthedocs.io/en/latest/]]**
55 A domain specific language to describe neuron models in NEST.|**[[NEURON>>url:https://www.neuron.yale.edu/neuron/docs]]**
graber 24.1 56 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 28.1 57 NeuroM is a Python toolkit for the analysis and processing of neuron morphologies.|
58 |**[[PyNN>>url:http://neuralensemble.org/docs/PyNN/]]**
59 A Python package for simulator-independent specification of neuronal network models.|**[[SpiNNaker Software>>url:https://spinnakermanchester.github.io/]]**
60 The Software used to compile and execute Neural Networks described in PyNN on SpiNNaker hardware.|**[[TVB image processing pipeline>>url:https://ebrains.eu/]]**
61 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.|
62 |**[[TVB-HPC>>url:https://github.com/the-virtual-brain/tvb-hpc/tree/master/docs]]**
graber 24.1 63 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 28.1 64 "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.|**[[The Virtual Brain Web-App>>url:http://docs.thevirtualbrain.org/]]**
65 The Virtual Brain Web App at HBP.|
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graber 24.1 67 === Neurorobotics ===
68 |**[[Neurorobotics Platform>>url:https://www.neurorobotics.net/Documentation/nrp/user_manual/index.html]]**
graber 28.1 69 The NRP supports closed-loop neuroscience and embodied AI by connecting brains and bodies in simulation.|**[[SpiNNaker-NRP integration>>url:https://spinnakermanchester.github.io/common_pages/5.0.0/How_to_use_Jupyter_notebooks_on_SpiNNaker.pdf]]**
70 Allows the NRP to use SpiNNaker as a brain for robotic simulations.
graber 21.1 71 === Medical data analytics ===
graber 22.1 72 |**[[Bids Manager & Pipeline>>url:https://github.com/Dynamap/BIDS_Manager]]**
73 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]]**
74 3D visualization software for intracranial EEG.
75 === Neuromorphic computing ===
graber 28.1 76 |**[[BrainScaleS>>url:https://wiki.ebrains.eu/bin/view/Collabs/neuromorphic/BrainScaleS/]]**
graber 23.1 77 Neural network emulation in 1000x accelerated biological real-time.|**[[Neuromorphic Platform Python client>>url:https://electronicvisions.github.io/hbp-sp9-guidebook/]]**
graber 28.1 78 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]]**
79 Jupyter notebook service running next to the SpiNNaker 1Million machine in Manchester.|
graber 23.1 80 |**[[SpiNNaker Local Boards>>url:https://spinnakermanchester.github.io/]]**
81 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/]]**
82 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 28.1 83 The SpiNNaker batch execution service allowing Neuromorphic Computing Platform jobs to be run on the SpiNNaker 1Million machine in Manchester.|
84 |**[[SpiNNaker Software>>url:https://spinnakermanchester.github.io/]]**
85 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 86 Allows the NRP to use SpiNNaker as a brain for robotic simulations.
graber 24.1 87 === High-performance computing ===
88 |**[[Fenix>>url:https://fenix-ri.eu/about-fenix/documentation]]**
89 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]]**
90 A plugin for SLURM used for the co-allocation of compute and data resources.|**[[Unicore>>url:https://www.unicore.eu/documentation/]]**
graber 28.1 91 A set of software components for federated access to high-performance compute and data resources.|
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sarakonradi 9.1 94 === Support ===
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sarakonradi 27.1 96 Contact the [[EBRAINS High Level Support Team (HLST)>>https://ebrains.eu/support/]] if you have questions about our tools, services and workflows.