Version 16.1 by sarakonradi on 2021/04/27 15:14
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2 == Findable. Accessible. User-facing. ==
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sarakonradi 16.1 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 Service Category (SC), and their documentation links. ===
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sarakonradi 16.1 8 | [[fairgraph>>url:https://fairgraph.readthedocs.io/en/latest/]]
9 Python API for the Human Brain Project Neural Activity Resource, capable of changing, and working with Metadata | [[Arbor>>url:https://arbor.readthedocs.io/en/v0.5/]]
graber 15.1 10 Arbor is a library for implementing performance portable network simulations of multi-compartment neuron models. |
sarakonradi 16.1 11 | [[Bids Manager & Pipeline>>url:https://github.com/Dynamap/BIDS_Manager]]
12 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. | [[BluePyMM>>url:https://bluepymm.readthedocs.io/en/latest/index.html]]
13 Model Management Python Library | [[BluePyOpt>>url:https://bluepyopt.readthedocs.io/en/latest/]]
graber 15.1 14 BluePyOpt is an extensible framework for data-driven model parameter optimisation that wraps and standardizes several existing open-source tools. |
sarakonradi 16.1 15 | [[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]] | [[CoreNeuron>>url:https://github.com/BlueBrain/CoreNeuron]]
16 CoreNeuron implements the core functionalities of the NEURON simulator targeting high efficiency when using millions of threads. | [[Elephant>>url:https://elephant.readthedocs.io/en/latest/index.html]]
graber 15.1 17 Elephant is an open-source Python library for the analysis of neurophysiology data, using Neo data structures. |
sarakonradi 16.1 18 | [[Fenix>>url:https://fenix-ri.eu/about-fenix/documentation]] | [[HBP Validation Framework - Python Client>>url:http://hbp-validation-client.readthedocs.io/]]
19 A Python package for working with the Human Brain Project Model Validation Framework. | [[HiBoP>>url:https://collab.humanbrainproject.eu/#/collab/78584/nav/531987?state=uuid%3Df72e40d9-a0bf-4ab7-8a27-462911107c5f]]
graber 15.1 20 3D visualization software for intracranial EEG. |
sarakonradi 16.1 21 | [[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]]
22 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. | [[Insite beta>>url:https://vrgrouprwth.github.io/insite/]]
23 Insite provides live access to running neuronal simulations for in-transit visualization and analysis. | [[Interactive Atlas Viewer>>url:https://interactive-viewer.readthedocs.io/en/latest/]]
graber 15.1 24 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. |
sarakonradi 16.1 25 | [[JuGEx>>url:https://www.fz-juelich.de/inm/inm-1/DE/Forschung/_docs/JuGex/JuGex_node.html]]
26 JuGEx links cytoarchitecture and gene expression to investigate multilevel human brain organization. | [[KnowledgeSpace>>url:https://knowledge-space.org/documentation]]
27 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. | [[Multi-scale brain simulation with TVB-NEST>>url:https://github.com/the-virtual-brain/tvb-multiscale/tree/master/docs]]
graber 15.1 28 Simulate multi-scale brain network models with TVB and NEST. |
sarakonradi 16.1 29 | [[NEST Desktop>>url:https://nest-desktop.readthedocs.io]]
30 A web-based GUI application for NEST simulator. | [[NEST>>url:https://nest-simulator.readthedocs.io/en/v2.20.0/]]
31 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 | [[NESTML>>url:https://nestml.readthedocs.io/en/latest/]]
graber 15.1 32 A domain specific language to describe neuron models in NEST. |
sarakonradi 16.1 33 | [[NEURON>>url:https://www.neuron.yale.edu/neuron/docs]]
34 Simulation enviroment for building and using computational models of neurons and networks of neurons | [[Neo>>url:https://neo.readthedocs.io/en/stable/]]
35 an object model for handling electrophysiology data in multiple formats. | [[Neo Viewer>>url:https://neo-viewer.brainsimulation.eu/]]
graber 15.1 36 Django/Angular software for graphing neural activity data (analog signals, spike trains etc.) read from Neo files. |
sarakonradi 16.1 37 | [[NeuroM>>url:https://neurom.readthedocs.io/en/v1.4.17/]]
38 NeuroM is a Python toolkit for the analysis and processing of neuron morphologies. | [[NeuroScheme>>url:https://neuroscheme-documentation.readthedocs.io/en/latest/]]
39 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 15.1 40 A Tool for the Generation and Visualization of Neuron Meshes and Adaptive On-the-Fly Refinement |
sarakonradi 16.1 41 | [[Neuromorphic Platform Python client>>url:https://electronicvisions.github.io/hbp-sp9-guidebook/]]
42 Client software for the Human Brain Project Neuromorphic Computing Platform. | [[Neurorobotics Platform>>url:https://www.neurorobotics.net/Documentation/nrp/user_manual/index.html]]
43 The NRP supports closed-loop neuroscience and embodied AI by connecting brains and bodies in simulation. | [[Nutil>>url:https://wiki.ebrains.eu/bin/view/Collabs/quint]]
graber 15.1 44 Nutil aims to both simplify and streamline the mechanism of pre-and-post processing 2D brain image data from mouse and rat. |
sarakonradi 16.1 45 | [[ODE-toolbox>>url:https://ode-toolbox.readthedocs.io/en/master/]]
46 Automatic selection and generation of integration schemes for systems of ordinary differential equations. | [[PyJuGex>>url:https://www.fz-juelich.de/inm/inm-1/DE/Forschung/_docs/JuGex/JuGex_node.html]]
47 JuGEx is an integrated framework of the AllenBrain and JuBrain atlases for statistical analysis of differential gene expression in the adult human brain. | [[PyNN>>url:http://neuralensemble.org/docs/PyNN/]]
graber 15.1 48 A Python package for simulator-independent specification of neuronal network models. |
sarakonradi 16.1 49 | [[QuickNII>>url:https://www.nitrc.org/docman/?group_id=1341]]
50 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. | [[SLURM plugin for the co-allocation of compute and data resources>>url:https://github.com/HumanBrainProject/coallocation-slurm-plugin/blob/master/README.md]]
graber 15.1 51 A plugin for SLURM used for the co-allocation of compute and data resources. | [[SpiNNaker Jupyter Service>>url:http://spinnakermanchester.github.io/common_pages/5.0.0/How_to_use_Jupyter_notebooks_on_SpiNNaker.pdf]] |
52 | [[SpiNNaker Local Boards>>url:https://spinnakermanchester.github.io/]] | [[SpiNNaker Machine>>url:https://spinnakermanchester.github.io/]] | [[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 16.1 53 | [[SpiNNaker Software>>url:http://spinnakermanchester.github.io/]] | [[SpiNNaker-NRP integration>>url:http://spinnakermanchester.github.io/common_pages/5.0.0/How_to_use_Jupyter_notebooks_on_SpiNNaker.pdf]] | [[TVB Brain Atlas Viewer>>url:#]]
graber 15.1 54 An interactive viewer of human brain function. |
sarakonradi 16.1 55 | [[TVB image processing pipeline>>url:https://drive.google.com/file/d/1VcXf3GX3KoihF4UzJQXzuGL4XWoqj5Jr/view]]
56 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]]
57 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 15.1 58 "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. |
sarakonradi 16.1 59 | [[The Virtual Brain Web-App>>url:http://docs.thevirtualbrain.org/]]
60 The Virtual Brain Web App at HBP. | [[Unicore>>url:https://www.unicore.eu/documentation/]]
61 A set of software components for federated access to high-performance compute and data resources. | [[ViSimpl>>url:https://visimpl-documentation.readthedocs.io/en/latest/]]
graber 15.1 62 ViSimpl integrates a set of visualization and interaction tools that provide a multi-view visual analysis of brain simultation data. |
sarakonradi 16.1 63 | [[VoluBA>>url:https://voluba-user-doc.apps-dev.hbp.eu/]]
graber 15.1 64 volumetric brain anchoring |
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sarakonradi 9.1 66 === Support ===
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68 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.