Version 19.1 by graber on 2021/04/29 15:59
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sarakonradi 9.1 1 (% style="text-align: center;" %)
2 == Findable. Accessible. User-facing. ==
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sarakonradi 17.1 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. ===
sarakonradi 9.1 6
graber 18.1 7 |**[[fairgraph>>url:https://fairgraph.readthedocs.io/en/latest/]]**
graber 19.1 8 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/]]**
9 Arbor is a library for implementing performance portable network simulations of multi-compartment neuron models.|
graber 18.1 10 |**[[Bids Manager & Pipeline>>url:https://github.com/Dynamap/BIDS_Manager]]**
graber 19.1 11 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]]**
12 Model Management Python Library|**[[BluePyOpt>>url:https://bluepyopt.readthedocs.io/en/latest/]]**
13 BluePyOpt is an extensible framework for data-driven model parameter optimisation that wraps and standardizes several existing open-source tools.|
graber 18.1 14 |**[[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]]**
graber 19.1 15 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]]**
16 Elephant is an open-source Python library for the analysis of neurophysiology data, using Neo data structures.|
graber 18.1 17 |**[[Fenix>>url:https://fenix-ri.eu/about-fenix/documentation]]**|**[[HBP Validation Framework - Python Client>>url:http://hbp-validation-client.readthedocs.io/]]**
graber 19.1 18 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]]**
19 3D visualization software for intracranial EEG.|
graber 18.1 20 |**[[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 19.1 21 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/]]**
22 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/]]**
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.|
graber 18.1 24 |**[[JuGEx>>url:https://www.fz-juelich.de/inm/inm-1/DE/Forschung/_docs/JuGex/JuGex_node.html]]**
graber 19.1 25 JuGEx links cytoarchitecture and gene expression to investigate multilevel human brain organization.|**[[KnowledgeSpace>>url:https://knowledge-space.org/documentation]]**
26 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]]**
27 Simulate multi-scale brain network models with TVB and NEST.|
graber 18.1 28 |**[[NEST Desktop>>url:https://nest-desktop.readthedocs.io]]**
graber 19.1 29 A web-based GUI application for NEST simulator.|**[[NEST>>url:https://nest-simulator.readthedocs.io/en/v2.20.0/]]**
30 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/]]**
31 A domain specific language to describe neuron models in NEST.|
graber 18.1 32 |**[[NEURON>>url:https://www.neuron.yale.edu/neuron/docs]]**
graber 19.1 33 Simulation enviroment for building and using computational models of neurons and networks of neurons|**[[Neo>>url:https://neo.readthedocs.io/en/stable/]]**
34 an object model for handling electrophysiology data in multiple formats.|**[[Neo Viewer>>url:https://neo-viewer.brainsimulation.eu/]]**
35 Django/Angular software for graphing neural activity data (analog signals, spike trains etc.) read from Neo files.|
graber 18.1 36 |**[[NeuroM>>url:https://neurom.readthedocs.io/en/v1.4.17/]]**
graber 19.1 37 NeuroM is a Python toolkit for the analysis and processing of neuron morphologies.|**[[NeuroScheme>>url:https://neuroscheme-documentation.readthedocs.io/en/latest/]]**
38 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/]]**
39 A Tool for the Generation and Visualization of Neuron Meshes and Adaptive On-the-Fly Refinement|
graber 18.1 40 |**[[Neuromorphic Platform Python client>>url:https://electronicvisions.github.io/hbp-sp9-guidebook/]]**
graber 19.1 41 Client software for the Human Brain Project Neuromorphic Computing Platform.|**[[Neurorobotics Platform>>url:https://www.neurorobotics.net/Documentation/nrp/user_manual/index.html]]**
42 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]]**
43 Nutil aims to both simplify and streamline the mechanism of pre-and-post processing 2D brain image data from mouse and rat.|
graber 18.1 44 |**[[ODE-toolbox>>url:https://ode-toolbox.readthedocs.io/en/master/]]**
graber 19.1 45 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]]**
46 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/]]**
47 A Python package for simulator-independent specification of neuronal network models.|
graber 18.1 48 |**[[QuickNII>>url:https://www.nitrc.org/docman/?group_id=1341]]**
graber 19.1 49 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]]**
50 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]]**|
graber 18.1 51 |**[[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]]**|
52 |**[[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 19.1 53 An interactive viewer of human brain function.|
graber 18.1 54 |**[[TVB image processing pipeline>>url:https://drive.google.com/file/d/1VcXf3GX3KoihF4UzJQXzuGL4XWoqj5Jr/view]]**
graber 19.1 55 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]]**
56 This is a Python package for generating code for parameter sweeps and Bayesian inversion.|**[[The Virtual Brain>>url:http://docs.thevirtualbrain.org/index.html]]**
57 "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 18.1 58 |**[[The Virtual Brain Web-App>>url:http://docs.thevirtualbrain.org/]]**
graber 19.1 59 The Virtual Brain Web App at HBP.|**[[Unicore>>url:https://www.unicore.eu/documentation/]]**
60 A set of software components for federated access to high-performance compute and data resources.|**[[ViSimpl>>url:https://visimpl-documentation.readthedocs.io/en/latest/]]**
61 ViSimpl integrates a set of visualization and interaction tools that provide a multi-view visual analysis of brain simultation data.|
graber 18.1 62 |**[[VoluBA>>url:https://voluba-user-doc.apps-dev.hbp.eu/]]**
graber 19.1 63 volumetric brain anchoring|
graber 12.1 64
sarakonradi 9.1 65 === Support ===
66
67 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.