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5	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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	8	+
	9	+
8	8	=== Collaboratory ===
9	9	|**[[Collaboratory>>url:https://wiki.ebrains.eu/bin/view/Collabs/the-collaboratory/]]**
10	10	Workspaces in the Cloud for your research, development, documentation, and collaboration.
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25	25	volumetric brain anchoring|
26	26
27	27	=== Data analysis ===
28		-|**[[Elephant>>url:https://elephant.readthedocs.io/en/latest/index.html]]**
	30	+|**[[Elephant>>url:https://elephant.readthedocs.io/en/v0.6.4/index.html]]**
	31	+Elephant is an open-source Python library for the analysis of neurophysiology data, using Neo data structures.|**[[Elephant>>url:https://elephant.readthedocs.io/en/latest/index.html]]**
29	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/]]**
30		-A Python package for working with the Human Brain Project Model Validation Framework.|**[[Neo>>url:https://neo.readthedocs.io/en/stable/]]**
31		-an object model for handling electrophysiology data in multiple formats.|
32		-|**[[Neo Viewer>>url:https://neo-viewer.brainsimulation.eu/]]**
	33	+A Python package for working with the Human Brain Project Model Validation Framework.|
	34	+|**[[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/]]**
33	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/]]**
	37	+NeuroScheme is a tool for navigating, exploring, creating and interacting with NeuroScience data using abstract, schematic or expressive representations.|
	38	+|**[[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|**[[Nutil>>url:https://wiki.ebrains.eu/bin/view/Collabs/quint]]**
	40	+Nutil aims to both simplify and streamline the mechanism of pre-and-post processing 2D brain image data from mouse and rat.|**[[Nutil>>url:https://www.nitrc.org/plugins/mwiki/index.php/nutil:MainPage]]**
	41	+Nutil aims to both simplify and streamline the mechanism of pre-and-post processing 2D brain image data from mouse and rat.|
	42	+|**[[ViSimpl>>url:https://visimpl-documentation.readthedocs.io/en/latest/]]**
38	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.|
40		-
	44	+ilastik is a simple, user-friendly tool for interactive image classification, segmentation and analysis.
41	41	=== Simulation ===
42		-|**[[Arbor>>url:https://arbor.readthedocs.io/en/v0.5/]]**
	46	+|**[[Arbor>>url:https://arbor.readthedocs.io/en/latest/index.html]]**
	47	+Arbor is a performance portable library for simulation of large networks of multi-compartment neurons on hybrid/accelerated/many core computer architectures.|**[[Arbor>>url:https://arbor.readthedocs.io/en/v0.5/]]**
43	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/]]**
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]]**
	49	+Model Management Python Library|
	50	+|**[[BluePyOpt>>url:https://bluepyopt.readthedocs.io/en/latest/]]**
	51	+BluePyOpt is an extensible framework for data-driven model parameter optimisation that wraps and standardizes several existing open-source tools.|**[[CoreNeuron>>url:https://github.com/BlueBrain/CoreNeuron]]**
48	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]]**
49	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	50	|**[[Multi-scale brain simulation with TVB-NEST>>url:https://github.com/the-virtual-brain/tvb-multiscale/tree/master/docs]]**
51	51	Simulate multi-scale brain network models with TVB and NEST.|**[[NEST>>url:https://nest-simulator.readthedocs.io/en/v2.20.0/]]**
52	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]]**
53		-A web-based GUI application for NEST simulator.|
54		-|**[[NESTML>>url:https://nestml.readthedocs.io/en/latest/]]**
	57	+A web-based GUI application for NEST simulator|
	58	+|**[[NEST Desktop>>url:https://nest-desktop.readthedocs.io]]**
	59	+A web-based GUI application for NEST simulator.|**[[NESTML>>url:https://nestml.readthedocs.io/en/latest/]]**
55	55	A domain specific language to describe neuron models in NEST.|**[[NEURON>>url:https://www.neuron.yale.edu/neuron/docs]]**
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/]]**
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	+Simulation enviroment for building and using computational models of neurons and networks of neurons|
	62	+|**[[NeuroM>>url:https://neurom.readthedocs.io/en/v1.4.17/]]**
	63	+NeuroM is a Python toolkit for the analysis and processing of neuron morphologies.|**[[PyNN>>url:http://neuralensemble.org/docs/PyNN/]]**
	64	+A Python package for simulator-independent specification of neuronal network models.|**[[TVB image processing pipeline>>url:https://ebrains.eu/]]**
61	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	62	|**[[TVB-HPC>>url:https://github.com/the-virtual-brain/tvb-hpc/tree/master/docs]]**
63	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]]**
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66	66
67	67	=== Neurorobotics ===
68	68	|**[[Neurorobotics Platform>>url:https://www.neurorobotics.net/Documentation/nrp/user_manual/index.html]]**
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.
	73	+The NRP supports closed-loop neuroscience and embodied AI by connecting brains and bodies in simulation.
71	71	=== Medical data analytics ===
72	72	|**[[Bids Manager & Pipeline>>url:https://github.com/Dynamap/BIDS_Manager]]**
73	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]]**
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91	91	A set of software components for federated access to high-performance compute and data resources.|
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	97	+
94	94	=== Support ===
95	95
96		-Contact the [[EBRAINS High Level Support Team (HLST)>>https://ebrains.eu/support/]] if you have questions about our tools, services and workflows.
	100	+Contact the [[EBRAINS High Level Support Team (HLST)>>https://ebrains.eu/support/]] if you have questions about our tools, services and workflows.