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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. ===
6	6
7	7
	8	+
8	8	=== Collaboratory ===
	10	+
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.
11	11	=== Find data ===
...	...	@@ -15,7 +15,8 @@
15	15	Python API for the Human Brain Project Neural Activity Resource, capable of changing, and working with Metadata|
16	16
17	17	=== Share data ===
18		-|**[[Data curation>>url:https://wiki.ebrains.eu/bin/view/Collabs/data-curation ]]**
	20	+
	21	+|**[[Data curation>>https://wiki.ebrains.eu/bin/view/Collabs/data-curation]]**
19	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	20	The place to submit your dataset for publication along with a manuscript for a peer-reviewed journal.
21	21	=== Brain atlases ===
...	...	@@ -25,39 +25,41 @@
25	25	volumetric brain anchoring|
26	26
27	27	=== Data analysis ===
28		-|**[[Elephant>>url:https://elephant.readthedocs.io/en/latest/index.html]]**
	31	+|**[[Elephant>>url:https://elephant.readthedocs.io/en/v0.6.4/index.html]]**
	32	+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/]]**
	34	+A Python package for working with the Human Brain Project Model Validation Framework.|
	35	+|**[[Neo>>url:https://neo.readthedocs.io/en/stable/]]**
	36	+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/]]**
	38	+NeuroScheme is a tool for navigating, exploring, creating and interacting with NeuroScience data using abstract, schematic or expressive representations.|
	39	+|**[[NeuroTessMesh>>url:https://neurotessmesh-documentation.readthedocs.io/en/latest/]]**
	40	+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]]**
	41	+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]]**
	42	+Nutil aims to both simplify and streamline the mechanism of pre-and-post processing 2D brain image data from mouse and rat.|
	43	+|**[[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		-
	45	+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/]]**
	47	+|**[[Arbor>>url:https://arbor.readthedocs.io/en/latest/index.html]]**
	48	+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]]**
	50	+Model Management Python Library|
	51	+|**[[BluePyOpt>>url:https://bluepyopt.readthedocs.io/en/latest/]]**
	52	+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/]]**
	58	+A web-based GUI application for NEST simulator|
	59	+|**[[NEST Desktop>>url:https://nest-desktop.readthedocs.io]]**
	60	+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/]]**
	62	+Simulation enviroment for building and using computational models of neurons and networks of neurons|
	63	+|**[[NeuroM>>url:https://neurom.readthedocs.io/en/v1.4.17/]]**
	64	+NeuroM is a Python toolkit for the analysis and processing of neuron morphologies.|**[[PyNN>>url:http://neuralensemble.org/docs/PyNN/]]**
	65	+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.
	74	+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]]**
74	74	3D visualization software for intracranial EEG.
75	75	=== Neuromorphic computing ===
	80	+
76	76	|**[[BrainScaleS>>url:https://wiki.ebrains.eu/bin/view/Collabs/neuromorphic/BrainScaleS/]]**
77	77	Neural network emulation in 1000x accelerated biological real-time.|**[[Neuromorphic Platform Python client>>url:https://electronicvisions.github.io/hbp-sp9-guidebook/]]**
78	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.|
	84	+Jupyter notebook service running next to the SpiNNaker 1Million machine in Manchester.|
80	80	|**[[SpiNNaker Local Boards>>url:https://spinnakermanchester.github.io/]]**
81	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	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]]**
83		-The SpiNNaker batch execution service allowing Neuromorphic Computing Platform jobs to be run on the SpiNNaker 1Million machine in Manchester.|
	88	+The SpiNNaker batch execution service allowing Neuromorphic Computing Platform jobs to be run on the SpiNNaker 1Million machine in Manchester.|
84	84	|**[[SpiNNaker Software>>url:https://spinnakermanchester.github.io/]]**
85	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]]**
86	86	Allows the NRP to use SpiNNaker as a brain for robotic simulations.
87	87	=== High-performance computing ===
	93	+
88	88	|**[[Fenix>>url:https://fenix-ri.eu/about-fenix/documentation]]**
89	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	90	A plugin for SLURM used for the co-allocation of compute and data resources.|**[[Unicore>>url:https://www.unicore.eu/documentation/]]**
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91	91	A set of software components for federated access to high-performance compute and data resources.|
92	92
93	93
	100	+
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.
	103	+Contact the [[EBRAINS High Level Support Team (HLST)>>https://ebrains.eu/support/]] if you have questions about our tools, services and workflows.