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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		-
9		-
10	10	=== Collaboratory ===
11	11	|**[[Collaboratory>>url:https://wiki.ebrains.eu/bin/view/Collabs/the-collaboratory/]]**
12	12	Workspaces in the Cloud for your research, development, documentation, and collaboration.
13	13	=== Find data ===
14	14	|**[[EBRAINS Knowledge Graph>>url:https://kg.ebrains.eu/]]**
15		-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]]**
16		-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/]]**
17		-Python API for the Human Brain Project Neural Activity Resource, capable of changing, and working with Metadata|
18		-
	13	+A user-driven, data-sharing and data-management infrastructure accelerating scientific progress by providing access to large collections of curated, heterogeneous neuroscience data.
19	19	=== Share data ===
20		-|**[[Data curation>>url:https://wiki.ebrains.eu/bin/view/Collabs/data-curation ]]**
21		-The place to share your neuroscience data on the EBRAINS platform.|**[[Data publishing>>url:https://ebrains.eu/services/data-knowledge/share-data/guidelines/]]**
22		-The place to submit your dataset for publication along with a manuscript for a peer-reviewed journal.
	15	+|**[[KnowledgeSpace>>url:https://knowledge-space.org/documentation]]**
	16	+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/]]**
	17	+Python API for the Human Brain Project Neural Activity Resource, capable of changing, and working with Metadata
23	23	=== Brain atlases ===
24	24	|**[[Interactive Atlas Viewer>>url:https://interactive-viewer.readthedocs.io/en/latest/]]**
25	25	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]]**
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27	27	volumetric brain anchoring|
28	28
29	29	=== Data analysis ===
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]]**
	25	+|**[[Elephant>>url:https://elephant.readthedocs.io/en/latest/index.html]]**
32	32	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/]]**
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/]]**
	27	+A Python package for working with the Human Brain Project Model Validation Framework.|**[[Neo>>url:https://neo.readthedocs.io/en/stable/]]**
	28	+an object model for handling electrophysiology data in multiple formats.|
	29	+|**[[Neo Viewer>>url:https://neo-viewer.brainsimulation.eu/]]**
36	36	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/]]**
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/]]**
	31	+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/]]**
	32	+A Tool for the Generation and Visualization of Neuron Meshes and Adaptive On-the-Fly Refinement|
	33	+|**[[Nutil>>url:https://wiki.ebrains.eu/bin/view/Collabs/quint]]**
	34	+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/]]**
43	43	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]]**
44		-ilastik is a simple, user-friendly tool for interactive image classification, segmentation and analysis.
	36	+ilastik is a simple, user-friendly tool for interactive image classification, segmentation and analysis.|
	37	+
45	45	=== Simulation ===
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/]]**
	39	+|**[[Arbor>>url:https://arbor.readthedocs.io/en/v0.5/]]**
48	48	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]]**
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]]**
	41	+Model Management Python Library|**[[BluePyOpt>>url:https://bluepyopt.readthedocs.io/en/latest/]]**
	42	+BluePyOpt is an extensible framework for data-driven model parameter optimisation that wraps and standardizes several existing open-source tools.|
	43	+|**[[BrainScaleS>>url:https://wiki.ebrains.eu/bin/view/Collabs/neuromorphic/BrainScaleS/]]**
	44	+Neural network emulation in 1000x accelerated biological real-time.|**[[CoreNeuron>>url:https://github.com/BlueBrain/CoreNeuron]]**
52	52	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]]**
53	53	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.|
54	54	|**[[Multi-scale brain simulation with TVB-NEST>>url:https://github.com/the-virtual-brain/tvb-multiscale/tree/master/docs]]**
55	55	Simulate multi-scale brain network models with TVB and NEST.|**[[NEST>>url:https://nest-simulator.readthedocs.io/en/v2.20.0/]]**
56	56	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]]**
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/]]**
	50	+A web-based GUI application for NEST simulator.|
	51	+|**[[NESTML>>url:https://nestml.readthedocs.io/en/latest/]]**
60	60	A domain specific language to describe neuron models in NEST.|**[[NEURON>>url:https://www.neuron.yale.edu/neuron/docs]]**
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/]]**
	53	+Simulation enviroment for building and using computational models of neurons and networks of neurons|**[[NeuroM>>url:https://neurom.readthedocs.io/en/v1.4.17/]]**
	54	+NeuroM is a Python toolkit for the analysis and processing of neuron morphologies.|
	55	+|**[[PyNN>>url:http://neuralensemble.org/docs/PyNN/]]**
	56	+A Python package for simulator-independent specification of neuronal network models.|**[[SpiNNaker Software>>url:https://spinnakermanchester.github.io/]]**
	57	+The Software used to compile and execute Neural Networks described in PyNN on SpiNNaker hardware.|**[[TVB image processing pipeline>>url:https://ebrains.eu/]]**
65	65	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.|
66	66	|**[[TVB-HPC>>url:https://github.com/the-virtual-brain/tvb-hpc/tree/master/docs]]**
67	67	This is a Python package for generating code for parameter sweeps and Bayesian inversion.|**[[The Virtual Brain>>url:http://docs.thevirtualbrain.org/index.html]]**
...	...	@@ -70,7 +70,8 @@
70	70
71	71	=== Neurorobotics ===
72	72	|**[[Neurorobotics Platform>>url:https://www.neurorobotics.net/Documentation/nrp/user_manual/index.html]]**
73		-The NRP supports closed-loop neuroscience and embodied AI by connecting brains and bodies in simulation.
	66	+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]]**
	67	+Allows the NRP to use SpiNNaker as a brain for robotic simulations.
74	74	=== Medical data analytics ===
75	75	|**[[Bids Manager & Pipeline>>url:https://github.com/Dynamap/BIDS_Manager]]**
76	76	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]]**
...	...	@@ -94,7 +94,6 @@
94	94	A set of software components for federated access to high-performance compute and data resources.|
95	95
96	96
97		-
98	98	=== Support ===
99	99
100		-Contact the [[EBRAINS High Level Support Team (HLST)>>https://ebrains.eu/support/]] if you have questions about our tools, services and workflows.
	93	+Contact the [[EBRAINS High Level Support Team (HLST)>>https://ebrains.eu/support/]] if you have questions about our tools, services and workflows.