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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	9	=== Collaboratory ===
10		-
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 ===
...	...	@@ -17,8 +17,7 @@
17	17	Python API for the Human Brain Project Neural Activity Resource, capable of changing, and working with Metadata|
18	18
19	19	=== Share data ===
20		-
21		-|**[[Data curation>>https://wiki.ebrains.eu/bin/view/Collabs/data-curation]]**
	18	+|**[[Data curation>>url:https://wiki.ebrains.eu/bin/view/Collabs/data-curation ]]**
22	22	The place to share your neuroscience data on the EBRAINS platform.|**[[Data publishing>>url:https://ebrains.eu/services/data-knowledge/share-data/guidelines/]]**
23	23	The place to submit your dataset for publication along with a manuscript for a peer-reviewed journal.
24	24	=== Brain atlases ===
...	...	@@ -28,41 +28,39 @@
28	28	volumetric brain anchoring|
29	29
30	30	=== Data analysis ===
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]]**
	28	+|**[[Elephant>>url:https://elephant.readthedocs.io/en/latest/index.html]]**
33	33	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/]]**
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/]]**
	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/]]**
37	37	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/]]**
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/]]**
	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/]]**
44	44	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]]**
45		-ilastik is a simple, user-friendly tool for interactive image classification, segmentation and analysis.
	39	+ilastik is a simple, user-friendly tool for interactive image classification, segmentation and analysis.|
	40	+
46	46	=== Simulation ===
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/]]**
	42	+|**[[Arbor>>url:https://arbor.readthedocs.io/en/v0.5/]]**
49	49	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]]**
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]]**
	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]]**
53	53	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]]**
54	54	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.|
55	55	|**[[Multi-scale brain simulation with TVB-NEST>>url:https://github.com/the-virtual-brain/tvb-multiscale/tree/master/docs]]**
56	56	Simulate multi-scale brain network models with TVB and NEST.|**[[NEST>>url:https://nest-simulator.readthedocs.io/en/v2.20.0/]]**
57	57	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]]**
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/]]**
	53	+A web-based GUI application for NEST simulator.|
	54	+|**[[NESTML>>url:https://nestml.readthedocs.io/en/latest/]]**
61	61	A domain specific language to describe neuron models in NEST.|**[[NEURON>>url:https://www.neuron.yale.edu/neuron/docs]]**
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/]]**
	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/]]**
66	66	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.|
67	67	|**[[TVB-HPC>>url:https://github.com/the-virtual-brain/tvb-hpc/tree/master/docs]]**
68	68	This is a Python package for generating code for parameter sweeps and Bayesian inversion.|**[[The Virtual Brain>>url:http://docs.thevirtualbrain.org/index.html]]**
...	...	@@ -71,26 +71,25 @@
71	71
72	72	=== Neurorobotics ===
73	73	|**[[Neurorobotics Platform>>url:https://www.neurorobotics.net/Documentation/nrp/user_manual/index.html]]**
74		-The NRP supports closed-loop neuroscience and embodied AI by connecting brains and bodies in simulation.
	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.
75	75	=== Medical data analytics ===
76	76	|**[[Bids Manager & Pipeline>>url:https://github.com/Dynamap/BIDS_Manager]]**
77	77	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]]**
78	78	3D visualization software for intracranial EEG.
79	79	=== Neuromorphic computing ===
80		-
81	81	|**[[BrainScaleS>>url:https://wiki.ebrains.eu/bin/view/Collabs/neuromorphic/BrainScaleS/]]**
82	82	Neural network emulation in 1000x accelerated biological real-time.|**[[Neuromorphic Platform Python client>>url:https://electronicvisions.github.io/hbp-sp9-guidebook/]]**
83	83	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]]**
84		-Jupyter notebook service running next to the SpiNNaker 1Million machine in Manchester.|
	79	+Jupyter notebook service running next to the SpiNNaker 1Million machine in Manchester.|
85	85	|**[[SpiNNaker Local Boards>>url:https://spinnakermanchester.github.io/]]**
86	86	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/]]**
87	87	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]]**
88		-The SpiNNaker batch execution service allowing Neuromorphic Computing Platform jobs to be run on the SpiNNaker 1Million machine in Manchester.|
	83	+The SpiNNaker batch execution service allowing Neuromorphic Computing Platform jobs to be run on the SpiNNaker 1Million machine in Manchester.|
89	89	|**[[SpiNNaker Software>>url:https://spinnakermanchester.github.io/]]**
90	90	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]]**
91	91	Allows the NRP to use SpiNNaker as a brain for robotic simulations.
92	92	=== High-performance computing ===
93		-
94	94	|**[[Fenix>>url:https://fenix-ri.eu/about-fenix/documentation]]**
95	95	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]]**
96	96	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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97	97	A set of software components for federated access to high-performance compute and data resources.|
98	98
99	99
100		-
101	101	=== Support ===
102	102
103		-Contact the [[EBRAINS High Level Support Team (HLST)>>https://ebrains.eu/support/]] if you have questions about our tools, services and workflows.
	96	+Contact the [[EBRAINS High Level Support Team (HLST)>>https://ebrains.eu/support/]] if you have questions about our tools, services and workflows.