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1		-XWiki.annedevismes
	1	+XWiki.graber

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2		-== 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. ==
	2	+=== 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. ===
3	3
4		-
5		-
6		-
7	7	=== Collaboratory ===
8	8
9	9	|**[[Collaboratory>>url:https://wiki.ebrains.eu/bin/view/Collabs/the-collaboratory/]]**
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24	24
25	25	=== Brain atlases ===
26	26
	24	+|**[[PyJuGEx>>url:https://www.fz-juelich.de/inm/inm-1/DE/Forschung/_docs/JuGex/JuGex_node.html]]**
	25	+Find a set of differentially expressed genes between two user defined volumes of interest based on JuBrain maps.|**[[Julich-Brain Gene Expression>>url:https://www.fz-juelich.de/inm/inm-1/DE/Forschung/_docs/JuGex/JuGex_node.html]]**
	26	+Decoding the chain from genes to cognition requires detailed insights how areas with specific gene activities and microanatomical architectures contribute to brain function and dysfunction.|**[[QuickNII>>url:https://wiki.ebrains.eu/bin/view/Collabs/quicknii-and-visualign]]**
	27	+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.|
27	27	|**[[siibra-explorer>>url:https://siibra-explorer.readthedocs.io/en/latest/]]**
28		-siibra-explorer is a browser-based viewer for the visual exploration of the EBRAINS atlases at microscopic detail, as well as the discovery of related multimodal data features. It is tightly integrated with the EBRAINS Knowledge Graph, allowing the seamless querying of semantically and spatially anchored datasets.|**[[QuickNII>>url:https://wiki.ebrains.eu/bin/view/Collabs/quicknii-and-visualign]]**
29		-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.|**[[VoluBA>>url:https://voluba-user-doc.apps-dev.hbp.eu/]]**
30		-VoluBA (Volumetric Brain Anchoring) is an online service for anchoring of high-resolution volumes of interest from imaging experiments to very large reference volumes.|**[[siibra-python>>url:https://siibra-python.readthedocs.io/en/latest/]]**
31		-siibra-python is a comprehensive Python client providing access to EBRAINS atlases and offering an easy and well-structured way to include maps, reference templates, region definitions and linked datasets in reproducible programmatic workflows.
	29	+siibra-explorer is a browser-based viewer for the visual exploration of the EBRAINS atlases at microscopic detail, as well as the discovery of related multimodal data features. It is tightly integrated with the EBRAINS Knowledge Graph, allowing the seamless querying of semantically and spatially anchored datasets.|**[[siibra-python>>url:https://siibra-python.readthedocs.io/en/latest/]]**
	30	+siibra-python is a comprehensive Python client providing access to EBRAINS atlases and offering an easy and well-structured way to include maps, reference templates, region definitions and linked datasets in reproducible programmatic workflows.|**[[VoluBA>>url:https://voluba-user-doc.apps-dev.hbp.eu/]]**
	31	+VoluBA (Volumetric Brain Anchoring) is an online service for anchoring of high-resolution volumes of interest from imaging experiments to very large reference volumes.|
32	32
33	33	=== Data analysis ===
34	34
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51	51	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]]**
52	52	Model Management Python Library|**[[BluePyOpt>>url:https://bluepyopt.readthedocs.io/en/latest/]]**
53	53	BluePyOpt is an extensible framework for data-driven model parameter optimisation that wraps and standardizes several existing open-source tools.|
	54	+
54	54	|**[[CoreNeuron>>url:https://github.com/BlueBrain/CoreNeuron]]**
55	55	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]]**
56	56	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.|**[[Multi-scale brain simulation with TVB-NEST>>url:https://github.com/the-virtual-brain/tvb-multiscale/tree/master/docs]]**
57	57	Simulate multi-scale brain network models with TVB and NEST.|
	59	+
58	58	|**[[NEST>>url:https://nest-simulator.readthedocs.io]]**
59	59	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]]**
60	60	A web-based GUI application for NEST simulator.|**[[NESTML>>url:https://nestml.readthedocs.io/en/latest/]]**
61	61	A domain specific language to describe neuron models in NEST.|
	64	+
62	62	|**[[NEURON>>url:https://www.neuron.yale.edu/neuron/docs]]**
63	63	Simulation enviroment for building and using computational models of neurons and networks of neurons|**[[NeuroM>>url:https://neurom.readthedocs.io/en/v1.4.17/]]**
64	64	NeuroM is a Python toolkit for the analysis and processing of neuron morphologies.|**[[PyNN>>url:http://neuralensemble.org/docs/PyNN/]]**
65	65	A Python package for simulator-independent specification of neuronal network models.|
	69	+
66	66	|**[[TVB image processing pipeline>>url:https://ebrains.eu/]]**
67	67	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]]**
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]]**
69	69	"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.|
	74	+
70	70	|**[[The Virtual Brain Web-App>>url:http://docs.thevirtualbrain.org/]]**
71		-The Virtual Brain Web App at HBP.
	76	+The Virtual Brain Web App at HBP.|**[[NeuroR>>url:https://elephant.readthedocs.io/en/latest/index.html]]**NeuroR is a collection of tools to repair morphologies.|**[[Local Field Potentials in Python>>url:https://lfpy.readthedocs.io/]]**LFPy is a Python module for the calculation of extracellular potentials and magnetic signals from activity in multicompartment neuron and network models.|
72	72
	78	+|**[[Snudda>>url:https://github.com/Hjorthmedh/Snudda/wiki]]**Snudda is a tool that allows the user to place neurons within multiple volumes, then performs touch detection to infer where putative synapses are based on reconstructed neuron morphologies.
	79	+
	80	+
73	73	=== Neurorobotics ===
74	74
75	75	|**[[Neurorobotics Platform>>url:https://www.neurorobotics.net/Documentation/nrp/user_manual/index.html]]**
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78	78	=== Medical data analytics ===
79	79
80	80	|**[[Bids Manager & Pipeline>>url:https://github.com/Dynamap/BIDS_Manager]]**
81		-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]]**
82		-3D visualization software for intracranial EEG.
	89	+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.|**[[Brainstorm>>url:https://neuroimage.usc.edu/brainstorm/Introduction]]**Brainstorm is a collaborative, open-source application dedicated to the analysis of brain recordings:
	90	+MEG, EEG, fNIRS, ECoG, depth electrodes and multiunit electrophysiology.|**[[HiBoP>>url:https://collab.humanbrainproject.eu/#/collab/78584/nav/531987?state=uuid%3Df72e40d9-a0bf-4ab7-8a27-462911107c5f]]**3D visualization software for intracranial EEG.|
83	83
	92	+|**[[ImaGIN>>url:https://wiki.ebrains.eu/bin/view/Collabs/quicknii-and-visualign]]**SPM-based Matlab toolbox for processing intracranial EEG recordings (SEEG and ECOG).|**[[IntranAt Electrodes>>url:https://intranat.readthedocs.io/]]**A software to visualize electrodes implantation on image data and prepare database for group studies.
	93	+
84	84	=== Neuromorphic computing ===
85	85
86	86	|**[[BrainScaleS>>url:https://wiki.ebrains.eu/bin/view/Collabs/neuromorphic/BrainScaleS/]]**