Last modified by graber on 2023/09/28 09:25
From version 30.1
edited by graber
on 2021/06/15 08:51
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To version 36.1
edited by graber
on 2022/07/08 08:00
Change comment: There is no comment for this version

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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 +
8 8  === Collaboratory ===
9 9  
10 10  |**[[Collaboratory>>url:https://wiki.ebrains.eu/bin/view/Collabs/the-collaboratory/]]**
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19 19  
20 20  === Share data ===
21 21  
22 -|**[[Data curation>>https://wiki.ebrains.eu/bin/view/Collabs/data-curation]]**
24 +|**[[Data curation>>url:https://wiki.ebrains.eu/bin/view/Collabs/data-curation ]]**
23 23  The place to share your neuroscience data on the EBRAINS platform.|**[[Data publishing>>url:https://ebrains.eu/services/data-knowledge/share-data/guidelines/]]**
24 24  The place to submit your dataset for publication along with a manuscript for a peer-reviewed journal.
25 25  
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28 28  |**[[Interactive Atlas Viewer>>url:https://interactive-viewer.readthedocs.io/en/latest/]]**
29 29  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]]**
30 30  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/]]**
31 -volumetric brain anchoring|
33 +volumetric brain anchoring|**[[siibra-explorer>>url:https://siibra-explorer.readthedocs.io/en/latest/]]**
34 +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.|\\
35 +|**[[siibra-python>>url:https://siibra-python.readthedocs.io/en/latest/]]**
36 +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.
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 -|**[[BrainScaleS>>url:https://wiki.ebrains.eu/bin/view/Collabs/neuromorphic/BrainScaleS/]]**
55 -Neural network emulation in 1000x accelerated biological real-time.|**[[CoreNeuron>>url:https://github.com/BlueBrain/CoreNeuron]]**
59 +|**[[CoreNeuron>>url:https://github.com/BlueBrain/CoreNeuron]]**
56 56  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]]**
57 -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.|
58 -|**[[Multi-scale brain simulation with TVB-NEST>>url:https://github.com/the-virtual-brain/tvb-multiscale/tree/master/docs]]**
59 -Simulate multi-scale brain network models with TVB and NEST.|**[[NEST>>url:https://nest-simulator.readthedocs.io/en/v2.20.0/]]**
61 +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]]**
62 +Simulate multi-scale brain network models with TVB and NEST.|
63 +|**[[NEST>>url:https://nest-simulator.readthedocs.io]]**
60 60  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]]**
61 -A web-based GUI application for NEST simulator.|
62 -|**[[NESTML>>url:https://nestml.readthedocs.io/en/latest/]]**
63 -A domain specific language to describe neuron models in NEST.|**[[NEURON>>url:https://www.neuron.yale.edu/neuron/docs]]**
65 +A web-based GUI application for NEST simulator.|**[[NESTML>>url:https://nestml.readthedocs.io/en/latest/]]**
66 +A domain specific language to describe neuron models in NEST.|
67 +|**[[NEURON>>url:https://www.neuron.yale.edu/neuron/docs]]**
64 64  Simulation enviroment for building and using computational models of neurons and networks of neurons|**[[NeuroM>>url:https://neurom.readthedocs.io/en/v1.4.17/]]**
65 -NeuroM is a Python toolkit for the analysis and processing of neuron morphologies.|
66 -|**[[PyNN>>url:http://neuralensemble.org/docs/PyNN/]]**
67 -A Python package for simulator-independent specification of neuronal network models.|**[[SpiNNaker Software>>url:https://spinnakermanchester.github.io/]]**
68 -The Software used to compile and execute Neural Networks described in PyNN on SpiNNaker hardware.|**[[TVB image processing pipeline>>url:https://ebrains.eu/]]**
69 -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.|
70 -|**[[TVB-HPC>>url:https://github.com/the-virtual-brain/tvb-hpc/tree/master/docs]]**
69 +NeuroM is a Python toolkit for the analysis and processing of neuron morphologies.|**[[PyNN>>url:http://neuralensemble.org/docs/PyNN/]]**
70 +A Python package for simulator-independent specification of neuronal network models.|
71 +|**[[TVB image processing pipeline>>url:https://ebrains.eu/]]**
72 +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]]**
71 71  This is a Python package for generating code for parameter sweeps and Bayesian inversion.|**[[The Virtual Brain>>url:http://docs.thevirtualbrain.org/index.html]]**
72 -"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.|**[[The Virtual Brain Web-App>>url:http://docs.thevirtualbrain.org/]]**
73 -The Virtual Brain Web App at HBP.|
74 +"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.|
75 +|**[[The Virtual Brain Web-App>>url:http://docs.thevirtualbrain.org/]]**
76 +The Virtual Brain Web App at HBP.
74 74  
75 75  === Neurorobotics ===
76 76  
77 77  |**[[Neurorobotics Platform>>url:https://www.neurorobotics.net/Documentation/nrp/user_manual/index.html]]**
78 -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]]**
79 -Allows the NRP to use SpiNNaker as a brain for robotic simulations.
81 +The NRP supports closed-loop neuroscience and embodied AI by connecting brains and bodies in simulation.
80 80  
81 81  === Medical data analytics ===
82 82  
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107 107  
108 108  === Support ===
109 109  
110 -Contact the [[EBRAINS High Level Support Team (HLST)>>https://ebrains.eu/support/]] if you have questions about our tools, services and workflows.
112 +Contact the [[EBRAINS High Level Support Team (HLST)>>https://ebrains.eu/support/]] if you have questions about our tools, services and workflows.