Tools and services documentation
Last modified by graber on 2023/09/28 09:25
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.
Collaboratory
| Collaboratory Workspaces in the Cloud for your research, development, documentation, and collaboration. |
Find data
| EBRAINS Knowledge Graph A user-driven, data-sharing and data-management infrastructure accelerating scientific progress by providing access to large collections of curated, heterogeneous neuroscience data. | KnowledgeSpace 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 Python API for the Human Brain Project Neural Activity Resource, capable of changing, and working with Metadata | |
| Model Catalog The EBRAINS Model Catalog allows you to find information about neuroscience models developed and/or used within the EBRAINS research infrastructure, and about results obtained using those models, in particular about how those models have been validated against experimental findings. |
Share data
| Data curation The place to share your neuroscience data on the EBRAINS platform. | Data publishing The place to submit your dataset for publication along with a manuscript for a peer-reviewed journal. |
Brain atlases
| PyJuGEx Find a set of differentially expressed genes between two user defined volumes of interest based on JuBrain maps. | Julich-Brain Gene Expression 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 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. |
| siibra-explorer 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 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 VoluBA (Volumetric Brain Anchoring) is an online service for anchoring of high-resolution volumes of interest from imaging experiments to very large reference volumes. |
| VisuAlign VisuAlign is a tool for applying user-guided nonlinear refinements (inplane) to an existing, affine 2D-to-3D registration, such as created using QuickNII. | WebAlign WebAlign is an online tool for spatial registration of histological section images from rodent brains to reference 3D atlases. | WebWarp WebWarp is an online tool for nonlinear refinement of spatial registration of histological section images from rodent brains to reference 3D atlases. |
Data analysis
| Elephant Elephant is an open-source Python library for the analysis of neurophysiology data, using Neo data structures. | HBP Validation Framework - Python Client A Python package for working with the Human Brain Project Model Validation Framework. | Neo an object model for handling electrophysiology data in multiple formats. |
| Neo Viewer Django/Angular software for graphing neural activity data (analog signals, spike trains etc.) read from Neo files. | NeuroScheme NeuroScheme is a tool for navigating, exploring, creating and interacting with NeuroScience data using abstract, schematic or expressive representations. | NeuroTessMesh A Tool for the Generation and Visualization of Neuron Meshes and Adaptive On-the-Fly Refinement |
| Nutil Nutil aims to both simplify and streamline the mechanism of pre-and-post processing 2D brain image data from mouse and rat. | ViSimpl ViSimpl integrates a set of visualization and interaction tools that provide a multi-view visual analysis of brain simultation data. | ilastik ilastik is a simple, user-friendly tool for interactive image classification, segmentation and analysis. |
| Brain-cockpit Web-based application to explore large fMRI datasets and inter-subject alignments. | Cobrawap Cobrawap is a Python-based, adaptable, and reusable pipeline for analyzing cortical wave activity. | Viziphant Viziphant provides an easy way to generate plots and interactive visualizations of neuroscientific data and analysis results |
| MeshView MeshView is a web application for real-time 3D display of surface mesh data representing structural parcellations from volumetric atlases, such as the Waxholm Space Atlas of the Sprague Dawley Rat Brain. | LocaliZoom Web application for viewing of series of high-resolution 2D images that have been anchored to reference atlases. | BluePyEfe BluePyEfe eases the process of reading and extracting electircal features from experimental recordings. |
| eFEL: Electrophys Feature Extraction Library Automatically extract eFeatures from time series data recorded from neurons, both in vitro and in silico. | Model Validation API The EBRAINS Model Validation Service is a web service to support the structured validation of neuroscience models. | Frites Frites is an open-source Python software to analyze neurophysiological data using information theoretical (IT) measures |
| Synaptic events analyzer Fitting synaptic events using data and model in NeuroInformatics Platform |
Simulation
| Arbor Arbor is a library for implementing performance portable network simulations of multi-compartment neuron models. | BluePyMM Model Management Python Library | BluePyOpt BluePyOpt is an extensible framework for data-driven model parameter optimisation that wraps and standardizes several existing open-source tools. |
| CoreNeuron CoreNeuron implements the core functionalities of the NEURON simulator targeting high efficiency when using millions of threads. | Hodgkin Huxley Neuron Builder 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 Simulate multi-scale brain network models with TVB and NEST. |
| NEST 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 A web-based GUI application for NEST simulator. | NESTML A domain specific language to describe neuron models in NEST. |
| NEURON Simulation enviroment for building and using computational models of neurons and networks of neurons | NeuroM NeuroM is a Python toolkit for the analysis and processing of neuron morphologies. | PyNN A Python package for simulator-independent specification of neuronal network models. |
| TVB image processing pipeline 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 This is a Python package for generating code for parameter sweeps and Bayesian inversion. | The Virtual Brain "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 The Virtual Brain Web App at HBP. | NeuroR NeuroR is a collection of tools to repair morphologies. | LFPy LFPy is a Python module for the calculation of extracellular potentials and magnetic signals from activity in multicompartment neuron and network models. |
| Snudda 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. | BlueNaaS-Subcellular BlueNaaS-Subcellular is designed as a web based environment for the creation and simulation of reaction-diffusion models. | libsonata A C++ / Python API for reading SONATA circuit files. |
| Brain Scaffold Builder The BSB is a framework for reconstructing and simulating multi-paradigm neuronal network models. It removes much of the repetitive work associated with writing the required code and lets you focus on the parts that matter. It helps write organized, well-parametrized and explicit code understandable and reusable by your peers. | InSite Insite provides a middleware that enables users to acquire data from NEST, Abror and TVB via the in-transit paradigm. | Subcellular model building and calibration toolset Tools for data-driven building of subcellular biochemical signaling pathway models, including interoperable modules for model building, calibration, and model analysis. |
| Arbor GUI Arbor GUI is a comprehensive tool for building single cell models using Arbor. It strives to be self-contained, fast, and easy to use. | SSBtoolkit The SSB computational toolkit was developed to easily predict classical pharmacodynamic models of drug-GPCR (class A) interactions given just as input structural information of the receptor and the ligand. | Synaptic plasticity Configure and test different synaptic plasticity models and protocols |
Neurorobotics
| Neurorobotics Platform The NRP supports closed-loop neuroscience and embodied AI by connecting brains and bodies in simulation. |
Medical data analytics
| Bids Manager & Pipeline 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 Brainstorm is a collaborative, open-source application dedicated to the analysis of brain recordings: MEG, EEG, fNIRS, ECoG, depth electrodes and multiunit electrophysiology. | HiBoP 3D visualization software for intracranial EEG. |
| ImaGIN SPM-based Matlab toolbox for processing intracranial EEG recordings (SEEG and ECOG). | IntranAt Electrodes A software to visualize electrodes implantation on image data and prepare database for group studies. | Medical Informatics Platform (MIP) The MIP is an open-source platform enabling federated data analysis in a secure environment for centers interested in initiating or joining disease-oriented federations with the aim of analyzing large-scale distributed clinical datasets. |
| Human Intracerebral EEG Platform (HIP) The HIP is a state-of-the-art open-source platform, offering integrated tools and workflows for optimized collection, storage, sharing, processing and analysis of multiscale Human intracerebral EEG data. |
Neuromorphic computing
| BrainScaleS Neural network emulation in 1000x accelerated biological real-time. | Neuromorphic Platform Python client Client software for the Human Brain Project Neuromorphic Computing Platform. | SpiNNaker Jupyter Service Jupyter notebook service running next to the SpiNNaker 1Million machine in Manchester. | |
| SpiNNaker Local Boards 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 The SpiNNaker 1Million core machine in Manchester consisting of 1200 SpiNNaker boards. | SpiNNaker Remote Access The SpiNNaker batch execution service allowing Neuromorphic Computing Platform jobs to be run on the SpiNNaker 1Million machine in Manchester. | |
| SpiNNaker Software The Software used to compile and execute Neural Networks described in PyNN on SpiNNaker hardware. | SpiNNaker-NRP integration Allows the NRP to use SpiNNaker as a brain for robotic simulations. |
High-performance computing
| Fenix Delivering e-infrastructure services federated as the Fenix Infrastructure. | SLURM plugin for the co-allocation of compute and data resources A plugin for SLURM used for the co-allocation of compute and data resources. | Unicore A set of software components for federated access to high-performance compute and data resources. |
Sensitve Data
| Health Data Cloud EBRAINS Service for Sensitive Data provides a federated network of protected and audited secure Virtual Research Environments that enables users to demonstrate compliance with EU data protection law when processing human data such as digital human brain twins. The service is provided by Europe’s largest University Hospital, Charité Berlin. |
Support
Contact the EBRAINS High Level Support Team (HLST) if you have questions about our tools, services and workflows.