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Resources

This index covers digital systems: data repositories where research outputs are deposited and retrieved, and software tools and digital services that researchers use to manage, process, discover, or access data. Entities with institutional identity (facilities, institutes, consortia) belong in Actors. Formal specifications belong in Standards.

General-purpose repositories and publication archives

Open repositories, preprint servers, and publication archives used across research domains.

  • arXiv is the original open-access preprint repository, covering physics, mathematics, computer science, and quantitative biology.
  • bioRxiv is the open preprint server for biological sciences.
  • DANS (Data Archiving and Networked Services) is the Dutch national research data repository, operated by KNAW and NWO.
  • data.gouv.fr is the French government open data portal, the umbrella infrastructure within which Recherche Data Gouv and Health Data Hub operate.
  • Figshare is a general-purpose repository accepting all file types with DOI assignment.
  • HAL (Hyper Articles en Ligne) is the French national open-access publication archive, with mandatory deposit under French open science mandates.
  • medRxiv is the preprint server for clinical medicine, epidemiology, and public health.
  • OSF (Open Science Framework) is a platform for pre-registration, data and code sharing, and preprints.
  • Recherche Data Gouv is the French national multidisciplinary research data repository.
  • Software Heritage is the universal software source code archive, integrated with HAL for code deposit.
  • Zenodo is the CERN general-purpose repository assigning DOIs to any research output.

Research data management tools and identifiers

Cross-domain tools for data management planning, persistent identification, and FAIR guidance.

  • Barometre Science Ouverte (Baromètre de la Science Ouverte) is the French Ministry open science monitoring dashboard, the empirical evidence base for Ouvrir la Science.
  • bio.tools is the ELIXIR registry of bioinformatics tools, databases, and web services.
  • DataCite is the international DOI registration agency for research data and software, underpinning Zenodo, OpenNeuro, and DANDI Archive.
  • Dataverse is open-source research data repository software, the platform on which Recherche Data Gouv and DataverseNL (DANS) are built.
  • FAIRsharing is a curated registry of data standards, repositories, and data policies.
  • ORCID (Open Researcher and Contributor ID) provides persistent digital identifiers for researchers.
  • OPIDoR is the French national research data management tools suite.
  • Protocols.io is an open-access platform for creating, versioning, and sharing step-by-step research protocols.
  • RDMkit is the ELIXIR research data management toolkit for life sciences FAIR guidance.
  • re3data (Registry of Research Data Repositories) is a global registry of research data repositories across all disciplines.
  • Open Neuroscience is a community-led database of open-source neuroscience projects spanning hardware, software, and data.
  • OpenDOAR (Directory of Open Access Repositories) is the global quality-assured directory of open access publication repositories.

Neuroimaging repositories

Open repositories for brain imaging data across MRI, PET, EEG, MEG, and related modalities.

  • ANC (Austrian NeuroCloud) is a FAIR-enabling open repository for neurocognitive research data, BIDS- and HED-compliant and a Neurobagel federated search node.
  • AfNiA (African Neuroimaging Archive) is a CAMERA initiative building an open archive of annotated brain MRI from across Africa.
  • C-BIG (Clinical Biospecimen Imaging and Genetic Repository) is the MNI open science repository for clinical, neuroimaging, genomic, and biospecimen data, built on LORIS.
  • CIMBI (Center for Integrated Molecular Brain Imaging) is a Copenhagen multimodal PET, MRI, genetic, and biobank database for serotonergic system research, run with NRU Copenhagen.
  • EBRAINS is the EU brain research infrastructure supporting BIDS, NWB, and openMINDS, with brain atlas and simulation services.
  • INDI (International Neuroimaging Data-sharing Initiative) is a Child Mind Institute programme releasing open neuroimaging collections such as ABIDE, ADHD-200, and CoRR.
  • NEMAR (NeuroElectroMagnetic data Archive and tools Resource) is an open EEG, MEG, and iEEG portal mirroring datasets from OpenNeuro with added HPC processing.
  • NeuroVault hosts unthresholded statistical maps, parcellations, and atlases for meta-analysis.
  • Neurosynth is a platform for automated fMRI meta-analysis, mapping activation coordinates to Cognitive Atlas terms.
  • NIMH Data Archive is the NIH NIMH controlled-access repository for human subjects neuroscience data, including the ABCD Study.
  • NITRC (Neuroimaging Informatics Tools and Resources Clearinghouse) is the NIH-funded neuroimaging tools registry and image repository.
  • NIF (Neuroscience Information Framework) provides RRID identifiers and a registry of recommended neuroscience repositories.
  • Neurostars is the INCF-operated community Q&A forum for open neuroscience tools and standards.
  • OASIS (Open Access Series of Imaging Studies) is a series of MRI datasets on ageing and Alzheimer’s disease, distributed via XNAT Central and OpenNeuro.
  • OpenNeuro is an open repository for BIDS-formatted MRI, EEG, MEG, iEEG, and PET datasets.
  • Public-nEUro is a GDPR-compliant European open-access repository for human brain imaging data in BIDS format.
  • RDR (Radboud Data Repository) is the institutional open data repository of Radboud University, the designated archive for Donders Institute open datasets.

Bioimaging

Archives, management platforms, and format tools for biological microscopy data.

  • Bio-Formats is the OME Java library for reading proprietary microscopy file formats, embedded in OMERO and most open-source bioimaging software.
  • BIII (BioImage Informatics Index) is the ELIXIR-affiliated community registry of bioimaging software tools, workflows, and training materials.
  • BioImage Archive is the EMBL-EBI broad-intake repository for biological image data accompanying publications.
  • EMPIAR (Electron Microscopy Public Image Archive) is the EMBL-EBI repository for raw cryo-electron microscopy image data.
  • IDR (Image Data Resource) is the EMBL-EBI reference image repository built on OMERO.
  • NeuroMorpho.Org is the open archive for digitally reconstructed neuron and glia morphologies, standardising them in SWC format.
  • OMERO (OME Remote Objects) is the OME institutional image management platform, deployed at Euro-BioImaging and France BioImaging nodes.

Neurophysiology repositories

  • DANDI Archive (Distributed Archives for Neurophysiology Data Integration) is the open archive for neurophysiology data funded by the NIH BRAIN Initiative, requiring NWB format.
  • EMBER Archive is the data archive for the NIH BRAIN Initiative BBQS programme, using NWB and BIDS.
  • G-Node (German Neuroinformatics Node) is the German national repository for electrophysiology and neuroimaging data.
  • PhysioNet is the MIT open repository for physiological signal and clinical data, hosting EDF recordings and the MIMIC critical-care database.

Computational models

  • ModelDB is the primary open repository for published computational neuroscience models, with strong support for NeuroML format.
  • OpenSourceBrain (Open Source Brain) is a platform for sharing and developing standardised computational models, using NeuroML as its primary format.
  • The Virtual Brain is an open-source platform for simulating personalised whole-brain network models, distributed within the EBRAINS ecosystem.

Neuroscience data management tools

Tools and platforms for managing, harmonising, and federating neuroscience datasets across sites.

  • BrainLife.io is a cloud platform for BIDS and NWB analysis with automatic provenance tracking.
  • DMP Online is the UK Digital Curation Centre’s data management plan authoring service, sharing a codebase with DMPTool.
  • DMPTool is the US data management plan authoring service, providing NIH-aligned templates.
  • Data Stewardship Wizard (DSW) is an open-source ELIXIR tool for structured DMP creation, with a French instance operated by IFB.
  • FAIR-Checker is an IFB-developed online tool for assessing the FAIRness of web-accessible research resources.
  • Madbot (Metadata And Data Brokering Online Tool) is an IFB-developed web application for FAIR metadata management and automated data submission.
  • Bonsai is an open-source event-based data acquisition and experimental control framework for neuroscience, outputting to DANDI Archive in NWB format.
  • SND (Swedish National Data Service) is Sweden’s national research data repository, providing discovery, DOI assignment, deposit, and preservation.
  • DataLad is a distributed data management system providing version control and provenance tracking for large research datasets.
  • JATOS (Just Another Tool for Online Studies) is an open-source server platform for hosting online behavioural studies, with direct export to OSF.
  • OpenSesame is an open-source graphical experiment builder for cognitive neuroscience, deploying online via JATOS.
  • PEP (Polymorphic Encryption and Pseudonymisation) is a cryptographic framework for privacy-preserving storage of sensitive medical research data, built for the Personalized Parkinson Project.
  • LORIS (Longitudinal Online Research and Imaging System) is an open-source platform for multisite neuroimaging data management, used by ADNI, CONP, and Ontario Brain Institute.
  • LONI IDA (Image and Data Archive) is the USC controlled-access repository hosting ADNI, PPMI, ABIDE, and other landmark neuroimaging cohorts.
  • Neo is an open-source Python I/O library for reading electrophysiology data across many proprietary and open formats.
  • Neurobagel enables federated participant-level cohort search across BIDS datasets without centralising data.
  • XNAT (Extensible Neuroimaging Archive Toolkit) is a DICOM management and pipeline platform used at EBRAINS member sites.

Genomics, single-cell, and multiomics

Sequence archives, controlled-access repositories, expression databases, and single-cell portals.

  • BioSamples is the EMBL-EBI registry of biological sample metadata, assigning each sample a stable accession referenced across sequence and omics archives.
  • Brain-CODE is the Ontario Brain Institute neuroinformatics platform, federating data across LORIS, XNAT, and CONP.
  • CELLxGENE is the Chan Zuckerberg Initiative portal for curated single-cell transcriptomics data, requiring Cell Ontology and AnnData format.
  • ClinVar is the NCBI database of clinical variant interpretations, curated by ClinGen expert panels.
  • dbGaP (database of Genotypes and Phenotypes) is the NIH controlled-access repository for GWAS and human genotype-phenotype data.
  • dbSNP is the NCBI reference database for small-scale human genomic variants.
  • dbVar is the NCBI open-access archive for human genomic structural variation, the structural-variant counterpart to dbSNP.
  • DDBJ (DNA Data Bank of Japan) is Japan’s INSDC member repository for open nucleotide sequences, synchronising with ENA and GenBank.
  • EGA (European Genome-phenome Archive) is the EMBL-EBI controlled-access repository for sensitive human genomics and phenotypic data.
  • ENA (European Nucleotide Archive) is the EMBL-EBI open-access raw sequence archive and INSDC partner.
  • EVA (European Variation Archive) is the EMBL-EBI open-access variant archive.
  • NCBI GEO (Gene Expression Omnibus) is the primary open-access repository for gene expression and functional genomics data.
  • NeMO Archive (Neuroscience Multi-Omic Archive) is the primary NIH BRAIN Initiative and BICAN multi-omics repository for single-cell brain atlas data.
  • Seurat is the R package providing the standard data object for single-cell RNA-seq analysis, the R-ecosystem counterpart to AnnData.
  • SRA (Sequence Read Archive) is the NCBI public repository for high-throughput sequencing data and an INSDC partner.
  • Synapse AMP-AD is the Sage Bionetworks platform hosting the AMP-AD Knowledge Portal, CommonMind, and PsychENCODE open Alzheimer’s datasets.

Rare disease

  • Orphanet is the European rare disease reference portal, providing ORPHAcodes and the ORDO ontology.

Clinical research

Platforms for clinical trial registration, data capture, health data warehousing, and trial data sharing.

  • BNDMR (Base Nationale de Données Maladies Rares) is the French national patient registry for rare diseases, operated by AP-HP using Orphanet ORPHAcodes.
  • CleanWEB is the AP-HP institutional eCRF platform for regulatory-grade clinical trials.
  • ClinicalTrials.gov is the US national clinical trial registry and results database.
  • CTIS (Clinical Trials Information System) is the mandatory EU registration and results portal for all EU/EEA clinical trials.
  • EDS AP-HP (Entrepôt de Données de Santé AP-HP) is the AP-HP clinical data warehouse, using OMOP CDM and HL7 FHIR.
  • Health Data Hub is the French national health data platform providing access to the SNDS via a secure Datalab, using OMOP CDM.
  • i2b2 (Informatics for Integrating Biology and the Bedside) is a clinical data warehousing platform deployed at AP-HP alongside OMOP CDM.
  • REDCap (Research Electronic Data Capture) is a secure web-based eCRF and clinical data capture platform.
  • SNDS (Système National des Données de Santé) is the French national health data system, a core resource for epidemiological and health economics research.
  • VIVLI is a global platform for clinical trial individual patient data sharing via a controlled-access enclave.