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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, founded in 1991, covering physics, mathematics, computer science, and quantitative biology.
  • bioRxiv is the Cold Spring Harbor Laboratory open preprint server for biological sciences, providing immediate open access with DOI assignment and ORCID integration.
  • data.gouv.fr is the French government open data portal operated by Etalab/DINUM, the umbrella infrastructure within which Recherche Data Gouv and Health Data Hub operate.
  • Figshare is a Digital Science general-purpose repository accepting all file types with DOI assignment and ORCID integration.
  • HAL is the French national open-access publication archive operated by CCSD/CNRS, with mandatory deposit under ANR Open Science Policy, CNRS Open Science, and Inserm Open Science.
  • medRxiv is the preprint server for clinical medicine, epidemiology, and public health, operated jointly by Cold Spring Harbor Laboratory, Yale University, and BMJ.
  • OSF (Open Science Framework) is the Center for Open Science platform for pre-registration, data and code sharing, and preprints.
  • Recherche Data Gouv is the French national multidisciplinary research data repository recommended by ANR Open Science Policy, CNRS Open Science, and Inserm Open Science.
  • Software Heritage is the universal software source code archive providing SWHIDs and integrated with HAL for code deposit under French open science mandates.
  • Zenodo is the CERN general-purpose repository assigning DOIs to any research output, recommended for EU-funded projects.

Research data management tools and identifiers

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

  • bio.tools is the ELIXIR registry of bioinformatics tools, databases, and web services, assigning persistent biotools IDs and using the EDAM ontology to annotate tool function and data types.
  • DataCite is the international DOI registration agency for research data and software, underpinning Zenodo, OpenNeuro, DANDI Archive, and Recherche Data Gouv.
  • FAIRsharing is a curated registry of data standards, repositories, and data policies.
  • ORCID provides persistent digital identifiers for researchers, embedded across repositories, funders, and publishers.
  • OPIDoR is the French national RDM tools suite operated by INIST-CNRS, comprising DMP OPIDoR, Cat OPIDoR, DORANum, and JurisDoR.
  • Protocols.io is an open-access platform for creating, versioning, and sharing step-by-step research protocols with DOI assignment.
  • RDMkit is the ELIXIR research data management toolkit providing life sciences FAIR guidance.
  • re3data is a widely used global registry of research data repositories across all disciplines.
  • Open Neuroscience (open-neuroscience.com) is a community-led database of open-source neuroscience projects spanning hardware, software, analysis tools, and data repositories.
  • OpenDOAR is the global quality-assured directory of open access publication repositories, operated by Jisc.

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 at the University of Salzburg, BIDS- and HED-compliant, registered on re3data, and the first official European Neurobagel federated search node.
  • C-BIG is the Montreal Neurological Institute’s open science repository for clinical, neuroimaging, genomic, and biospecimen data, built on LORIS and part of TOSI.
  • EBRAINS is the EU brain research infrastructure supporting BIDS, NWB, and openMINDS, with brain atlas services and simulation environments.
  • NEMAR is an open-access EEG, MEG, and iEEG data portal that automatically mirrors datasets from OpenNeuro and adds HPC processing via the Neuroscience Gateway.
  • NeuroVault hosts unthresholded statistical maps, parcellations, and atlases and enables meta-analysis workflows.
  • Neurosynth is a platform for large-scale automated fMRI meta-analysis, mapping activation coordinates to Cognitive Atlas terms.
  • NIMH Data Archive (NDA) is the NIH NIMH controlled-access repository for human subjects neuroscience data, including the ABCD Study.
  • NITRC is the NIH-funded neuroimaging tools registry and image repository, hosting 800+ tools and a searchable collection of MRI datasets.
  • NIF (Neuroscience Information Framework) provides RRID identifiers for research resources and maintains a registry of recommended neuroscience repositories.
  • Neurostars is the INCF-operated community Q&A forum serving as the primary support channel for open neuroscience tools and standards.
  • OpenNeuro is an open repository for BIDS-formatted datasets (MRI, EEG, MEG, iEEG, PET) released under CC0/PDDL licences.
  • Public-nEUro is a GDPR-compliant European open-access repository for human brain imaging data in BIDS format.

Bioimaging

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

  • Bio-Formats is the OME Java library for reading over 160 proprietary microscopy file formats, embedded in OMERO, Fiji, and most open-source bioimaging software.
  • BIII (BioImage Informatics Index / BISE) is the ELIXIR-affiliated community-curated registry of bioimaging software tools, workflows, and training materials, annotated using the EDAM-Bioimaging ontology.
  • BioImage Archive is the EMBL-EBI broad-intake repository for all 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, hosting published microscopy datasets.
  • NeuroMorpho.Org is the open archive for digitally reconstructed neuron and glia morphologies, standardising all reconstructions in SWC format.
  • OMERO is the OME institutional image management platform, deployed at Euro-BioImaging and France BioImaging nodes worldwide.

Neurophysiology repositories

  • DANDI Archive is the open archive for neurophysiology data funded by the NIH BRAIN Initiative, requiring NWB format for all submissions.
  • EMBER Archive is the official data archive for the NIH BRAIN Initiative’s BBQS programme, storing multimodal neurophysiological and behavioural datasets using NWB, BIDS, and DANDI storage infrastructure.
  • G-Node (German Neuroinformatics Node) is the German national neuroinformatics repository for electrophysiology and neuroimaging data.

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.
  • DataLad is a distributed data management system providing version control and provenance tracking for large research datasets.
  • LORIS is an open-source platform for multisite neuroimaging data management, developed at MNI and used by ADNI, CONP, and Ontario Brain Institute.
  • LONI IDA (Image and Data Archive) is the USC Stevens Neuroimaging and Informatics Institute 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 a wide range of proprietary and open formats, endorsed by INCF.
  • Neurobagel enables federated participant-level cohort search across BIDS datasets without centralising data.
  • XNAT 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.

  • Brain-CODE is the Ontario Brain Institute neuroinformatics platform serving 240+ researchers, 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 and pathogenicity classifications, curated by ClinGen expert panels.
  • dbGaP 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, assigning stable RefSNP identifiers to over 1.1 billion unique variants as of 2024.
  • DDBJ is the Japanese national sequence database and INSDC partner that mirrors ENA and SRA data.
  • EGA is the EMBL-EBI and CRG controlled-access repository for sensitive human genomics and phenotypic data.
  • ENA is the EMBL-EBI open-access raw sequence archive and INSDC partner.
  • EVA is the EMBL-EBI open-access variant archive covering short variants and structural variants.
  • NCBI GEO is the primary open-access repository for gene expression and functional genomics data.
  • NeMO Archive is the primary NIH BRAIN Initiative and BICAN multi-omics repository, focusing on 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 a public repository for high-throughput sequencing data, operated by NCBI/NIH 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 managed by INSERM, 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 Telemedicine Technologies eClinical suite and the AP-HP institutional eCRF platform for regulatory-grade clinical trials.
  • ClinicalTrials.gov is the US national clinical trial registry and results database, operated by NLM/NIH.
  • CTIS is the EU Clinical Trials Information System, the mandatory registration and results portal for all EU/EEA clinical trials.
  • EDS AP-HP is the AP-HP clinical data warehouse covering 19 million patients, using OMOP CDM and HL7 FHIR, with the Cohort360 query tool.
  • Health Data Hub is the French national health data platform providing access to the SNDS (67 million people) via a secure Datalab, using OMOP CDM.
  • i2b2 is a clinical data warehousing platform deployed at AP-HP alongside OMOP CDM.
  • REDCap is a secure web-based eCRF and clinical data capture platform with 7,000+ institutional partners in 159 countries.
  • SNDS (Système National des Données de Santé) is the French national health data system and the 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.