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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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Brain Observatory Storage Service and Database (BossDB) Resource Report Resource Website 10+ mentions |
Brain Observatory Storage Service and Database (BossDB) (RRID:SCR_017273) | BossDB, bossDB, BOSS DB | 3d spatial image, data or information resource, data repository, database, image, service resource, storage service resource | BossDB (Brain Observatory Storage Service and Database) is a cloud-based ecosystem for the storage and management of public large-scale volumetric neuroimaging and connectomics datasets. This includes volumetric Electron Microscopy and X-Ray Micro/Nanotomography data with support for multi-channel image data, segmentations, annotations, meshes, and connectomes. BossDB integrates with community resources for data access, processing, visualization, and analysis, and includes an API that enables metadata management, rendering, datatype conversions, and ingest. | Johns Hopkins University Applied Physics Laboratory, JHU/APL, database, electron microscopy, xray, data, storage, archive, BRAIN Initiative, EM, XRM, XNH, ecosystem |
is used by: BICCN is recommended by: National Library of Medicine is recommended by: BRAIN Initiative is related to: Scalable Analytics for Brain Exploration Research is related to: Ecosystem for Multi-modal Brain-behavior Experimentation and Research has parent organization: BRAIN Initiative has parent organization: Johns Hopkins University; Maryland; USA |
BRAIN Initiative ; NIMH R24 MH114785 |
DOI:10.1101/217745 | Open | https://github.com/jhuapl-boss/boss/ | SCR_017273 | Brain Observatory Storage Service, bossDB, Block and Object Storage Service, BOSSDB, Block and Object Storage Service Database, Brain Observatory Storage Service and Database, BossDB | 2026-08-29 11:25:33 | 31 | |||||
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Strains, SNPs and Polymorphisms Resource Report Resource Website 1+ mentions |
Strains, SNPs and Polymorphisms (RRID:SCR_017518) | data or information resource, service resource | MGI integrates comparative data on inbred strain characteristics including SNPs, polymorphisms, and quantitative phenotypes. | Integrate, comparative, data, inbred, strain, SNP, polymorhism, quantitative, phenotype | has parent organization: Mouse Genome Informatics (MGI) | Free, Freely available | SCR_017518 | 2026-08-29 11:25:43 | 4 | ||||||||||
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3D Genome Resource Report Resource Website 10+ mentions |
3D Genome (RRID:SCR_017525) | service resource | Genome Browser for study of 3D genome organization and gene regulation and data visualization. Used to visualizing chromatin interaction data, browse other omics data such as ChIP-Seq or RNA-Seq for same genomic region, and gain complete view of both regulatory landscape and 3D genome structure for any given gene., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | 3D, genome, organization, gene, regulation, data, visualization, chromatin, interaction, omic, ChIPseq, RNAseq, regulatory, structure |
is related to: Encode has parent organization: Pennsylvania State University |
THIS RESOURCE IS NO LONGER IN SERVICE | SCR_017525 | 2026-08-29 11:26:00 | 20 | ||||||||||
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Cardiff Study of all Wales and North West of England Twins Resource Report Resource Website |
Cardiff Study of all Wales and North West of England Twins (RRID:SCR_017480) | CaStANET | data or information resource | Study of twins and their families provides tool for disentangling genetic and environmental origins of traits. Study collected behavioral and psychopathological information using self-, parent and teacher reports, and focused on contributions of genetic and environmental risk factors to psychological health of young people. | Twins, family, genetic, environmental, origin, trait, collected, behavioral, psychopathological, data | PMID:17539361 | SCR_017480 | 2026-08-29 11:26:00 | 0 | ||||||||||
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DIANA-mirExTra Resource Report Resource Website 1+ mentions |
DIANA-mirExTra (RRID:SCR_017498) | analysis service resource, data access protocol, production service resource, service resource, software resource, web service | Software tool for analysis of expression data for microRNA function. | Analysis, expression, data, microRNA, function, DIANA tool | is provided by: DIANA Tools | Free, Freely available | http://diana.imis.athena-innovation.gr/DianaTools/ | SCR_017498 | Mirextra 2.0 | 2026-08-29 11:25:42 | 1 | ||||||||
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Epigenie Resource Report Resource Website |
Epigenie (RRID:SCR_017494) | data or information resource, portal, topical portal | Collection of epigenetic data browsers and repositories. Repository of epigenetics tools and databases by EpiGenie team. | Repository, epigenetic, tool, database, EpiGenie, data | Free, Available for download, Freely available | SCR_017494 | 2026-08-29 11:25:36 | 0 | |||||||||||
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gene Expression Analysis Resource Resource Report Resource Website 50+ mentions |
gene Expression Analysis Resource (RRID:SCR_017467) | gEAR | analysis service resource, data or information resource, portal, production service resource, service resource, software resource | Portal for visualization and analysis of multi omic data in public and private domains. Enables upload, visualization and analysis of scRNA-seq data. | Visualization, analysis, multi, omic, data, upload, scRNA-seq, BRAIN Initiative |
is recommended by: BRAIN Initiative has parent organization: University of Maryland School of Medicine; Maryland; USA |
Hearing Health Foundation (Hearing Restoration Project) ; NIDCD R01 DC013817; NIMH MH114788; NIMH R24 MH114815 |
Restricted | SCR_017467 | gene Expression Analysis Resource | 2026-08-29 11:26:00 | 91 | |||||||
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Analysis, Visualization, and Informatics Lab-space (AnVIL) Resource Report Resource Website 10+ mentions |
Analysis, Visualization, and Informatics Lab-space (AnVIL) (RRID:SCR_017469) | AnVIL | data or information resource, data repository, portal, project portal, service resource, storage service resource | Portal to facilitate integration and computing on and across large datasets generated by NHGRI programs, as well as initiatives funded by National Institutes of Health or by other agencies that support human genomics research. Resource for genomic scientific community, that leverages cloud based infrastructure for democratizing genomic data access, sharing and computing across large genomic, and genomic related data sets. Component of federated data ecosystem, and is expected to collaborate and integrate with other genomic data resources through adoption of FAIR (Findable, Accessible, Interoperable, Reusable) principles, as their specifications emerge from scientific community. Will provide collaborative environment, where datasets and analysis workflows can be shared within consortium and be prepared for public release to broad scientific community through AnVIL user interfaces. | Dataset, NHGRI, program, NIH, initiative, funded, human, genomic, data, access, sharing, FAIR, analysis, workflow |
is recommended by: NIDDK Information Network (dkNET) is recommended by: National Library of Medicine is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases |
NIH | Restricted | https://www.genome.gov/Funded-Programs-Projects/Computational-Genomics-and-Data-Science-Program/Genomic-Analysis-Visualization-Informatics-Lab-space-AnVIL | SCR_017469 | Visualization, and Informatics Lab-space, AnVIL, Analysis Visualization and Informatics Lab-space, Analysis | 2026-08-29 11:25:41 | 31 | ||||||
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Hemodialysis Pilot Studies Consortium Resource Report Resource Website |
Hemodialysis Pilot Studies Consortium (RRID:SCR_017468) | HDPSC | consortium, data or information resource, organization portal, portal | Consortium to design and conduct pilot and feasibility studies of novel therapies to reduce morbidity and mortality for patients treated with maintenance hemodialysis. Data Coordinating Center (DCC) for consortium provides scientific expertise and operational support for pilot studies that will be conducted at HDPSC Participating Clinical Centers. Data Coordinating Center for Hemodialysis Pilot Studies Consortium. | Novel, therapy, reduce, morbidity, patient, maintenance, hemodialysis, data, coordinating, center | has parent organization: University of Pennsylvania Perelman School of Medicine; Pennsylvania; USA | NIDDK ; NIH |
SCR_017468 | 2026-08-29 11:25:35 | 0 | |||||||||
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LAN toolbox Resource Report Resource Website 1+ mentions |
LAN toolbox (RRID:SCR_017629) | LANtoolbox | 1d time-series analysis software, data analysis software, data processing software, software application, software resource, software toolkit, time-series analysis software | Software toolbox for neuroscientist data (EEG and reaction time for time being). Used to create shared language among different algorithms and softwares in this field (e.g. Fieldtrip, Eeglab, Chronux, Brainstorm, etc), in order to facilitate implementation of experimental analysis by users. Code and scripts for EEG analysis for MATLAB. | Neuroscientist, data, EEG, experimental, analysis, code, script | is related to: MATLAB | Free, Available for download, Freely available | SCR_017629 | Laboratory of Analysis in Neurosciences Toolbox, EEG Toolbox | 2026-08-29 11:25:47 | 2 | ||||||||
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Italian Twin Registry Resource Report Resource Website |
Italian Twin Registry (RRID:SCR_017476) | data or information resource, portal, topical portal | Portal with information about twins in Italy. | Twins, Italy, data, registry | Free, Freely available | SCR_017476 | National Register of Twins | 2026-08-29 11:25:41 | 0 | ||||||||||
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Data Information System - DAISY Resource Report Resource Website 1+ mentions |
Data Information System - DAISY (RRID:SCR_017472) | DAISY | software resource, web application | Open source web application that allows biomedical research institutions to map their data and data flows in accordance with GDPR's accountability requirement. | Map, data, flow, GDPR | Free, Available for download, Freely available | https://github.com/elixir-luxembourg/daisy | SCR_017472 | DAta Information SYstem | 2026-08-29 11:26:00 | 2 | ||||||||
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Mediation Analysis of Causality under Confounding Resource Report Resource Website |
Mediation Analysis of Causality under Confounding (RRID:SCR_017442) | MACC | data analysis software, data processing software, software application, software resource | Software package to perform causal mediation analysis under confounding or correlated errors. Includes single level mediation model, two level and three level mediation model for data with hierarchical structures. Under two or three level mediation model, correlation parameter is identifiable and is estimated based on hierarchical likelihood, marginal likelihood or two stage method. | Casual, mediation, analysis, confounding, correlated, error, data, hierarchical, structure, parameter, BRAIN Initiative |
is recommended by: BRAIN Initiative is listed by: CRAN |
NIBIB EB022911 | Free, Available for downloads, Freely available | SCR_017442 | Mediation Analysis of Causality under Confounding, macc | 2026-08-29 11:26:00 | 0 | |||||||
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Transcriptomics Explorer Resource Report Resource Website 100+ mentions |
Transcriptomics Explorer (RRID:SCR_017567) | data analysis software, data processing software, data visualization software, service resource, software application, software resource | Software tool to visualize and analyze transcriptomics data and transcriptomic cell types for mouse and human, all directly in web browser. To explore gene expression heatmap across cell types in datasets, search for genes of interest, explore tSNE visualization, colored by cell types or expression of genes of interest, visualize dataset’s sampling strategy to see how cells and nuclei were sampled across brain areas, cortical layer, and other dimensions, find cell type of interest in one visualization and see its characteristics in different visualization.Used for Allen Brain Map Cell Types Database to Browse Data: Human - Multiple Cortical Areas, and Mouse - Cortex and Hippocampus. | Visualize, analyze, transcriptomic, data, cell, type, mouse, human, Allen, database, multiple, cortical, area, cortex, hippocampus | works with: Allen Brain Atlas | Free, Freely available | https://celltypes.brain-map.org/rnaseq/human/cortex, https://celltypes.brain-map.org/rnaseq/mouse/cortex-and-hippocampus, | SCR_017567 | 2026-08-29 11:25:44 | 108 | |||||||||
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Willoughby–Hoye Python Scripts A-D Resource Report Resource Website 1+ mentions Issue |
Willoughby–Hoye Python Scripts A-D (RRID:SCR_017562) | data analysis software, data processing software, software application, software resource | Software tool as scripts for calculating NMR chemical shifts. Warning - this group of Python scripts used to process NMR data, described in Willoughby et al, 2014, has been found to contain bug. Please see PMID:31591889. | Python, NMR, script, caluclating, chemical, shift, data | NIA R01 AG039468 | PMID:24556787 PMID:31591889 |
Free, Freely available | SCR_017562 | 2026-08-29 11:26:01 | 1 | |||||||||
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shinyGEO Resource Report Resource Website |
shinyGEO (RRID:SCR_017605) | analysis service resource, production service resource, service resource, software resource, web application | Web based tool to download gene expression datasets from GEO in order to perform differential expression and survival analysis for gene of interest. Produces publication ready graphics and generates R code ensuring that all analyses are reproducible. Web based application for analyzing gene expression omnibus datasets. | Gene, expression, dataset, GEO, differencial, analysis, gene, graphic, omnibus, data, bio.tools |
uses: Shiny is listed by: Debian is listed by: bio.tools has parent organization: Eastern Connecticut State University; Connecticut; United States works with: Gene Expression Omnibus (GEO) |
Google Summer of Code | PMID:27503226 | Free, Available for download, Freely available | biotools:shinygeo | https://gdancik.github.io/shinyGEO/, https://bio.tools/shinygeo | SCR_017605 | 2026-08-29 11:25:46 | 0 | ||||||
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SciGraph Resource Report Resource Website 1+ mentions |
SciGraph (RRID:SCR_017576) | data processing software, data visualization software, software application, software resource, standalone software | Software tool to represent ontologies and data described using ontologies as Neo4j graph. Ontology serving middleware tool using Neo4J as base server, able to ingest ttl files, and serve them to quickly create services that can underpin autocomplete, term lookup and tree traversal. | Ontology, data, Neo4j graph, server, ttl, file |
is used by: SPARC Portal is used by: SciCrunch is used by: CINERGI is used by: Human Brain Project |
Free, Available for download, Freely available | SCR_017576 | 2026-08-29 11:25:44 | 3 | ||||||||||
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PoloPlus USB Drive software Resource Report Resource Website 10+ mentions |
PoloPlus USB Drive software (RRID:SCR_017614) | data analysis software, data processing software, software application, software resource | Software to perform Probit and Logit analsis with grouped data. Original Polo Software available through USB Drive. Able to work on all versions of Windows as all files are kept on USB. | LeOra Software LLC, grouped, data, analysis, USB, drive, probit, logit | Restricted | SCR_017614 | Probit Or LOgit Plus USB Drive, PoloPlus USB Drive | 2026-08-29 11:26:01 | 35 | ||||||||||
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StatPackets Resource Report Resource Website |
StatPackets (RRID:SCR_017613) | data or information resource, narrative resource, standard specification | Standardized method to export statistical data, associated with KOMP project. Standard way to keep data and results of analyzing that data together. | Standardized, method, export, statistical, data, KOMP, result, analysis, together | is related to: Knockout Mouse Project | Free, Freely available | SCR_017613 | 2026-08-29 11:25:37 | 0 | ||||||||||
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EBRAINS Knowledge Graph Resource Report Resource Website 1+ mentions |
EBRAINS Knowledge Graph (RRID:SCR_017612) | data management software, data or information resource, database, service resource, software application, software resource | Metadata management system built for EBRAINS. Multi modal metadata store which brings together information from different areas of Human Brain Project as well as from external partners. Graph database tracks linkage between experimental data and neuroscientific data science supporting more extensive data reuse and complex computational research.Supports rich terminologies, ontologies and controlled vocabularies. Built by design to support iterative elaborations of common standards and supports these by probabilistic suggestion and review systems. | Metadata, managing, system, neuroscience, experimental, data, human, brain, graph, database, terminology, ontology |
is related to: Human Brain Project is related to: MarmotGraph |
European Union’s Horizon 2020 Framework Programme for Research and Innovation 720270; European Union’s Horizon 2020 Framework Programme for Research and Innovation 785907 |
Free, Freely available | https://kg.humanbrainproject.eu/ | SCR_017612 | New Enabling Infrastructure for Neuroscience Knowledge Graph, EBRAINS Knowledge Graph (KG), HBP Knowledge Graph | 2026-08-29 11:25:46 | 8 |
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