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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
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ewas-galaxy Resource Report Resource Website 1+ mentions |
ewas-galaxy (RRID:SCR_018085) | data analysis software, data processing software, software application, software resource, software toolkit | Software suite for population epigenetics integrated into Galaxy. Galaxy Docker repository for population epigenetics data analysis. | Population epigenetics, Galaxy, docker repository, data analysis | is related to: Galaxy | DOI:10.1101/553784 | Free, Available for downolad, Freely available | https://galaxyproject.org/use/ewas-galaxy/ | SCR_018085 | SciCrunch Registry | Epigenome-Wide Association Studies- Galaxy, EWAS-Galaxy | 2026-10-31 12:16:57 | 1 | |||||||
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GNomEx Resource Report Resource Website 1+ mentions |
GNomEx (RRID:SCR_011805) | GNomEx | data repository, service resource, storage service resource | A Genomic Laboratory Information Management System (LIMS) and Data repository that can function as an experiment tracking and workflow management system for Core Facilities as well as an advanced data repository for storing and sharing genomic data sets. |
is listed by: OMICtools has parent organization: University of Utah; Utah; USA |
PMID:20828407 | OMICS_01005 | https://uofuhealth.utah.edu/huntsman/shared-resources/gba/bioinformatics/software/ | http://hci-scrum.hci.utah.edu/gnomexdoc/ | SCR_011805 | SciCrunch Registry | 2026-10-31 12:15:29 | 5 | |||||||
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mitochondria simulator Resource Report Resource Website 1+ mentions |
mitochondria simulator (RRID:SCR_023430) | software application, software resource | Software repository for mtDNA assembly project. | mitochondria, assembly, de bruijn graph, data mining, mtDNA assembly project, | Free, Available for download, Freely available | SCR_023430 | SciCrunch Registry | mitochondria-simulator | 2026-10-31 12:21:44 | 8 | ||||||||||
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hgu133plus2 Resource Report Resource Website |
hgu133plus2 (RRID:SCR_026448) | software resource, software toolkit | Software R package for Affymetrix Affymetrix HG-U133_Plus_2 Array annotation data assembled using data from public repositories. | annotation data assembled package, | Free, Free available, | SCR_026448 | SciCrunch Registry | 2026-10-31 12:24:00 | 0 | |||||||||||
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Trace Archive Resource Report Resource Website 100+ mentions |
Trace Archive (RRID:SCR_013788) | data repository, service resource, storage service resource | An online repository which houses sequencing data from gel and capillary platforms (such as Applied Biosystems ABI 3730®). Most sequences are derived from Whole Genome Shotgun sequencing. Large data sets as well as only a few sequences can be obtained. | repository, sequencing data, gel platform, capillary platform, whole genome shotgun sequencing |
is recommended by: NIDDK Information Network (dkNET) is related to: NCBI Assembly Archive Viewer |
r3d100010905 | https://www.ncbi.nlm.nih.gov/Traces | SCR_013788 | SciCrunch Registry | Trace Archive, NCBI Trace Archive | 2026-10-31 12:16:03 | 144 | ||||||||
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Mammalian Phosphorylation Resource Resource Report Resource Website |
Mammalian Phosphorylation Resource (RRID:SCR_008210) | MPR | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE, documented on 6/24/13. A repository of information on commercially available phospho-specific antibodies to human phosphorylation sites. It provides a BLAST search for phosphorylation sites using as query the amino acid sequence surrounding the site. It also provides direct links to the relevant antibodies from many companies including BD Pharmingen, Biosource International, Cell Signaling Technology (CST), Santa Cruz Biotechnologies, Upstate Biotechnology. | amino acid, antibody, human, mammalian, phosphorylation, protein property databases, repository, sequence, blast, data analysis resource |
is listed by: 3DVC has parent organization: Center for Cancer Research |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-21274 | SCR_008210 | SciCrunch Registry | Mammalian Phosphorylation Resource | 2026-10-31 12:20:32 | 0 | |||||||
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PRO-ACT database Resource Report Resource Website |
PRO-ACT database (RRID:SCR_023520) | data or information resource, database | Publicly available repository of merged ALS clinical trials data. | amyotrophic lateral sclerosis, ALS, clinical trials data, | Amyotrophic Lateral Sclerosis | ALS Therapy Alliance | PMID:25298304 | Free, Freely available | SCR_023520 | SciCrunch Registry | Pooled Resource Open Access ALS Clinical Trials Database | 2026-10-31 12:20:56 | 0 | |||||||
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Proteome Commons Resource Report Resource Website 10+ mentions |
Proteome Commons (RRID:SCR_006234) | Proteome Commons | community building portal, data or information resource, data repository, database, portal, service resource, software resource, storage service resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 17, 2013. A public resource for sharing general proteomics information including data (Tranche repository), tools, and news. Joining or creating a group/project provides tools and standards for collaboration, project management, data annotation, permissions, permanent storage, and publication. | proteomics, protein, peptide, data sharing, data, tool, news, annotation, proteome, genome |
is listed by: re3data.org has parent organization: University of Michigan; Ann Arbor; USA is parent organization of: Proteome Commons Tranche repository |
NCI ; Clinical Proteomics Technologies for Cancer ; NCRR P41-RR018627 |
PMID:20356086 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_151800 | SCR_006234 | SciCrunch Registry | ProteomeCommons.org, ProteomeCommons | 2026-10-31 12:14:30 | 12 | |||||
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EBRAINS Resource Report Resource Website 50+ mentions |
EBRAINS (RRID:SCR_019260) | data or information resource, data repository, portal, project portal, service resource, storage service resource | Research infrastructure for the EU Human Brain Project. Provides digital tools and services which can be used to address challenges in brain research and brain inspired technology development. Digital research infrastructure, created by EU-funded Human Brain Project, that gathers extensive range of data and tools for brain-related research. EBRAINS will capitalize on the work performed by the Human Brain Project teams in digital neuroscience, brain medicine, and brain-inspired technology.You can share your neuroscience data, models and software. | EU Human Brain Project, European Union Human Brain Project, human brain project, human brain, OpenMINDs, FAIR |
lists: QuickNII and VisuAlign lists: QuickNII is listed by: FAIRsharing is related to: openMINDS metadata framework is related to: Julich-Brain Cytoarchitectonic Atlas is related to: BRAIN Initiative is related to: openMINDS chemicals metadata model is related to: openMINDS computation metadata model is related to: openMINDS specimenPrep metadata model is related to: openMINDS core metadata model is related to: openMINDS controlledTerms metadata model is related to: openMINDS publications metadata model is related to: openMINDS stimulation metadata model |
EU | Free, Freely available | r3d100013325 | https://doi.org/10.17616/R31NJMRX | SCR_019260 | SciCrunch Registry | ebrains, Ebrains | 2026-10-31 12:17:14 | 78 | ||||||
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USC Multimodal Connectivity Database Resource Report Resource Website 10+ mentions |
USC Multimodal Connectivity Database (RRID:SCR_012809) | UMCD | data or information resource, data repository, database, service resource, storage service resource | Web-based repository and analysis site for connectivity matrices that have been derived from neuroimaging data including different imaging modalities, subject groups, and studies. Users can analyze connectivity matrices that have been shared publicly and upload their own matrices to share or analyze privately. | fmri, dti, dsi, mri, eeg, meg, data set, image, computational hosting, connectivity, neuroimaging, data sharing, brain, rendering, diffusion-weighted mri, functional connectivity, graph theory, resting-state fmri, structural connectivity, image display, magnetic resonance, python, rendering, visualization, connectivity matrix, network, brain network, matrix, de-identified, male, female, apoe, child, adult |
is used by: NIF Data Federation is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: MGH-USC Human Connectome Project |
Normal, Lesioned, Attention deficit-hyperactivity disorder, Autism Spectrum Disorder, Obsessive-Compulsive Disorder, BDD, APOE 4/4, APOE 3/4, APOE 3/3, Alzheimer's disease | NRSA ; NIH Blueprint for Neuroscience Research ; NIA F31AG035438-01; NIDA HHSN271200800035C |
PMID:23226127 PMID:20850551 |
The community can contribute to this resource, Some features require an account | nlx_83091 | http://www.nitrc.org/projects/umcd | http://jessebrown.webfactional.com/welcome/default/index | SCR_012809 | SciCrunch Registry | UCLA Connectivity Database, UCLA Multimodal Connectivity Database: Web-based brain network analysis and data sharing, UCLA Multimodal Connectivity Database | 2026-10-31 12:15:44 | 26 | ||
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IPBIR - Integrated Primate Biomaterials and Information Resource Resource Report Resource Website |
IPBIR - Integrated Primate Biomaterials and Information Resource (RRID:SCR_004614) | IPBIR | biomaterial supply resource, cell repository, material resource | The purpose of the IPBIR - Integrated Primate Biomaterials and Information Resource is to assemble, characterize, and distribute high-quality DNA samples of known provenance with accompanying demographic, geographic, and behavioral information in order to stimulate and facilitate research in primate genetic diversity and evolution, comparative genomics, and population genetics. Further research in these areas will advance our understanding of human origins, the biological basis of cognitive processes, evolutionary history and relationships, and social structure, and will provide critical scientific information needed to facilitate conservation of biological diversity. The derived DNA will be openly available to the broad scientific community who agree to restrict use to non-commercial purposes. DNA and cell culture samples are distributed only to qualified professional persons who are associated with recognized research, medical, or educational organizations engaged in research. | demographic data, geographic data, behavioral data, genetic diversity, evolution, comparative genomics, population genetics, dna, cell culture, frozen |
is listed by: One Mind Biospecimen Bank Listing has parent organization: Coriell Cell Repositories |
All | NSF 0629321 | Public, Non-commercial, The derived DNA will be openly available to the broad scientific community | nlx_143841 | SCR_004614 | SciCrunch Registry | Integrated Primate Biomaterials and Information Resource, IPBIR Repository, IPBIR - Integrated Primate Biomaterials Information Resource, Integrated Primate Biomaterials Information Resource | 2026-10-31 12:19:09 | 0 | |||||
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ROAR Resource Report Resource Website 10+ mentions |
ROAR (RRID:SCR_005951) | ROAR | data or information resource, database, registry | Listing of institutional repositories for depositing preprints of published materials with the aim of promoting the development of open access by providing timely information about the growth and status of repositories throughout the world. Open access to research maximizes research access and thereby also research impact, making research more productive and effective. Repository Types: * Research Institutional or Departmental * Research Multi-institution Repository * Research Cross-Institutional * e-Journal/Publication * e-Theses * Database/A&I Index * Research Data * Open and Linked Data * Learning and Teaching Objects * Demonstration * Web Observatory * Other Repository Software: * ARNO * Bepress * CDS Invenio * ContentDM by OCLC * DIGIBIB * DigiTool * DiVA * DoKS * DSpace * EDOC * EPrints * Equella * ETD-db * Fedora ** Fez * Greenstone * HAL * i-Tor * IntraLibrary * Keystone DLS * MiTOS * MyCoRe * Open Journal System * Open Repository * OPUS (Open Publications System) * Other softwares (various) * PMB Services * SBCAT * SciX * SobekCM * WIKINDX * Zentity | archive, repository, registry, software, open access |
is listed by: FORCE11 is related to: ROARMAP: Registry of Open Access Repositories Mandatory Archiving Policies is related to: ROARMAP: Registry of Open Access Repositories Mandatory Archiving Policies has parent organization: University of Southampton; Southampton; United Kingdom |
JISC | Open unspecified license, The community can contribute to this resource | nlx_151309 | SCR_005951 | SciCrunch Registry | Registry of Open Access Repositories | 2026-10-31 12:20:11 | 22 | ||||||
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Digital Asset Management System Resource Report Resource Website |
Digital Asset Management System (RRID:SCR_000491) | DAMS | data repository, image repository, service resource, software repository, software resource, storage service resource | A digital repository designed to store and manage digital assets of UC San Diego. The flexible architecture can accept a variety of data formats, schemas and web services when ingesting digital assets. It stores digital content files and allows for the creation, indexing and searching of associated metadata to locate and retrieve the content files. Content can be composed of files in any format, including text, sound, video, and images. The DAMS is also designed to facilitate the transfer and submission of the Library's digital assets to Chronopolis and the California Digital Library's Merritt, and can easily be extended to serve other purposes. Additionally, the DAMS is able to export data in many formats, including METS, HTML, OAI, RSS, CSV. Future plans include linking data sets with other universities and organizations. For more information about the DAMS, including the data model and technical diagram, see Github, https://github.com/ucsdlib: * DAMS Manual, https://github.com/ucsdlib/dams/wiki/DAMS-Manual * DAMS Hydra Head, https://github.com/ucsdlib/damspas * DAMS REST API, https://github.com/ucsdlib/dams/wiki/REST-API * DAMS Ontology, https://github.com/ucsdlib/dams/tree/master/ontology Additional information on Hydra is available at Project Hydra and Duraspace. | digital repository, store and manage digital assets of UC San Diego, digital repository designed to store and manage digital assets, |
is listed by: GitHub is related to: UC3 Merritt is related to: chronopolis has parent organization: University of California at San Diego; California; USA |
Restricted | nlx_158282 | https://github.com/ucsdlib/dams | http://libraries.ucsd.edu/about/digital-library/dams.html | SCR_000491 | SciCrunch Registry | UC San Diego Library DAMS repository, UC San Diego Library Digital Asset Management System | 2026-10-31 12:12:39 | 0 | |||||
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Cell Type Ontology Resource Report Resource Website 10+ mentions |
Cell Type Ontology (RRID:SCR_004251) | CL | controlled vocabulary, data or information resource, ontology | Ontology designed as a structured controlled vocabulary for cell types. It was constructed for use by the model organism and other bioinformatics databases. It includes cell types from prokaryotes, mammals, and fungi. The ontology is available in the formats adopted by the Open Biological Ontologies umbrella and is designed to be used in the context of model organism genome and other biological databases. | cell ontology, ontology repository |
is listed by: BioPortal is listed by: Ontology Lookup Service is related to: CELDA Ontology is related to: OBO is related to: Cell Line Knowledge Base |
BBSRC ; MRC ; NIH ; NSF DBI-9978564; NSF PGRP-0321666 |
PMID:15693950 | Free, Freely available | nlx_26501 | http://purl.bioontology.org/ontology/CL | http://cellontology.org, http://www.obofoundry.org/cgi-bin/detail.cgi?id=cell, | SCR_004251 | SciCrunch Registry | cellontology.org, Obo-cell-type, Cell Ontology | 2026-10-31 12:18:23 | 10 | |||
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OntoSoft Resource Report Resource Website |
OntoSoft (RRID:SCR_017328) | data or information resource, portal, software repository, software resource | A repository for geosciences software. Registry for software for geoscientists. Part of NSF EarthCube OntoSoft project. | registry, software, repository, geoscientist | has parent organization: University of Southern California; Los Angeles; USA | Restricted | SCR_017328 | SciCrunch Registry | 2026-10-31 12:16:51 | 0 | ||||||||||
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Marmoset Brain Connectivity Atlas Resource Report Resource Website 10+ mentions |
Marmoset Brain Connectivity Atlas (RRID:SCR_015964) | atlas, data or information resource, data repository, database, service resource, storage service resource | Brain connectivity atlas to create systematic, digital repository for data on connections between different cortical areas, in primate species. Data repository for connections between different cortical areas in marmoset monkeys. Allows access to data set and enables other interpretations of data, in light of future evolution of knowledge about marmoset cortex. | cortex, marmoset, monkey, cerebral, brain, architecture, primate |
has parent organization: Monash University; Melbourne; Australia has parent organization: Nencki Institute of Experimental Biology; Warsaw; Poland works with: Nencki-Monash template |
Australian Research Council CE140100007; Australian Research Council DP140101968; European Regional Development Fund ; International Neuroinformatics Coordinating Facility ; NIDA R01 DA036400; NIMH R01 MH087988 |
DOI:10.1038/s41467-020-14858-0 PMID:27099164 |
Free, Freely available | http://marmoset.braincircuits.org, http://analysis.marmosetbrain.org | SCR_015964 | SciCrunch Registry | Marmoset Monkey Cerebral Cortex Connectivity Atlas | 2026-10-31 12:16:36 | 26 | ||||||
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rOpenSci Resource Report Resource Website 1+ mentions |
rOpenSci (RRID:SCR_013986) | software repository, software resource | A software repository which provides and builds open source tools for open science. rOpenSci provides packages that allow access to data repositories through the R statistical programming environment. R packages are grouped by what the tools do: acquire data, full-text of journal articles, altmetrics, data-publication, reproducibility, and data visualization. | software repository, R code, R statistical programming environment, open science |
is listed by: Connected Researchers is related to: R Project for Statistical Computing is related to: Connected Researchers |
SCR_013986 | SciCrunch Registry | 2026-10-31 12:21:27 | 9 | |||||||||||
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ConnectomeDB Resource Report Resource Website 50+ mentions |
ConnectomeDB (RRID:SCR_004830) | ConnectomeDB | data or information resource, data repository, database, image collection, image repository, service resource, storage service resource | Data management platform that houses all data generated by the Human Connectome Project - image data, clinical evaluations, behavioral data and more. ConnectomeDB stores raw image data, as well as results of analysis and processing pipelines. Using the ConnectomeDB infrastructure, research centers will be also able to manage Connectome-like projects, including data upload and entry, quality control, processing pipelines, and data distribution. ConnectomeDB is designed to be a data-mining tool, that allows users to generate and test hypotheses based on groups of subjects. Using the ConnectomeDB interface, users can easily search, browse and filter large amounts of subject data, and download necessary files for many kinds of analysis. ConnectomeDB is designed to work seamlessly with Connectome Workbench, an interactive, multidimensional visualization platform designed specifically for handling connectivity data. De-identified data within ConnectomeDB is publicly accessible. Access to additional data may be available to qualified research investigators. ConnectomeDB is being hosted on a BlueArc storage platform housed at Washington University through the year 2020. This data platform is based on XNAT, an open-source image informatics software toolkit developed by the NRG at Washington University. ConnectomeDB itself is fully open source. | brain, connectivity, human, adult human, evaluation, clinical, behavior, data set, diffusion imaging, resting-state fmri, task-evoked fmri, t1-weighted mri, t2-weighted mri, structural mapping, myelin mapping, magnetoencephalography, electroencephalography, fmri, twin |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: XNAT - The Extensible Neuroimaging Archive Toolkit has parent organization: Washington University in St. Louis; Missouri; USA works with: Connectome Workbench |
Healthy, Twin, Non-twin sibling | NIH Blueprint for Neuroscience Research ; Washington University in St. Louis; Missouri; USA ; McDonnell Center for Systems Neuroscience ; NIMH 1U54MH091657 |
PMID:22366334 | Account required, Open unspecified license, Acknowledgement required, See Data Use Terms, The community can contribute to this resource | nlx_143923 | SCR_004830 | SciCrunch Registry | 2026-10-31 12:18:29 | 63 | |||||
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MetabolomeXchange Resource Report Resource Website 1+ mentions |
MetabolomeXchange (RRID:SCR_014664) | data or information resource, database, portal | International effort whose objective is to improve and encourage the exchange of Metabolomics data. Datasets are stored in external data repositories independent of MetabolomeXchange; however, MetabolomeXchange allows users to browse datasets directly then proceed to the external repository for more information. | metabolomics, dataset, exchange, international, portal, consortium |
is listed by: Metabolomics Workbench is affiliated with: Omics Discovery Index |
European Union COSMOS EC312941 | Open source | r3d100013740 | https://github.com/leidenuniv-lacdr-abs | SCR_014664 | SciCrunch Registry | 2026-10-31 12:19:18 | 6 | |||||||
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Kinetic Models of Biological Systems (KiMoSys) Resource Report Resource Website 1+ mentions |
Kinetic Models of Biological Systems (KiMoSys) (RRID:SCR_017423) | data access protocol, data repository, service resource, software resource, storage service resource, web service | Web application for quantitative KInetic MOdels of biological SYStems. Platform includes public data repository of relevant published measurements, including metabolite concentrations, flux data, and enzyme measurements and tools in order to build ODE-based kinetic model. Designed to search, exchange and disseminate experimental data and associated kinetic models for systems modeling community. | Quantitative, kinetic, model, biological, system, data, storage, search, exchange, experiment |
is recommended by: NIDDK Information Network (dkNET) is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases |
EU ; Portuguese national funding agency for science ; research and technology. |
Restricted | r3d100011562 | https://doi.org/10.17616/R3864V | https://fairsharing.org/FAIRsharing.6erywc | SCR_017423 | SciCrunch Registry | , Kinetic Models of Biological Systems (KiMoSys), KInetic MOdels of biological SYStems, KiMoSys | 2026-10-31 12:16:51 | 1 |
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