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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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U.S. Antarctic Program Data Coordination Center Resource Report Resource Website 1+ mentions |
U.S. Antarctic Program Data Coordination Center (RRID:SCR_002221) | USAP-DCC | data or information resource, data repository, database, service resource, storage service resource | Assists scientists in finding Antarctic scientific data of interest and submitting data for long-term preservation in accordance with their obligations under the National Science Foundation (NSF) Office of Polar Programs (OPP) Data Policy. | antarctica, southern ocean, polar |
is listed by: CINERGI has parent organization: Marine Geoscience Data System |
NSF | Free, Freely available | r3d100010660, nlx_154744 | https://doi.org/10.17616/R31898 | http://www.usap-data.org/ | SCR_002221 | SciCrunch Registry | 2026-09-19 12:49:54 | 6 | |||||
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Arvados Resource Report Resource Website 1+ mentions |
Arvados (RRID:SCR_002223) | arvados | data repository, service resource, storage service resource | Bioinformatics platform for storing, organizing, processing, and sharing genomic and other biomedical big data. Designed to make it easier for bioinformaticians to develop analyses, developers to create genomic web applications and IT administers to manage large-scale compute and storage genomic resources. Designed to run on top of cloud operating systems such as Amazon Web Services and OpenStack. Currently, there are implementations that work on AWS and Xen+Debian/Ubuntu. Functionally, Arvados has two major sets of capabilities: (a) data management and (b) compute management. | mapreduce/hadoop, genomic, biomedical, data sharing, compute, data management, cloud | is listed by: Debian | Free, Freely available | OMICS_01835 | https://sources.debian.org/src/arvados/ | SCR_002223 | SciCrunch Registry | 2026-09-19 12:49:55 | 3 | |||||||
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National Oceanographic Data Center Resource Report Resource Website 10+ mentions |
National Oceanographic Data Center (RRID:SCR_002189) | NODC | data or information resource, data repository, database, service resource, storage service resource | Accepts and provides access to biology data, buoy data, chlorophyll, nutrients, ocean currents, oxygen, plankton, profile data, salinity, satellite data, sea level, snow and ice, temperature, waves. Please note that routine underway oceanographic shipboard data collected with standard equipment aboard the UNOLS fleet (e.g. CTD, ADCP, XBT, MET, TSG) are routinely transmitted to NODC via Rolling Deck to Repository (R2R). NODC Provides: * The World's largest collection of freely available oceanographic data * Water temperatures dating back to the late 1700's and measuring thousands of meters deep * A State of the Ocean Climate from NODC's Ocean Climate Lab and Satellite Team's scientific analyses * Scientific journals, rare books, historical photo collections and maps through the NOAA Central Library, a division of NODC * Data management expertise including metadata training through NODC's National Coastal Data Development Center | oceanographic data, water temperature, ocean climate, marine, ocean |
is listed by: CINERGI has parent organization: National Oceanic and Atmospheric Administration |
U.S. Department of Commerce | Free, Freely available | nlx_154699 | SCR_002189 | SciCrunch Registry | National Oceanographic Data Center (NODC) | 2026-09-19 12:49:54 | 31 | ||||||
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FR-HIT Resource Report Resource Website 10+ mentions |
FR-HIT (RRID:SCR_002181) | FR-HIT | software resource | An efficient fragment recruitment software program for next generation sequences against microbial reference genomes. It produces similar sensitivity of BLASTN, but runs at a 100 times higher speed. The algorithm adopts a seeding heuristic strategy with overlapping k-mer hashing to locate candidate matching blocks on the reference sequences, and then apply an effective filtering within the candidate blocks to filter out blocks that do not meet the minimum criteria for containing an alignment with specified parameters. For each candidate block that passed the filter, the best matching sub-regions between a candidate block and a read are determined, and used subsequently by the banded Smith-Waterman algorithm to carry out the actual alignment efficiently, which will finally verify if this can be a valid recruitment hit. | metagenomics, bioinformatics, sequence analysis, next-generation sequencing |
is listed by: OMICtools has parent organization: Google Code |
Free, Freely available | OMICS_01850 | SCR_002181 | SciCrunch Registry | FR-HIT: Metagenome Fragment Recruitment at High Identity with Tolerance, Metagenome Fragment Recruitment at High Identity with Tolerance, Fragment Recruitment at High Identity with Tolerance | 2026-09-19 12:49:54 | 11 | |||||||
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Biological Magnetic Resonance Data Bank (BMRB) Resource Report Resource Website 500+ mentions |
Biological Magnetic Resonance Data Bank (BMRB) (RRID:SCR_002296) | BioMagResBank, BMRB | data or information resource, data repository, database, service resource, storage service resource | Public depository that collects, annotates, archives, and disseminates important spectral and quantitative data derived from nuclear magnetic resonance spectroscopic investigations of biological macromolecules and metabolites. Provides reference information and maintains a collection of NMR pulse sequences and computer software for biomolecular NMR. | magnetic resonance, data bank, depository, database, data repository, spectral data, quantitative data, nmr, spectroscopy, macromolecule, metabolite, metabolomics, FASEB list |
is recommended by: NIDDK Information Network (dkNET) is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases is listed by: DataCite is listed by: 3DVC is listed by: re3data.org is related to: Worldwide Protein Data Bank (wwPDB) is related to: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) is related to: Nucleic Acid Database is related to: DNA DataBank of Japan (DDBJ) is related to: PDBe - Protein Data Bank in Europe is related to: NRG-CING is related to: Worldwide Protein Data Bank (wwPDB) is related to: PDBj - Protein Data Bank Japan is related to: CCPN Data Model has parent organization: University of Wisconsin-Madison; Wisconsin; USA is parent organization of: NMR Restraints Grid |
NLM LM05799 | PMID:18288446 PMID:17984079 PMID:12766409 PMID:36478084 |
Free, Freely available | r3d100010191, nif-0000-21058 | SCR_002296 | SciCrunch Registry | BMRB, BioMagResBank, Biological Magnetic Resonance DataBank, BioMag Res Bank | 2026-09-19 12:49:56 | 790 | |||||
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metaRNASeq Resource Report Resource Website 10+ mentions |
metaRNASeq (RRID:SCR_002174) | software resource | Software package for meta-analysis of RNA-seq data. This package implements two p-value combination techniques (inverse normal and Fisher methods). It also provides a vignette explaining how to combine data from multiple RNA-seq experiments. | standalone software, unix/linux, mac os x, windows, r |
is listed by: OMICtools is related to: SMAGEXP has parent organization: CRAN |
PMID:24678608 | Free, Available for download, Freely available | OMICS_03527 | SCR_002174 | SciCrunch Registry | metaRNASeq: Meta-analysis of RNA-seq data | 2026-09-19 12:49:54 | 35 | |||||||
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BioAfrica HIV Informatics in Africa Resource Report Resource Website 1+ mentions |
BioAfrica HIV Informatics in Africa (RRID:SCR_002295) | data or information resource, portal, topical portal | The BioAfrica HIV-1 Proteomics Resource is a website that contains detailed information about the HIV-1 proteome and protease cleavage sites, as well as data-mining tools that can be used to manipulate and query protein sequence data, a BLAST tool for initiating structural analyses of HIV-1 proteins, and a proteomics tools directory. HIV Proteomics Resource contains information about each HIV-1 gene product in regard to expression, post-transcriptional / post-translational modifications, localization, functional activities, and potential interactions with viral and host macromolecules. The Proteome section contains extensive data on each of 19 HIV-1 proteins, including their functional properties, a sample analysis of HIV-1HXB2, structural models and links to other online resources. The HIV-1 Protease Cleavage Sites section provides information on the position, subtype variation and genetic evolution of Gag, Gag-Pol and Nef cleavage sites. | expression, functional, gene, aids, cleavage, database, hiv, hiv/aids databases, interaction, localization, model, modification, post-transcriptional, post-translational, protease, protein, proteome, proteomic, publication, research, sequence, software, structural, journal article | has parent organization: University of KwaZulu-Natal; Durban; South Africa | nif-0000-21050 | SCR_002295 | SciCrunch Registry | HIV Informatics in Africa | 2026-09-19 12:49:56 | 5 | |||||||||
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ARK-Genomics: Centre for Functional Genomics Resource Report Resource Website 10+ mentions |
ARK-Genomics: Centre for Functional Genomics (RRID:SCR_002214) | ARK Genomics | access service resource, core facility, data or information resource, database, organization portal, portal, service resource | Portal for studies of genome structure and genetic variation, gene expression and gene function. Provides services including DNA sequencing of model and non-model genomes using both Next Generation and Sanger sequencing , Gene expression analysis using both microarrays and Next Generation Sequencing, High throughput genotyping of SNP and copy number variants, Data collection and analysis supported in-house high performance computing facilities and expertise, Extensive EST clone collections for a number of animal species, all of commercially available microarray tools from Affymetrix, Illumina, Agilent and Nimblegen, Parentage testing using microsatellites and smaller SNP panels. ARK-Genomics has developed network of researchers whom they support through each stage of their genomics research, from grant application, experimental design and technology selection, performing wet laboratory protocols, through to analysis of data often in conjunction with commercial partners. | gene expression, farm, function, gene, genetic, animal, dna, genome, genomic, genotype, knowledge base, model, structure, variation, job, comparative genome hybridization, parentage testing, microsatellite |
is listed by: ScienceExchange is related to: Roslin Institute Labs and Facilities has parent organization: Roslin Institute works with: University of Edinburgh GenePool Next Generation Sequencing and Bioinformatics |
BBSRC | Free, Freely available | nif-0000-20966, SciEx_157 | https://genomics.ed.ac.uk/ | SCR_002214 | SciCrunch Registry | ARK Genomics, Roslin Institute ARK-Genomics | 2026-09-19 12:49:56 | 13 | |||||
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Genoscope Resource Report Resource Website 100+ mentions |
Genoscope (RRID:SCR_002172) | Genoscope | institution | French national sequencing center with the following resources: * Sequencing ** Genoscope Projects * Environmental genomics ** Microbial diversity in wastewater ** Metabolic genomics * Bioinformatics ** Atelier for comparative genomics ** Computational Systems Biology ** Servers resources *** GGB for Generic Genome Browser: graphic interface for various databases (sequence, annotation, syntenies...) for a given organism. *** MaGe for Magnifying Microbial Genomes: annotation system for microbial genomes. | environmental genomics, biocatalysis, environment, genomics, sequencing, bioinformatics, biodiversity, blast, blat, ggb, mage, metabolic, whole genome shotgun, chromosome 3, cdna, chromosome 14, alternative splicing, o��kopleura dioica, mutation, enzymatic cloning, screening, synteny, data set, genome, sequence, annotation, genome browser, FASEB list | has parent organization: CEA; Gif sur Yvette; France | Free, Freely available | Wikidata: Q3100800, ISNI: 0000 0004 0641 2997, grid.434728.e, nif-0000-20957 | https://ror.org/028pnqf58 | SCR_002172 | SciCrunch Registry | Genoscope - Centre National de S�quen�age, Genoscope - French National Sequencing Center, French National Sequencing Center, Genoscope - Centre National de Sequencage | 2026-09-19 12:49:54 | 165 | ||||||
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DEMI Resource Report Resource Website 1+ mentions |
DEMI (RRID:SCR_002291) | software resource | R package for estimating differential expression from multiple indicators that capitalizes on the high number of concurrent measurements. It extends to various experimental designs and target categories (transcripts, genes, genomic regions) as well as small sample sizes. | standalone software, affymetrix, mac os x, unix/linux, windows, r |
is listed by: OMICtools has parent organization: CRAN |
PMID:24586062 | Free, Available for download, Freely available, Acknowledgement requested | OMICS_03438 | http://cran.r-project.org/web/packages/demi/ | SCR_002291 | SciCrunch Registry | demi: Differential Expression from Multiple Indicators, Differential Expression from Multiple Indicators | 2026-09-19 12:49:56 | 6 | ||||||
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EarthChem Resource Report Resource Website 10+ mentions |
EarthChem (RRID:SCR_002207) | EarthChem | data or information resource, data repository, database, service resource, storage service resource | Accepts and makes available geochemical, geochronlogical, and petrological data (analytical and synthesis) through this community-driven effort to facilitate the preservation, discovery, access and visualization of data generated. * PetDB holds geochemical data from sub-oceanic igneous and metamorphic rocks generated at mid-ocean ridges including back-arc basins, young seamounts, and old oceanic crust. Data are compiled primarily from the published literature. * SedDB integrates marine and terrestrial sediment geochemical data compiled primarily from the published literature. * Deep Lithosphere Data Set contains geochemical and petrological data from lower crust and upper mantle xenoliths. (more info) * VentDB contains hydrothermal spring geochemistry that hosts and serves the full range of compositional data acquired on seafloor hydrothermal vents from all tectonic settings. * NAVDAT - The Western North American Volcanic and Intrusive Rock Database * Geochron is an application that helps with the onerous task of data management for geochronological and thermochronological studies. * EarthChemPortal is the one-stop-shop for geochemical data that gives users the ability to search federated databases PetDB, NAVDAT, and GEOROC simultaneously, integrated into a common output format. (more info) * The EarthChem Library is a repository for geochemical datasets (analytical data, experimental data, synthesis databases) and other digital resources relevant to the field of geochemistry, contributed by the geochemistry community. * SESAR - System for Earth SAmple Registration | geochemical, geochronological, petrological |
is listed by: CINERGI has parent organization: Columbia University; New York; USA is parent organization of: VentDB is parent organization of: PetDB is parent organization of: SedDB is parent organization of: System for Earth Sample Registration |
NSF | Free, Available for download, Freely available | nlx_154721, r3d100011538 | https://doi.org/10.17616/R3V644 | SCR_002207 | SciCrunch Registry | IEDA: EarthChem | 2026-09-19 12:49:54 | 30 | |||||
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flowCore Resource Report Resource Website 100+ mentions |
flowCore (RRID:SCR_002205) | software resource | A Bioconductor software package for high throughput flow cytometry that provides S4 data structures and basic functions. | software package, mac os x, unix/linux, windows, r, cell based assay, flow cytometry, infrastructure |
is used by: flowBeads is listed by: OMICtools has parent organization: Bioconductor |
PMID:19358741 | Artistic License, v2 | OMICS_05596 | SCR_002205 | SciCrunch Registry | flowCore: Basic structures for flow cytometry data | 2026-09-19 12:49:54 | 376 | |||||||
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MetPetDB Resource Report Resource Website 1+ mentions |
MetPetDB (RRID:SCR_002208) | MetPetDB | data or information resource, data repository, database, service resource, storage service resource | Database / data repository for metamorphic petrology that is being designed and built by a global community of metamorphic petrologists in collaboration with computer scientists at Rensselaer Polytechnic Institute as part of the National Cyberinfrastructure Initiative. | metamorphic, petrology, geology, geochemistry |
is listed by: CINERGI has parent organization: Rensselaer Polytechnic Institute; New York; USA |
NSF EAR 0949318 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154722, r3d100012514 | SCR_002208 | SciCrunch Registry | 2026-09-19 12:49:54 | 1 | |||||||
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Human Brain Project EU Resource Report Resource Website 50+ mentions |
Human Brain Project EU (RRID:SCR_002241) | HBP EU, HBP, European HBP, | data or information resource, funding resource, organization portal, portal | Global, collaborative effort for neuroscience, medicine and computing to understand brain, its diseases and its computational capabilities. Goal is to obtain access to research, data sources, platforms and infrastructures offered by other organisations, and enabling organizations outside HBP to use HBP platforms to pursue their own research. Coordinating these activities is the responsibility of the European Research Programme. | brain, ethics, neuroscience, medicine, computing, treatment, brain disease, neuroinformatics, software development, computational modeling, software, connectomics |
is related to: BigBrain is related to: Julich-Brain Cytoarchitectonic Atlas is parent organization of: subcellular application is parent organization of: Subcellular App |
Restricted | nlx_155553 | SCR_002241 | SciCrunch Registry | European Human Brain Project | 2026-09-19 12:49:55 | 69 | |||||||
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edX Resource Report Resource Website 10+ mentions |
edX (RRID:SCR_002240) | edX | online course, training resource | Massive, open, online courses (MOOCs) and interactive online classes in subjects including law, history, science, engineering, business, social sciences, computer science, public health, and artificial intelligence (AI). This non-profit was created by founding partners Harvard and MIT bringing the best of higher education to students around the world. Online courses are designed to be interesting, fun and rigorous. They are the best online courses, from the best professors and the best schools, spanning dozens of subjects. Some edX courses now offer ID verified Certificates of Achievement. A new way to demonstrate your achievement and showcase your knowledge. | education |
has parent organization: Harvard University; Cambridge; United States has parent organization: Massachusetts Institute of Technology; Massachusetts; USA; |
Free, Freely available | nlx_155551 | SCR_002240 | SciCrunch Registry | 2026-09-19 12:49:55 | 22 | ||||||||
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CIGAL Resource Report Resource Website 1+ mentions |
CIGAL (RRID:SCR_002232) | CIGAL | software resource | Software program that provides accurate real-time stimulus control, behavioral and physiological recording, and synchronization with external devices. It can also provide continuous real-time feedback of task performance and physiological responses. Task programming typically involves a simple text file specifying basic parameter settings (e.g. screen color) and a list of stimulus events, which can include images, animated movies, sound files, text stimuli, video graphics, or commands that communicate with external hardware devices. Multiple video and auditory stimuli can be presented simultaneously. Multi-channel response recording and real-time feedback features require no user programming. Advanced users can add customized stimulus events using CIGAL's real-time programming capabilities. Output files can be automatically created in a variety of output formats (e.g. FSL 3-column files, XML Events files, CSV trial tables). | magnetic resonance, stimulus control, behavioral recording, physiological recording |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Duke University; North Carolina; USA |
Free, Available for download, Freely available | nlx_155528 | http://www.nitrc.org/projects/cigal | http://fourier.biac.duke.edu/wiki/doku.php/jvs:cigal | SCR_002232 | SciCrunch Registry | Compilable Imaging Graphics and Analytical Language | 2026-09-19 12:49:55 | 6 | |||||
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NIfTImatlab Resource Report Resource Website 1+ mentions |
NIfTImatlab (RRID:SCR_002230) | NIfTImatlab | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 28, 2025. Software tool that allows the user to operate on NIfTI image files from Matlab. | matlab, nifti, image | has parent organization: New York University; New York; USA | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_155526 | SCR_002230 | SciCrunch Registry | NYU CBI NIfTI Matlab tool | 2026-09-19 12:49:55 | 1 | |||||||
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Neotoma Paleoecology Database Resource Report Resource Website 10+ mentions |
Neotoma Paleoecology Database (RRID:SCR_002190) | Neotoma | analysis service resource, data analysis service, data or information resource, data repository, database, production service resource, service resource, storage service resource | Paleoecology database for plio-pleistocene to holocene fossil data with a centralized structure for interdisciplinary, multiproxy analyses and common tool development; discipline-specific data can also be easily accessed. Data currently include North American Pollen (NAPD) and fossil mammals (FAUNMAP). Other proxies (plant macrofossils, beetles, ostracodes, diatoms, etc.) and geographic areas (Europe, Latin America, etc.) will be added in the near future. Data are derived from sites from the last 5 million years. | data sharing, paleoecology, plio-pleistocene, holocene, fossil |
is listed by: CINERGI has parent organization: Pennsylvania State University |
NSF | Free, Available for download, Freely available | nlx_154700, r3d100011761 | SCR_002190 | SciCrunch Registry | NeotomaDB, Neotoma DB | 2026-09-19 12:49:54 | 38 | ||||||
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4D Atlases Construction Resource Report Resource Website 1+ mentions |
4D Atlases Construction (RRID:SCR_002227) | software resource | Software package for constructing longitudinal atlases, which are the necessary steps for many brain-related applications. | magnetic resonance, altas, brain, software package |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: University of North Carolina at Chapel Hill School of Medicine; North Carolina; USA |
PMID:34891818 PMID:31115143 |
Free, Available for download, Freely available | nlx_155688 | http://www.nitrc.org/projects/atlas4d | http://www.med.unc.edu/bric/ideagroup/free-softwares/4d-atlases-construction | SCR_002227 | SciCrunch Registry | 4D Atlas Construction Toolbox, 4D Atlas Construction | 2026-09-19 12:49:57 | 3 | |||||
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Concierge Resource Report Resource Website 10+ mentions |
Concierge (RRID:SCR_002386) | Concierge | data management software, software application, software resource | A data management tool which stores, classifies and manages digital resources such as publications, experimental data, presentation files, etc, together with its metadata. A key feature of the software is a high level of extensibility. By installing optional plug-ins, users can customize and extend the usability of the software based on their needs. It has a function of sharing data with open digital archives based on the XooNIps system, such as neuroinformatics platforms in operation and publicly available at J-Node (http://www.neuroinf.jp). The Concierge Project is a part of neuroinformatics research by Laboratory for Neuroinformatics in RIKEN Brain Science Institute. Concierge's primary goal is to encourage research resource sharing in neuroscience communities. A key feature of the software is its pluggable configuration. Based on the basic functions, various applications can be developed as plug-ins. It has already developed several application plug-ins specific to neuroscience research, e.g. literature manager, electronic laboratory notebook, etc. | literature manager, labnote, electronic laboratory notebook, plug-in, resource management, resource sharing |
is related to: XooNIps - Neuroinformatics Base Platform System has parent organization: RIKEN Brain Science Institute |
PMID:18974800 | Open unspecified license; Mac OS X and Windows XP versions | nif-0000-00379 | SCR_002386 | SciCrunch Registry | Concierge: Personal Database Software for Managing Digital Research Resources, Concierge Project, Concierge: Personal Database Software for Digital Research Resources, The Concierge Project: Personal Database Software for Digital Research Resources | 2026-09-19 12:49:58 | 12 |
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The NIDDK Information Network (dkNET) serves the needs of basic and clinical investigators by providing seamless access to large pools of data and research resources relevant to the mission of The National Institute of Diabetes Digestive and Kidney Diseases (NIDDK). dkNET is hosted at University of California San Diego, and is supported by NIH NIDDK grant U24DK097771.
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