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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Caenorhabditis Genetics Center Resource Report Resource Website 1000+ mentions |
Caenorhabditis Genetics Center (RRID:SCR_007341) | CGC | organism supplier, material resource, biomaterial supply resource, cell repository | Center that acquires, maintains, and distributes genetic stocks and information about stocks of the small free-living nematode Caenorhabditis elegans for use by investigators initiating or continuing research on this genetic model organism. A searchable strain database, general information about C. elegans, and links to key Web sites of use to scientists, including WormBase, WormAtlas, and WormBook are available. | non-human animal, caenorhabditis elegans, chromosome, database, model, mutant, nematode, nomenclature, model organism, protein, transgenic, web accessible database, genetic stock, germplasm, genotype, FASEB list |
is used by: NIF Data Federation is listed by: One Mind Biospecimen Bank Listing is related to: C. elegans Gene Knockout Consortium is related to: Expression Patterns for C. elegans promoter GFP fusions has parent organization: University of Minnesota Twin Cities; Minnesota; USA |
NIH OD010440 | nif-0000-00240 | https://orip.nih.gov/comparative-medicine/programs/invertebrate-models http://www.cbs.umn.edu/research/resources/cgc |
http://biosci.umn.edu/CGC/, http://www.cgc.cbs.umn.edu | SCR_007341 | 2026-02-16 09:46:56 | 3842 | ||||||
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MAxEntScan Resource Report Resource Website 50+ mentions |
MAxEntScan (RRID:SCR_016707) | MAxEntScan | service resource, software application, software resource, simulation software | Software tool as a framework for modeling the sequences of short sequence motifs based on the maximum entropy principle (MEP). Used for sequence motifs such as those involved in RNA splicing. | modeling, sequence, short, motif, maximum, entropy, principle, MEP, RNA, splicing |
is listed by: OMICtools has parent organization: Massachusetts Institute of Technology; Massachusetts; USA; |
NSF Grant 0218506; NIH ; Lee Kuan Yew Scholarship for the goverment of Singapore |
PMID:15285897 | Free, Available for download, Freely available | SCR_016707 | Maximum Entropy Scan, MAxEntScan, MAximumEntropyScan | 2026-02-16 09:49:05 | 65 | ||||||
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CoSMoS_Analysis Resource Report Resource Website 10+ mentions |
CoSMoS_Analysis (RRID:SCR_016896) | CoSMoS Analysis | software application, data processing software, data analysis software, image analysis software, software resource | Software tools for analyzing co-localization single-molecule spectroscopy image data. | co-localization, single, molecule, spectroscopy, image, data, analysis | NIGMS ; NIH |
Free, Available for download, Freely available | SCR_016896 | co-localization single-molecule spectroscopy, Co-localization Single-Molecule Spectroscopy Analysis, co-localization single molecule spectroscopy, CoSMoS | 2026-02-16 09:49:07 | 17 | ||||||||
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ValIdated Systematic IntegratiON of epigenomic data Resource Report Resource Website 1+ mentions |
ValIdated Systematic IntegratiON of epigenomic data (RRID:SCR_016921) | VISION | project portal, database, catalog, portal, data or information resource | International project to analyze mouse and human hematopoiesis, and provide a tractable system with clear clinical significance and importance to NIDDK. Collection of information from the flood of epigenomic data on hematopoietic cells as catalogs of validated regulatory modules, quantitative models for gene regulation, and a guide for translation of research insights from mouse to human. | analyze, mouse, human, hematopoietic, cell, blood, component, collection, epigenomic, data, catalog, gene, regulation | is listed by: NIDDK Information Network (dkNET) | National Institute for Diabetes and Digestive Diseases ; NIH ; NIDDK |
SCR_016921 | ValIdated Systematic IntegratiON of epigenomic data, ValIdated Systematic IntegratiON | 2026-02-16 09:49:07 | 9 | ||||||||
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PanoramaWeb Resource Report Resource Website |
PanoramaWeb (RRID:SCR_017136) | web service, data access protocol, data repository, software resource, storage service resource, service resource, data or information resource | Repository software for targeted mass spectrometry assays from Skyline. Targeted proteomics knowledge base. Public repository for quantitative data sets processed in Skyline. Facilitates viewing, sharing, and disseminating results contained in Skyline documents. | repository, software, targeted, mass, spectrometry, data, proteomic, quantitative, viewing, sharing, disseminating, result, , bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: University of Washington; Seattle; USA works with: Skyline |
NIGMS R01 GM103551; NIGMS R01 GM121696; NHGRI U54 HG008097; NIH R01 AR071762; University of Washington Proteomics Resource |
DOI:10.1074/mcp.RA117.000543 | Free, Freely available | biotools:panorama | https://bio.tools/panorama | SCR_017136 | 2026-02-16 09:49:10 | 0 | ||||||
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NIH Figshare Archive Resource Report Resource Website 1+ mentions |
NIH Figshare Archive (RRID:SCR_017580) | NIH Figshare | data repository, database, storage service resource, service resource, data or information resource | Repository to make datasets resulting from NIH funded research more accessible, citable, shareable, and discoverable. Data submitted will be reviewed to ensure there is no personally identifiable information in data and metadata prior to being published and in line with FAIR -Findable, Accessible, Interoperable, and Reusable principles. Data published on Figshare is assigned persistent, citable DOI (Digital Object Identifier) and is discoverable in Google, Google Scholar, Google Dataset Search, and more.Complited on July,2020. Researches can continue to share NIH funded data and other research product on figshare.com. | Respository, data, NIH funded, data set, FAIR |
is recommended by: NIDDK Information Network (dkNET) is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases is related to: FigShare is related to: FigsharePlus |
NIH | Restricted | SCR_017580 | NIH, Figshare, Fig Share, NIH Figshare, NIH Fig share, National Institute of Health | 2026-02-16 09:49:16 | 9 | |||||||
|
AmoebaDB Resource Report Resource Website 1+ mentions |
AmoebaDB (RRID:SCR_017592) | analysis service resource, database, production service resource, service resource, data or information resource | Integrated genomic and functional genomic database for Entamoeba and Acanthamoeba parasites. Contains genomes of three Entamoeba species and microarray expression data for E. histolytica. Integrates whole genome sequence and annotation and includes experimental data and environmental isolate sequences provided by community researchers. | Genomic, functional, database, Entamoeba, Acanthamoeba, parasite, microarray, expression, data, experimental, isolate, sequence, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: Eukaryotic Pathogen Database Resources |
NIDA ; Department of Health and Human Services ; NIH |
PMID:20974635 | Free, Freely available | biotools:amoebadb, r3d100012457 | https://bio.tools/amoebadb https://doi.org/10.17616/R3PX9Q |
SCR_017592 | 2026-02-16 09:49:16 | 7 | ||||||
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Distributed Archives for Neurophysiology Data Integration Resource Report Resource Website 50+ mentions |
Distributed Archives for Neurophysiology Data Integration (RRID:SCR_017571) | DANDI | service resource, data repository, storage service resource | DANDI is a platform for publishing, sharing, and processing neurophysiology data funded by the BRAIN Initiative. The archive is not just an endpoint to dump data, it is intended as a living repository that enables collaboration within and across labs, and for others, the entry point for research. | publishing data, sharing data, processing data, neurophysiology data, BRAIN Initiative, |
is used by: BICCN is recommended by: BRAIN Initiative is listed by: DataCite is listed by: FAIRsharing is related to: BRAIN Initiative is related to: Allen Institute for Brain Science is related to: NeuroSift is related to: Ecosystem for Multi-modal Brain-behavior Experimentation and Research |
NIH R24 MH117295 | Free, Freely available | DOI:10.25504/FAIRsharing.f2c119, DOI:10.48324, r3d100013638 | https://doi.org/10.48324/ https://dx.doi.org/10.48324/ https://fairsharing.org/10.25504/FAIRsharing.f2c119 https://doi.org/10.17616/R31NJN0M |
SCR_017571 | 2026-02-16 09:49:16 | 52 | ||||||
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Multi-omics Visualization Platform Resource Report Resource Website 1+ mentions |
Multi-omics Visualization Platform (RRID:SCR_018077) | MVP | software application, data processing software, data visualization software, data analysis software, software resource | Software tool as plugin to enable viewing of results produced from workflows integrating genomic sequencing data and mass spectrometry proteomics data. Plugin to Galaxy bioinformatics workbench which enables visualization of mass spectrometry-based proteomics data integrated with genomic and/or transcriptomic sequencing data. Useful for verifying quality of results and characterizing novel peptide sequences identified using multi-omic proteogenomic approach. | Proteogenomics, data, multi-omics, mass spectrometry, proteomics, genomics, transcriptomics, Galaxy Project, data visualization, bio.tools |
is listed by: bio.tools is listed by: Debian |
NIH U24 CA199347 | Free, Available for download, Freely available | biotools:mvp_a | http://galaxyp.org https://bio.tools/mvp_a |
SCR_018077 | Multi-omics Visualization Platform, Galaxy MVP | 2026-02-16 09:49:23 | 1 | |||||
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NIH COVID-19 Portfolio Resource Report Resource Website 10+ mentions |
NIH COVID-19 Portfolio (RRID:SCR_018295) | web service, data access protocol, software resource, service resource, data or information resource | NIH comprehensive, curated source for publications related to COVID-19. Includes articles from PubMed and pre-prints from arXiv, medRxiv, bioRxiv, and ChemRxiv. Updated daily. NIH Office of Portfolio Analysis has developed this resource to explore and analyze set of advances in COVID‑19 research as they accumulate in real time, and complements efforts by NLM to aggregate full text documents broadly related to COVID-19 and other outbreaks, and articles on COVID‑19 specific to PubMed database. | COVID-19 publication, COVID-19 article, COVID-19 data, COVID-19 full text document, COVID-19 pre-print | COVID-19 | NIH | Free, Freely available | SCR_018295 | iSearch COVID-19 portfolio, COVID-19 Portfolio Tool From the Office of Portfolio Analysis, iSearch COVID-19 Portfolio, COVID-19 Portfolio | 2026-02-16 09:49:27 | 17 | ||||||||
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Data and Computational Resources to Address COVID-19 Resource Report Resource Website |
Data and Computational Resources to Address COVID-19 (RRID:SCR_018274) | data or information resource, topical portal, disease-related portal, portal | COVID-19 open access data and computational resources provided by federal agencies, including NIH, public consortia, and private entities. Continuously updated as more information becomes available. These resources are being shared for scientific and public health interests, and content is responsibility of resource organizers. | COVID-19, COVID-19 data, federal agency data, computational resource, public health information, SARS-CoV-2, NIH |
lists: Nextstrain lists: outbreak.info lists: Research Data Alliance Working Group lists: UC Health clinical data warehouse lists: Vivli lists: Cloud resources for COVID-19 research lists: COVID-19 High Performance Computing Consortium lists: Data-Against-COVID Team lists: NASEM Standing Committee on Emerging Infectious Diseases and 21st Century Health Threats lists: NIAID Overview of Coronaviruses lists: Schema.org lists: Virus Pathogen Resource (ViPR) lists: Modeling Infectious Disease Agents Study online portal for COVID-19 lists: LitCovid lists: Broad Terra cloud commons for pathogen surveillance lists: COVID-19 research data on Figshare lists: Dimensions COVID-19 publications, datasets and clinical trials lists: COVID-19 Open Research Dataset lists: Global Initiative on Sharing All Influenza Data |
COVID-19 | NIH | Free, Freely available | SCR_018817 | SCR_018274 | Open Access Data and Computational Resources to Address COVID-19, NIH Open-Access Data and Computational Resources to Address COVID-19 | 2026-02-16 09:49:26 | 0 | ||||||
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GLYCAM-Web Resource Report Resource Website 50+ mentions |
GLYCAM-Web (RRID:SCR_018260) | web service, data access protocol, software resource, topical portal, portal, data or information resource | Web provides tools for modeling 3D structures of molecules and complexes containing carbohydrates including oligosaccharide conformation modeling and glycoprotein 3D structure modeling. Used to simplify prediction of three dimensional structures of carbohydrates and macromolecular structures involving carbohydrates. | Glycosylated SARS-Cov-2 Spike protein, SARS-Cov-2, SARS-Cov-2 Spike protein, spike protein, 3D structure, carbohydrate, oligosaccharide conformation, modeling, structure modeling, data | has parent organization: University of Georgia; Georgia; USA | COVID-19, COVID19 | NIH | Free, Freely available | SCR_018260 | GLYCAM | 2026-02-16 09:49:27 | 96 | |||||||
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Minimum Information about Biosynthetic Gene cluster Resource Report Resource Website 50+ mentions |
Minimum Information about Biosynthetic Gene cluster (RRID:SCR_023660) | MIBiG | data or information resource, database, project portal, portal | MIBiG is genomic standards consortium project and biosynthetic gene cluster database used as reference dataset. Provides community standard for annotations and metadata on biosynthetic gene clusters and their molecular products. Standardised data format that describes minimally required information to uniquely characterise biosynthetic gene clusters. MIBiG 2.0 is expended repository for biosynthetic gene clusters of known function. MIBiG 3.0 is database update comprising large scale validation and re-annotation of existing entries and new entries. Community driven effort to annotate experimentally validated biosynthetic gene clusters. | Genomic standards consortium project, community standard, annotations and metadata standards, biosynthetic gene clusters, sequence framework, biosynthetic gene cluster data, | Netherlands Organization for Scientific Research VENI grant ; NSF CAREER Award ; UK Biotechnology and Biological Sciences Research Council ; Novo Nordisk Foundation ; NIH U41 AT008718; Danish National Research Foundation ; NCCIH U24 AT010811; NCCIH F32 AT011475; Natural Sciences and Engineering Council of Canada Discovery grant ; European Union Horizon 2020 projects CARTNET ; Horizon 2020 Marie Skłodowska-Curie ; U.S. Department of Energy ; Portuguese Science and Technology Foundation ; U.S. National Science Foundation ; National Research Foundation of Korea ; NIGMS GM134688; NIAID R01AI155694; Netherlands eScience Center Accelerating Scientific Discoveries Grant ; Funds of the Chemical Industry Germany ; UK government Department for Environment ; Food and Rural Affairs ; German Chemical Industry ; Natural Sciences and Engineering Council of Canada |
PMID:36399496 DOI:10.1093/nar/gkz882 |
Free, Freely available | SCR_023660 | MIBiG 3.0, MIBiG 2.0 | 2026-02-16 09:50:45 | 55 | |||||||
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Mouse Models For Alzheimer's Disease Research Resource Report Resource Website 1+ mentions |
Mouse Models For Alzheimer's Disease Research (RRID:SCR_000708) | data or information resource, model, narrative resource | An information resource about several models for mice to develop Alzheimer's-related characteristics as they age. | alzheimer's, aging, mouse, mice, model, transgenic, research | has parent organization: Jackson Laboratory | Aging | NIH | Non-Commercial, Personal Use | nif-0000-00183 | http://jaxmice.jax.org/research/neurobiology/alzheimers-agedmodels.html, http://research.jax.org/grs/alzheimers.html | SCR_000708 | MMFADR | 2026-02-16 09:45:20 | 1 | |||||
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Knockout Mouse Project Resource Report Resource Website 10+ mentions |
Knockout Mouse Project (RRID:SCR_005571) | KOMP, NIH KOMP | data or information resource, project portal, portal | Project is providing critical tools for understanding gene function and genetic causes of human diseases. Project KOMP is focused on generating targeted knockout mutations in mouse ES cells. Second phase, KOMP2, relies upon successful generation of strains of knockout mice from these ES cells. Information from JAX about their contributions to KOMP project. | Generating, knockout, mutation, mouse, ES cell, embryonic, stem, c57bl/6 |
is listed by: NIDDK Information Network (dkNET) is listed by: NIDDK Research Resources is related to: KOMP2 is related to: KOMP2 is related to: StatPackets has parent organization: International Knockout Mouse Consortium has parent organization: National Institutes of Health is parent organization of: Knockout Mouse Project Repository is parent organization of: Knockout Mouse Project Repository at JAX |
NIH ; NIH Blueprint for Neuroscience Research |
Free, Freely available | nlx_145296, SCR_017527 | https://grants.nih.gov/grants/guide/rfa-files/rfa-rr-06-005.html | http://www.nih.gov/science/models/mouse/knockout/index.html | SCR_005571 | NIH Knockout Mouse Project, Knock-Out Mouse Project | 2026-02-16 09:46:29 | 10 | ||||
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Human Microbiome Project Resource Report Resource Website 100+ mentions |
Human Microbiome Project (RRID:SCR_012956) | HMP, NIH HMP, HMP1 | data or information resource, project portal, portal | NIH Project to generate resources to characterize the human microbiota and to analyze its role in human health and disease at several different sites on the human body, including nasal passages, oral cavities, skin, gastrointestinal tract, and urogenital tract using metagenomic and traditional approach to genomic DNA sequencing studies.HMP was supported by the Common Fund from 2007 to 2016. | generate, resource, human, body, microbiota, analyze, health, disease, metagenomic, DNA, sequesncing, data |
lists: Pathogen Portal lists: DNACLUST lists: QIIME lists: mothur lists: Greengenes lists: Ribosomal Database Project lists: DeconSeq lists: FragGeneScan lists: MetAMOS lists: MetaPhlAn lists: MetaPhyler lists: METAREP lists: PRINSEQ lists: TagCleaner lists: BioCyc lists: MG-RAST lists: Core Gene Evaluation Script lists: IMG System lists: RAST Server lists: GINGKO lists: inVUE lists: LEfSe lists: Metastats lists: MicrobiomeUtilities lists: Hypothesis Testing and Power Calculations for Comparing Metagenomic Samples from HMP lists: HMPTrees lists: Simrank lists: speciateIT lists: Unifrac lists: Fast-Unifrac lists: SitePainter lists: BMTagger lists: HUMAnN lists: Metapath lists: IMG System is related to: biobakery is related to: Integrative Human Microbiome Project is related to: MicrobiomeDB has parent organization: National Institutes of Health is parent organization of: HMP Data Analysis and Coordination Center |
NIH | nif-0000-25316 | https://www.hmpdacc.org/ihmp/ https://www.hmpdacc.org/hmp |
http://nihroadmap.nih.gov/hmp/ | SCR_012956 | Human Microbiome Project, NIH HMP, HMP1, HMP, NIH Human Microbiome Project | 2026-02-16 09:48:19 | 385 | |||||
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SegAN Resource Report Resource Website 1+ mentions |
SegAN (RRID:SCR_016215) | data processing software, software application, software resource, image analysis software | Image analysis software for medical image segmentation. The software is fueled by an end-to-end adversarial neural network that generates segmentation label maps. | neural, network, segmentation, pixel, spatial, image, medical, analysis, labelling, loss function, segmentor | NIH ; NLM ; LHNCBC HHSN276201500692P |
Free, Available for download | SCR_016215 | Semantic Segmentation with Adversarial Learning (SegAN), Semantic Segmentation with Adversarial Learning, SegAN: Semantic Segmentation with Adversarial Learning | 2026-02-16 09:48:59 | 4 | |||||||||
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Nonhuman Primate Reference Transcriptome Resource Resource Report Resource Website 10+ mentions |
Nonhuman Primate Reference Transcriptome Resource (RRID:SCR_017534) | NHPRTR | data or information resource, project portal, portal | Nonhuman Primate reference transcriptome resource consisting of deep sequencing complete transcriptomes (RNA-seq) from multiple NHP species. | Nonhuman, primate, reference, transcriptome, deep, sequencing, RNAseq, data, species | NIH | Free, Freely available | SCR_017534 | Nonhuman Primate Reference Transcriptome Resource | 2026-02-16 09:49:15 | 10 | ||||||||
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Mouse Connectome Project Resource Report Resource Website |
Mouse Connectome Project (RRID:SCR_017313) | MCP | data or information resource, project portal, portal | Project to create complete mesoscale connectivity atlas of the C57Black/6 mouse brain and to subsequently generate its global neural networks. | mesoscale, connectivity, atlas, C57Black/6, mouse, brain, neural, network |
is used by: BICCN has parent organization: University of Southern California; Los Angeles; USA |
NIH | Free, Freely available | SCR_017313 | The Mouse Connectome Project, Mouse Connectome Project | 2026-02-16 09:49:12 | 0 | |||||||
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Dynamic Regulatory Events Miner Resource Report Resource Website 1+ mentions |
Dynamic Regulatory Events Miner (RRID:SCR_003080) | DREM | data processing software, software application, software resource | The Dynamic Regulatory Events Miner (DREM) allows one to model, analyze, and visualize transcriptional gene regulation dynamics. The method of DREM takes as input time series gene expression data and static transcription factor-gene interaction data (e.g. ChIP-chip data), and produces as output a dynamic regulatory map. The dynamic regulatory map highlights major bifurcation events in the time series expression data and transcription factors potentially responsible for them. DREM 2.0 was released and supports a number of new features including: * new static binding data for mouse, human, D. melanogaster, A. thaliana * a new and more flexible implementation of the IOHMM supports dynamic binding data for each time point or as a mix of static/dynamic TF input * expression levels of TFs can be used to improve the models learned by DREM * the motif finder DECOD can be used in conjuction with DREM and help find DNA motifs for unannotated splits * new features for the visualization of expressed TFs, dragging boxes in the model view, and switching between representations | transcription, gene regulation, dynamics, time series, gene expression, static, dynamic, transcription factor-gene interaction, chip-chip, transcription factor, regulatory network, hidden markov model, systems biology, gene regulatory network, times series expression data, dynamic network, chip-seq | has parent organization: Carnegie Mellon University; Pennsylvania; USA | NIH ; NIGMS 1RO1 GM085022; NIAID DNO1 AI-5001; NSF 0448453 |
PMID:22897824 | Free, Available for download, Freely available | nif-0000-30478 | SCR_003080 | Dynamic Regulatory Events Miner (DREM) | 2026-02-16 09:46:07 | 5 |
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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 2U24DK097771-09.
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