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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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PanoramaWeb Resource Report Resource Website |
PanoramaWeb (RRID:SCR_017136) | software resource, data access protocol, web service, service resource, storage service resource, data repository, 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 | 2026-02-15 09:21:58 | 0 | ||||||
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NIH Figshare Archive Resource Report Resource Website 1+ mentions |
NIH Figshare Archive (RRID:SCR_017580) | NIH Figshare | database, service resource, storage service resource, data repository, 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 | 2026-02-15 09:22:03 | 9 | |||||||
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AmoebaDB Resource Report Resource Website 1+ mentions |
AmoebaDB (RRID:SCR_017592) | database, service resource, production service resource, data or information resource, analysis service 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 | 2026-02-15 09:22:09 | 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, storage service resource, data repository | 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 | 2026-02-15 09:22:05 | 52 | ||||||
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LIGER Resource Report Resource Website 10+ mentions |
LIGER (RRID:SCR_018100) | software application, data processing software, data analysis software, software resource | Software R package for integrating and analyzing multiple single-cell datasets. It relies on integrative non-negative matrix factorization to identify shared and dataset-specific factors. Used for analysis of multiple scRNA-seq data sets. | Single cell genomic, data integration, dataset, cell identity, integrative analysis, gene regulation, disease state, scRNA seq analysis, shared factor among data set, | has parent organization: Broad Institute | NIH | PMID:31178122 | Free, Available for download, Freely available | https://github.com/MacoskoLab/liger | SCR_018100 | Linked Inference of Genomic Experimental Relationships | 2026-02-15 09:21:32 | 12 | ||||||
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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) | disease-related portal, topical portal, data or information resource, 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 | 2026-02-15 09:22:20 | 0 | ||||||
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GLYCAM-Web Resource Report Resource Website 50+ mentions |
GLYCAM-Web (RRID:SCR_018260) | portal, software resource, data access protocol, web service, data or information resource, topical portal | 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 | 2026-02-15 09:22:12 | 96 | |||||||
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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 visualization software, data processing software, software resource, data analysis software | 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 | 2026-02-15 09:22:10 | 1 | |||||
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Wien Center For Alzheimer's Disease and Memory Disorders Resource Report Resource Website |
Wien Center For Alzheimer's Disease and Memory Disorders (RRID:SCR_008755) | portal, research forum portal, data or information resource, topical portal, disease-related portal | A joint program between Mount Sinai Medical Center and the University of Miami Department of Psychiatry that seeks an end to Alzheimer's disease and similar disorders through research, diagnosis, education and treatment. The goals are to improve memory and mental responsiveness of Alzheimer's patients, delay the onset of the disease and, ultimately, find a cure. The Wien Center typically conducts multidisciplinary initiatives utilizing clinical trials. | alzheimer's disease, memory disorder, dementia, clinical, diagnosis, treatment, late adult human |
has parent organization: University of Miami; Florida; USA is parent organization of: Florida Brain Bank |
Aging | NIH | Public | nlx_143957 | SCR_008755 | Wien Center for Alzheimer's Disease and Memory Disorders | 2026-02-15 09:19:55 | 0 | ||||||
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OHSU Brain Institute Resource Report Resource Website |
OHSU Brain Institute (RRID:SCR_008932) | OBI | topical portal, data or information resource, service resource, portal | A clinical care and research center for neurological conditions such as Alzheimer's, dementia and seizure disorders. It provides a dynamic setting for training healthcare professionals and neuroscience researchers to develop and implement evidence-based treatment. | alzheimer's disease, clinical care, research center, neurological condition, dementia, training | has parent organization: Oregon Health and Science University School of Medicine; Oregon; USA | Alzheimer's disease, Memory disorder, Arteriovenous malformations, Brain aneurysm, Brain trauma, Spinal Cord Trauma, Cerebrovascular disorder, Concussion, Head injury, Ischemic stroke, Hemorrhagic stroke, Stroke, Epilepsy, Seizure disorder, Parkinson's disease, Pituitary disorder, Mood disorder, Multiple Sclerosis, Neuropathic pain, Spine surgery, Surgical pain management, Traumatic brain injury, Trigeminal neuralgia, Brain disorder, Central nervous system disorder, Neurological disease, Neurodegenerative disorder, Neuromuscular disorder, Movement disorder, Metabolic disorder, Eating disorder, Diabetes, Neurodevelopmental disorder, Pain, Sensory failure, Brain injury, Spinal Cord Injury, Sleep disorder, Neuropsychiatric disorder, Amyotrophic Lateral Sclerosis, Aging, Brain tumor, Central nervous system tumor, Peripheral nerve disorder, Pituitary disorder, Mental disease | NIH | Public | nlx_151799 | SCR_008932 | Oregon Health and Science University Brain Institute | 2026-02-15 09:19:59 | 0 | |||||
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Molecular Libraries Program Resource Report Resource Website 10+ mentions |
Molecular Libraries Program (RRID:SCR_008847) | MLP | organization portal, portal, service resource, production service resource, data or information resource, material analysis service, topical portal, analysis service resource | High throughput screening services to identify small molecules that can be optimized as chemical probes to study the functions of genes, cells, and biochemical pathways, along with medicinal chemistry and informatics. This will lead to new ways to explore the functions of genes and signaling pathways in health and disease. The NIH Molecular Libraries Initiative NIH is designed to discover small molecules that interact with biologically important proteins and pathways and to provide open access to the bioassay and chemical data generated by its research centers. This will lead to new ways to explore the functions of genes and signaling pathways in health and disease. As these HTS Technologies were not previously available to the public sector, many investigators may not be familiar with the components and requirements of high throughput screening. A key challenge is to identify small molecules effective at modulating a given biological process or disease state. The Molecular Libraries Roadmap, through one of its components, the Molecular Libraries Probe Production Centers Network (MLPCN), offers biomedical researchers access to the large-scale screening capacity, along with medicinal chemistry and informatics necessary to identify chemical probes to study the functions of genes, cells, and biochemical pathways. This will lead to new ways to explore the functions of genes and signaling pathways in health and disease. There are two kinds of data that are available to the scientific community through a dedicated database: Chemical Compounds and Bioassay Results (NCBI). Various types of data, including informative records on substances, compound structures, and biologically active properties of small molecules are housed respectively within PubChem''''s three primary databases: PCSubstance, PCCompound, and PCBioAssay. To date, PubChem contains over 11 million substance records, details about approximately 5.5 million unique compound structures with links to bioassay descriptions, relevant literature, references, and assay data points and over 250 bioassays, a good percentage of which were contributed by the pilot phase of the MLP. The deposition will continue during the current MLPCN phase. NIH anticipates that these projects will also facilitate the development of new drugs, by providing early stage chemical compounds that will enable researchers in the public and private sectors to validate new drug targets, which could then move into the drug-development pipeline. This is particularly true for rare diseases, which may not be attractive for development by the private sector. Funding opportunities are available through the site. | molecule, compound, probe, small molecule, high throughput screening, gene, cell, biochemical pathway, drug development, protein, pathway |
is used by: LINCS Information Framework is related to: BARD is related to: NIH Clinical Collection is related to: PubChem has parent organization: National Institutes of Health |
NIH | nlx_146246 | SCR_008847 | Molecular Libraries, Molecular Libraries Initiative | 2026-02-15 09:19:57 | 15 | |||||||
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CBFBIRN Resource Report Resource Website 1+ mentions |
CBFBIRN (RRID:SCR_009543) | CBFBIRN | data set, service resource, storage service resource, data repository, data or information resource |
THIS RESOURCE IS NO LONGER IN SERVICE. Documented August 23, 2017. A web based central repository for individual and group analysis of Arterial Spin Labeling (ASL) data sets and ASL pulse sequences developed at CMFRI UCSD for MRI researchers. This resource currently hosts more 1300 ASL data sets from 22 projects and consists of mainly two main tools 1) The Cerebral Blood Flow Database and Analysis Pipeline (CBFDAP) is a web enabled data and workflow management system extended from the HID codebase on NITRC specialized for Arterial Spin Labeling data management and analysis (including group analysis) in a centralized manner. 2) Pulse Sequence Distribution System (PSDS) for managing dissamination of ASL pulse sequences developed at the UCSD CFMRI. This resource also includes web and video tutorials for end users. |
java, javascript, matlab, magnetic resonance, os independent, web environment, arterial spin labeling, mri |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: Cerebral Blood Flow Database and Analysis Pipeline has parent organization: University of California at San Diego; California; USA |
NIH | PMID:24151465 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_155722 | http://www.nitrc.org/projects/cbfbirn | SCR_009543 | Cerebral Blood Flow Biomedical Informatics Research Network | 2026-02-15 09:20:04 | 3 | ||||
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The Immunology Database and Analysis Portal (ImmPort) Resource Report Resource Website 500+ mentions |
The Immunology Database and Analysis Portal (ImmPort) (RRID:SCR_012804) | ImmPort | portal, ontology, database, service resource, storage service resource, data repository, data or information resource, controlled vocabulary, topical portal, disease-related portal | Data sharing repository of clinical trials, associated mechanistic studies, and other basic and applied immunology research programs. Platform to store, analyze, and exchange datasets for immune mediated diseases. Data supplied by NIAID/DAIT funded investigators and genomic, proteomic, and other data relevant to research of these programs extracted from public databases. Provides data analysis tools and immunology focused ontology to advance research in basic and clinical immunology. | immunology, basic, clinical, data, share, store, analyze, exchange, dataset, immune, mediated, disease, analysis, tool, FASEB list |
is recommended by: National Library of Medicine is recommended by: NIDDK Information Network (dkNET) is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases is listed by: NIDDK Research Resources is affiliated with: Cytokine Registry is related to: MetaCyto is related to: The 10000 Immunomes is related to: NIAID |
Immune mediated disease | NIH ; NIAID ; DAIT ; NIAID HHSN266200400076C; NIAID HHSN272201200028C |
PMID:24791905 | nlx_152691 | http://www.immport.org/immport-open/public/home/home http://www.immport.org/ |
http://www.immport.org | SCR_012804 | Immunology Data and Analysis Portal, ImmPort system, ImmPort, Immunology Database and Analysis Portal | 2026-02-15 09:20:38 | 987 | |||
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i2b2 Research Data Warehouse Resource Report Resource Website 1+ mentions |
i2b2 Research Data Warehouse (RRID:SCR_013276) | i2b2 | database, service resource, storage service resource, data repository, data or information resource | A data warehouse that integrates information on patients from multiple sources and consists of patient information from all the visits to Cincinnati Children''''s between 2003 and 2007. This information includes demographics (age, gender, race), diagnoses (ICD-9), procedures, medications and lab results. They have included extracts from Epic, DocSite, and the new Cerner laboratory system and will eventually load public data sources, data from the different divisions or research cores (such as images or genetic data), as well as the research databases from individual groups or investigators. This information is aggregated, cleaned and de-identified. Once this process is complete, it is presented to the user, who will then be able to query the data. The warehouse is best suited for tasks like cohort identification, hypothesis generation and retrospective data analysis. Automated software tools will facilitate some of these functions, while others will require more of a manual process. The initial software tools will be focused around cohort identification. They have developed a set of web-based tools that allow the user to query the warehouse after logging in. The only people able to see your data are those to whom you grant authorization. If the information can be provided to the general research community, they will add it to the warehouse. If it cannot, they will mark it so that only you (or others in your group with proper approval) can access it. | biomedical, computing, clinical data, platform, clinical, translational research, data sharing, framework, data analysis service, service resource, aging |
is listed by: Biositemaps is related to: SHRINE is related to: National Centers for Biomedical Computing |
NIH | Must login., Work with investigators on a case-by-case basis., The community can contribute to this resource | nif-0000-33024 | SCR_013276 | Informatics for Integrating Biology and the Bedside, Informatics for Integrating Biology and the Bedside Research Data Warehouse | 2026-02-15 09:20:39 | 1 | ||||||
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Monocle2 Resource Report Resource Website 100+ mentions |
Monocle2 (RRID:SCR_016339) | software application, data processing software, software resource, software toolkit, data analysis software | Software package for analyzing single cell gene expression, classifying and counting cells, performing differential expression analysis between subpopulations of cells, and reconstructing cellular trajcectories. Works well with very large single-cell RNA-Seq experiments containing tens of thousands of cells or more. Used in computational analysis of gene expression data in single cell gene expression studies to profile transcriptional regulation in complex biological processes and highly heterogeneous cell populations. | analysis, heterogenous, population, single, cell, gene, expression, data, large, single-cell RNA-Seq, transcriptional, regulation, heterogen | NIH DP2 HD088158; Alfred P. Sloan Foundation Research Fellowship |
PMID:24658644 | Free, Available for download, Freely available | SCR_016339 | Monocle 2 | 2026-02-15 09:21:05 | 203 | ||||||||
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MAST Resource Report Resource Website 50+ mentions |
MAST (RRID:SCR_016340) | MAST | software application, data processing software, software resource, software toolkit, data analysis software | Software as an open source package for assessing transcriptional changes and characterizing heterogeneity in single-cell RNA sequencing data. | model, based, analysis, single, cell, transcriptomics, RNA, sequencing, data | NIH DP2 DE023321; NIBIB R01 EB008400; Bill and Melinda Gates Foundation OPP1032317 |
DOI:10.5281/zenodo.18539 | Free, Available for download, Freely available | https://github.com/RGLab/MAST/ | SCR_016340 | Model based Analysis of Single Cell Transcriptomics | 2026-02-15 09:21:38 | 86 | ||||||
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NIAID Resource Report Resource Website 500+ mentions |
NIAID (RRID:SCR_016598) | NIAID | organization portal, portal, data or information resource, topical portal, disease-related portal | National Institute of Allergy and Infectious Diseases is a leading research institution to understand, treat, and prevent infectious, immunologic, and allergic diseases. | immunologic, allergic, infectious, disease, institute, treat, prevent |
lists: Nephele lists: PaVE lists: ChemokineDB lists: SPICE lists: TRIAGE lists: NGlycPred lists: dCAS lists: HASP lists: ABC Bacterial Transporter Systems Database lists: TB PORTALS lists: JOINSOLVER is related to: The Immunology Database and Analysis Portal (ImmPort) is related to: The 10000 Immunomes is related to: NIAID Overview of Coronaviruses is parent organization of: OMiCC is parent organization of: OCICB is parent organization of: NetCirChro |
NIH | SCR_016598 | National Institute of Allergy and Infectious Diseases | 2026-02-15 09:21:45 | 510 | ||||||||
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SPICE Resource Report Resource Website 50+ mentions |
SPICE (RRID:SCR_016603) | SPICE | software application, data visualization software, data processing software, software resource, data analysis software | Software application for data mining and visualization. Used for analyzes of large FLOWJO data sets from polychromatic flow cytometry and organizing the normalized data graphically. | data, mining, visualization, analysis, polychromatic, flow, cytometry, dataset, normalized, graphically, bio.tools |
is listed by: NIAID is listed by: Debian is listed by: bio.tools |
NIAID ; NIH |
PMID:21265010 | Free, Available for download, Freely available | biotools:spice | https://bio.tools/spice | SCR_016603 | Simplified Presentation of Incredibly Complex Evaluations | 2026-02-15 09:21:45 | 66 | ||||
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Cleveland Family Study Resource Report Resource Website 1+ mentions |
Cleveland Family Study (RRID:SCR_016585) | CFS | disease-related portal, topical portal, data or information resource, portal | Portal for family based study of sleep apnea. Contains data for quantifying the familial aggregation of sleep apnea. The polysomnographic (PSG) montage signals: EEG, ECG, EOG, EMG, SpO2, plethysmography, airflow (thermistor), nasal pressure, respiratory effort, position, snore. | data, polysomnography, sleep apnea, family, familial aggregation, EEG, ECG, longitudinal | is listed by: National Sleep Research Resource (NSRR) | sleep disorder | NHLBI HL46380; NHLBI T32 HL07567; NIH R01 46380; NCRR M01 RR00080 |
PMID:7881656 | SCR_016585 | Cleveland Family Study | 2026-02-15 09:21:44 | 3 | ||||||
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MAxEntScan Resource Report Resource Website 50+ mentions |
MAxEntScan (RRID:SCR_016707) | MAxEntScan | software application, simulation software, service resource, software resource | 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 | 2026-02-15 09:21:47 | 65 |
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Welcome to the Neuroscience Information Framework Project, designed to serve the biomedical research community. NIF maintains the largest searchable collection of neuroscience data, the largest catalog of biomedical resources, and the largest ontology for neuroscience on the web. We welcome all feedback and suggestions and are actively looking for resource providers to make their resources accessible through NIF. Learn about the tools available to help you share your data and discover a dynamic inventory of Web-based neuroscience resources.
