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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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nbdocker Resource Report Resource Website |
nbdocker (RRID:SCR_017159) | software application, software resource | Software tool as Jupyter Notebook extension for Docker. Each Docker container encapsulates its individual computing environment to allow different programming languages and computing environments to be included in one single notebook, provides user to document code as well as computing environment. | Jupyter, notebook, extension, docker, container, code, computing, environment, data | is related to: University of Washington; Seattle; USA | Institute of Technology at University of Washington Tacoma ; NHLBI U54 HL127624; NIGMS R01 GM126019 |
DOI:10.1101/309567 | Free, Available for download, Freely available | https://hub.docker.com/r/biodepot/nbdocker/ | SCR_017159 | 2026-09-05 06:33:02 | 0 | |||||||
|
ADMIXTOOLS Resource Report Resource Website 100+ mentions |
ADMIXTOOLS (RRID:SCR_018495) | software resource, software toolkit | Software package that supports formal tests of whether admixture occurred, and makes it possible to infer admixture proportions and dates. | Formal test support, admixture, infer admixture proportion, infer admixture date, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: Harvard University; Cambridge; United States |
NIGMS GM100233; U.S. National Science Foundation HOMINID |
PMID:22960212 | Free, Available for download, Freely available | biotools:admixtools | http://genetics.med.harvard.edu/reich/Reich_Lab/Software.html., https://bio.tools/admixtools | SCR_018495 | 2026-09-05 06:33:04 | 222 | ||||||
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FluCalc Resource Report Resource Website 1+ mentions |
FluCalc (RRID:SCR_019322) | data analytics software, software application, software resource | Software tool as MSS-MLE calculator for Luria–Delbrück fluctuation analysis. | Estimator, fluctuation calculation, MSS-MLE, Ma-Sandri-Sarkar Maximum Likelihood Estimator, calculator, fluctuation analysis | has parent organization: Tufts University; Massachusetts; USA | NIGMS GM105473; NIGMS GM60987 |
PMID:29043640 | Free, Available for download, Freely available | SCR_019322 | flucalc, fluctuation calculation | 2026-09-05 06:33:06 | 1 | |||||||
|
CellChat Resource Report Resource Website 500+ mentions |
CellChat (RRID:SCR_021946) | software resource, software toolkit | Software R toolkit for inference, visualization and analysis of cell-cell communication from single cell data.Quantitatively infers and analyzes intercellular communication networks from single-cell RNA-sequencing data. Predicts major signaling inputs and outputs for cells and how those cells and signals coordinate for functions using network analysis and pattern recognition approaches. Classifies signaling pathways and delineates conserved and context specific pathways across different datasets. | inference, visualization, analysis, cell-cell communication, single cell data, intercellular communication networks, single-cell RNA-sequencing data | Howard Hughes Medical Institute ; LEO Foundation ; NIGMS R01 GM123731; NIH P30 AR07504; NIH U01 AR073159; NSF DMS1763272; Pew Charitable Trust ; Simons Foundation ; UC Irvine |
PMID:33597522 | Free, Available for download, Freely available | http://www.cellchat.org/ | SCR_021946 | 2026-09-05 06:33:09 | 753 | ||||||||
|
SYGNAL Resource Report Resource Website 1+ mentions |
SYGNAL (RRID:SCR_023080) | software resource, software toolkit | Software pipeline to integrate correlative, causal and mechanistic inference approaches into unified framework that systematically infers causal flow of information from mutations to TFs and miRNAs to perturbed gene expression patterns across patients. Used to decipher transcriptional regulatory networks from multi-omic and clinical patient data. Applicable for integrating genomic and transcriptomic measurements from human cohorts. | Integrating genomic and transcriptomic measurements, human cohorts, transcriptional regulatory networks, integrate correlative, causal and mechanistic inference, unified framework, infers causal flow of information, mutations to TFs, miRNAs to perturbed gene expression patterns across patients, | American Cancer Society Research Scholar Grant ; NCI U24CA143835; NIGMS P50GM076547; NIGMS R01GM077398; NSF ABI NSF-1262637; NSF DBI-0640950 |
PMID:27426982 | Free, Available for download, Freely available | SCR_023080 | SYstems Genetic Network AnaLysis | 2026-09-05 06:33:13 | 1 | ||||||||
|
AmpliconArchitect Resource Report Resource Website 50+ mentions |
AmpliconArchitect (RRID:SCR_023150) | software resource, software toolkit | Software package designed to call circular DNA from short read WGS data.Used to identify one or more connected genomic regions which have simultaneous copy number amplification and elucidates architecture of amplicon.Used to reconstruct structure of focally amplified regions using whole genome sequencing and validate it extensively on multiple simulated and real datasets, across wide range of coverage and copy numbers. | call circular DNA, short read WGS data, connected genomic regions identification, simultaneous copy number amplification, amplicon | NHGRI HG010149; NIGMS R01GM114362; NSF NSF-DBI-1458557 |
DOI:10.1038/s41467-018-08200-y | SCR_023150 | 2026-09-05 06:33:13 | 53 | ||||||||||
|
iPOP Resource Report Resource Website 10+ mentions |
iPOP (RRID:SCR_008991) | iPOP | data or information resource, data set | Data set generated by personal omics profiling of Dr. Michael Snyder at Stanford University. It combines genomic, transcriptomic, proteomic, metabolomic, and autoantibody profiles from a single individual over a 14 month period. The analysis revealed various medical risks, including type II diabetes. It also uncovered extensive, dynamic changes in diverse molecular components and biological pathways across healthy and diseased conditions. | genomics, proteomics, transcriptional profiling, saliva, blood, maternal data, metabolomics, personalized medicine, adult human, genetics, transcriptome, male | has parent organization: Stanford University; Stanford; California | Healthy | Breetwor Family Foundation ; Korber Foundation ; Fundacion Marcelino Botin ; Fundacion Lilly ; NLM T15-LM007033; NIGMS R24-GM61374; NHLBI T32 HL094274; NHLBI KO8 HL083914; NIH New Investigator DP2 award OD004613; Spanish Ministry of Science and Innovation Projects ; Spanish Ministry of Science and Innovation Projects ; European Union FP7 Genica ; European Union FP7 TELOMARKER ; European Research Council Advanced Grant |
PMID:22424236 | Free for personal, Non-exclusive, Non-transferable, Non-commercial access., Please cite. | nlx_152492 | SCR_008991 | Snyderome, Integrated Personal Omics Profiling | 2026-09-05 06:33:29 | 14 | ||||
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Center for Computational Mass Spectrometry Resource Report Resource Website 1+ mentions |
Center for Computational Mass Spectrometry (RRID:SCR_008161) | CCMS | biomedical technology research center, training resource | Biomedical technology research center that focuses on the computational bottlenecks that impair the interpretation of data, bringing modern algorithmic approaches to mass spectrometry and building a new generation of reliable, open-access software tools to support both new mass spectrometry instrumentation and emerging applications. | systems biology technology center, mass spectrometry, algorithm, computational proteomics, proteomics |
is listed by: DataCite has parent organization: University of California at San Diego; California; USA has parent organization: University of California; California; USA is parent organization of: NeuroPedia |
NCRR ; NIGMS |
nlx_152677 | https://api.datacite.org/dois?prefix=10.25345 | SCR_008161 | UCSD Center for Computational Mass Spectrometry | 2026-09-05 06:33:28 | 7 | ||||||
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NIH / NCRR Mass Spectrometry Resource Washington University in St. Louis Resource Report Resource Website 1+ mentions |
NIH / NCRR Mass Spectrometry Resource Washington University in St. Louis (RRID:SCR_009009) | Mass Spectrometry Resource, WU Mass Spectrometry Resource | biomedical technology research center, training resource | Biomedical technology research center that develops mass spectrometry-based tools for the study of proteins, lipids and metaboilites. These include biomarker identification, stable isotope mass spectrometry and the analysis of intact proteins. Our goals are: * to conduct basic research in the science of mass spectrometry * to establish collaborative research projects with scientists at WU and at other institutions * to provide a service in mass spectrometry * to educate and train students in mass spectrometry * to disseminate results of our research and descriptions of the subject of mass spectrometry | systems biology technology center, mass spectrometry, protein, lipid, metaboilite, biomarker, isotope, analysis | has parent organization: Washington University School of Medicine in St. Louis; Missouri; USA | NIGMS ; NCRR 2P41RR00954 |
nlx_152688 | SCR_009009 | Mass Spectrometry Resource at Washington University in St. Louis, Washington University Mass Spectrometry Resource | 2026-09-05 06:33:30 | 1 | |||||||
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Resource for Integrated Glycotechnology Resource Report Resource Website |
Resource for Integrated Glycotechnology (RRID:SCR_009008) | Resource for Integrated Glycotechnology | biomedical technology research center, training resource | Biomedical technology research center that develops technologies to increase understanding of the molecular basis of the involvement of carbohydrates in protein-carbohydrate interactions in disease and to develop more powerful technologies necessary to achieve this goal. Complex carbohydrates play an important role in many biomedically important processes, including inflammatory response, hormone action, malignancy, viral and bacterial infections and cell differentiation. The resource combines complimentary technologies: synthetic chemistry, nuclear magnetic resonance, mass spectrometry, computational biology, protein expression and cell-based assays. As new technologies are developed, application to these processes will be pursued through collaborative and service projects. | systems biology technology center, protein-carbohydrate interaction, disease, synthetic chemistry, nuclear magnetic resonance, mass spectrometry, computational biology, protein expression, cell-based assay, glycan, enzyme, carbohydrate | has parent organization: University of Georgia; Georgia; USA | NIGMS 8 P41 GM103390-23; NCRR 5P41RR005351-23 |
nlx_152685 | SCR_009008 | 2026-09-05 06:33:30 | 0 | ||||||||
|
National Resource for Biomedical Accelerator Mass Spectrometry Resource Report Resource Website |
National Resource for Biomedical Accelerator Mass Spectrometry (RRID:SCR_009006) | Resource for Biomedical AMS | access service resource, biomedical technology research center, service resource, training resource | Biomedical technology research center that develops and refines accelerator mass spectrometry methods and instrumentation for the precise, quantitative and cost-effective measurement of the effects of drugs and toxicants on humans at safe doses. It facilitates the use of accelerator mass spectrometry in biomedical research and provides training and access for researchers. | systems biology technology center, accelerator mass spectrometry, radioisotope, isotope | has parent organization: Lawrence Livermore National Laboratory | NCRR ; NIGMS |
nlx_152682 | SCR_009006 | 2026-09-05 06:33:30 | 0 | ||||||||
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Integrated Technology Resource for Biomedical Glycomics Resource Report Resource Website 1+ mentions |
Integrated Technology Resource for Biomedical Glycomics (RRID:SCR_009003) | Integrated Technology Resource for Biomedical Glycomics | biomedical technology research center, training resource | Biomedical technology research center that develops and implements new technologies to investigate the glycome of cells, including glycoproteomics and glycoconjugate analysis, transcript analysis and bioinformatics. It develops the tools and technology to analyze in detail the glycoprotein and glycolipid expression of mouse embryonic stem cells and the cells into which they differentiate. The technology developed in the Center will allow an understanding of how glycosylation is controlled during differentiation and will allow the development of tools to promote the use of stem cells to treat human disease. In addition, the technology developed will be applicable to the study of other cell types, including cancer cells that are progressing to a more invasive phenotype. The technology developed will also allow others in the scientific community to participate in glycomics research through dissemination of the new methods developed and through the analytical services provided by the resource to other scientists requesting assistance in glycomic analyses. | systems biology technology center, glycome, cell, glycoproteomics, glycoconjugate analysis, transcript analysis, bioinformatics, glycoprotein, glycolipid, embryonic stem cell, glycosylation, stem cell, glycomics | has parent organization: University of Georgia; Georgia; USA | NCRR ; NIGMS |
nlx_152678 | SCR_009003 | NCRR Integrated Technology Resource for Biomedical Glycomics | 2026-09-05 06:33:29 | 1 | |||||||
|
SSRL Structural Molecular Biology Resource Report Resource Website 1+ mentions |
SSRL Structural Molecular Biology (RRID:SCR_009000) | SSRL SMB | biomedical technology research center, training resource | Biomedical technology research center that operates as a integrated center with three primary areas (or cores) of technological research and development and scientific focus: macromolecular crystallography (MC), X-ray absorption spectroscopy (XAS) and small-angle X-ray scattering/diffraction (SAXS) . Central to the core technological developments in all three areas is the development and utilization of improved detectors and instrumentation, especially to be able to take maximum advantage of the high brightness of SSRL?s third-generation synchrotron X-ray storage ring (SPEAR3). A primary focus is the use of enhanced computing and data management tools to provide more user-friendly, real-time and on-line instrumentation control, including full remote access for crystallography, data reduction and analysis. | synchrotron, radiation, structural biology, structural biology technology center, macromolecular crystallography, x-ray absorption spectroscopy, small-angle x-ray scattering, diffraction | has parent organization: Stanford University; Stanford; California | DOE ; NIGMS ; NCRR P41RR001209 |
nlx_152676 | SCR_009000 | Stanford Synchrotron Radiation Lightsource Structural Molecular Biology, Synchrotron Radiation Structural Biology Resource | 2026-09-05 06:33:29 | 1 | |||||||
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Rhode Island INBRE Molecular Informatics Core Facility Resource Report Resource Website 10+ mentions |
Rhode Island INBRE Molecular Informatics Core Facility (RRID:SCR_017685) | access service resource, core facility, service resource | Core provides sequencing and bioinformatics support for INBRE and non-INBRE researchers. Provides data science services adjacent to traditional bioinformatics; access to computational and software resources for INBRE network institutions, particularly primarily undergraduate institutions; training for students and faculty in data science methods. Maintains professional network with other core and user facilities in Rhode Island and beyond to maximize resources available to our users.Utilizes novel technologies such as virtual/augmented reality for use in teaching and research. | Analysis, interpretation, nucleotide, amino acid, sequence, protein, domain, structure, service, 3D visualization, modeling, USEDit |
has parent organization: University of Rhode Island; Rhode Island; USA has parent organization: USEDit |
NIGMS P20 GM103430 | Open | ABRF_3 | SCR_017685 | Rhode Island INBRE Molecular Informatics, RI-INBRE Bioinformatics Core; RI Genomics and Sequencing Center | 2026-09-05 06:34:10 | 16 | |||||||
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University of Delaware CBCB Bioinformatics Data Science Core Facility Resource Report Resource Website 10+ mentions |
University of Delaware CBCB Bioinformatics Data Science Core Facility (RRID:SCR_017696) | access service resource, core facility, service resource | CBCB Bioinformatics Data Science Core builds upon infrastructure of the Center for Bioinformatics and Computational Biology. Delaware Biotechnology Institute , Delaware Data Science Institute, and Protein Information Resource. Core helps with planning your research or analyzing your current data. Services:Consultation and Collaboration, Proposal Assistance,Training, Bioinformatics Software, Computational Hardware, Database and Web Services, Next Gen Analysis, Custom Analysis. | ABRF, USEDit, CBCB, Bioinformatics, core, Delaware, Biotechnology, Institute, data, analyzing, service, data science |
is listed by: ABRF CoreMarketplace is related to: USEDit has parent organization: University of Delaware; Delaware; USA |
NIGMS P20GM103446; NIH Office of the Director S10OD028725 |
Open | SCR_017712, ABRF_82 | SCR_017696 | Center for Bioinformatics and Computational Biology Bioinformatics Core, CBCB Bioinformatics Core | 2026-09-05 06:34:10 | 46 | |||||||
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University of North Dakota School of Medicine and Health Sciences Imaging Core Facility Resource Report Resource Website 1+ mentions |
University of North Dakota School of Medicine and Health Sciences Imaging Core Facility (RRID:SCR_017733) | access service resource, core facility, service resource | Provides advanced instrumentation for researchers interested in investigating biological processes at cellular, sub cellular and molecular level.Instrumentation include Confocal Microscope Systems :Zeiss LSM-510 Meta Confocal Microscope, Olympus FV1000 MPE Basic Multiphoton Microscope;Brightfield/Fluorescence: Nikon Eclipse TE300 (inverted) Fluorescent Microscope, Nikon Eclipse 80i (upright) Fluorescent Microscope, Leica Thunder Imager; TIRF Systems:Olympus TIRF Microscope; Transmission Electron Microscopy:Hitachi 7500 TEM, RCM MTX Ultramicrotomes;Scanning Electron Microscopy:Hitachi 4700 Field Emission SEM, Denton Desk II Sputter and Turbo-sputter Coaters.Light and electron microscopic facilities, complete with ancillary support equipment, are located in close proximity to each other within suite of rooms housed in medical school. | Light, electron, microscopy, imaging | NIGMS P20 GM113123; NIGMS U54 GM128729; UNDSMHS fund |
Open | ABRF_184 | SCR_017733 | Imaging Core | 2026-09-05 06:34:11 | 1 | ||||||||
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Wyoming University Jenkins Microscopy Core Facility Resource Report Resource Website |
Wyoming University Jenkins Microscopy Core Facility (RRID:SCR_017758) | access service resource, core facility, service resource | Core to assist researchers and students in their imaging needs of fluorescence and electron microscopy and to increase use of microscopes in science education. Consultation, training or touring facility is also available by appointment. | Microscopy, imaging, fluorescence, electron, consultation, training, service, core | NIGMS P20 GM121310; University of Wyoming Neuroscience COBRE and Neuroscience Core Center grant ; UW Sensory Biology COBRE grant |
Restricted | ABRF_268 | SCR_017758 | Jenkins Microscopy Facility | 2026-09-05 06:34:11 | 0 | ||||||||
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University of Nevada at Reno Nevada Proteomics Center Core Facility Resource Report Resource Website 1+ mentions |
University of Nevada at Reno Nevada Proteomics Center Core Facility (RRID:SCR_017761) | access service resource, core facility, service resource | Core offers mass spectral proteomic analysis. Assists with qualitative and quantitative characterization of proteins in biological matrices such as plasma/serum, tissue, cell lines and other biological material to gain understanding of physiological pathways, molecular interactions and regulatory signaling. | Mass, spectral, proteomic, analysis, qualitative, quantitative, protein, plasma, serum, tissue, cell, line, physiological, pathway, interaction, signaling, stury, service, core |
is listed by: ABRF CoreMarketplace has parent organization: University of Nevada at Reno; Nevada; USA |
NIGMS P20 GM103440 | Open | SCR_011043, SciEx_9701, ABRF_281 | https://coremarketplace.org/?FacilityID=281&citation=1 | SCR_017761 | Mick Hitchcock, Ph.D. Nevada Proteomics Center | 2026-09-05 06:34:11 | 6 | ||||||
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Kansas University at Lawrence Protein Production Group Core Facility Resource Report Resource Website |
Kansas University at Lawrence Protein Production Group Core Facility (RRID:SCR_017749) | PPG | access service resource, core facility, service resource | Core focuses on cloning, expression and purification of prokaryotic and eukaryotic proteins for COBRE and other investigators in Kansas and region. Laboratory maintains equipment to support production of properly folded proteins in quantities suitable for structural studies (X-ray and NMR), functional studies (catalytic or biological), label-free binding studies (SPR) and/or high throughput (HTP) screening studies. | Protein, production, purification, expression, cloning, service, core | NCRR P20 RR017708; NIGMS P20 GM103420; NIGMS P30 GM110761 |
Open | ABRF_249 | SCR_017749 | KU COBRE Protein Production Group | 2026-09-05 06:34:11 | 0 | |||||||
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University of Delaware BioImaging Center Core Facility Resource Report Resource Website 1+ mentions |
University of Delaware BioImaging Center Core Facility (RRID:SCR_017814) | access service resource, core facility, service resource | Microscopy facility that houses equipment including confocal microscopes: LSM780 confocal microscope (Located at CBBI),LSM880 confocal microscope (Located at DBI 117),electron microscopes and their accessory instrumentation:Thermo Scientific Apreo VS SEM microscope,Hitachi S-4700, Leica EM ACE600 and Tousimis Autosamdri-815B,CX7 high content analysis system. Our staff has technical expertise across different microscopy platforms and methodologies. | Microscopy, bioimaging, confocal, electron, microscope, analysis, service, core |
is listed by: ABRF CoreMarketplace has parent organization: University of Delaware; Delaware; USA |
NCRR S10 RR027273; NIGMS P20 GM103446; NIGMS P20 GM113125; NIH Office of the Director S10 OD016361; NIH Office of the Director S10 OD025165; NSF IIA 1301765; State of Delaware |
Open | ABRF_537 | https://coremarketplace.org/?FacilityID=537&citation=1 | SCR_017814 | Delaware University BioImaging Center Core Facility, University of Delaware Bio-Imaging Center | 2026-09-05 06:34:13 | 1 |
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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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