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SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.

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Resource Name Proper Citation Abbreviations Resource Type Description Keywords Resource Relationships Related Condition Funding Defining Citation Availability Specification URL Alternate IDs Alternate URLs Old URLs Parent Organization Resource ID Synonyms Record Last Update Mentions Count
Pavian
 
Resource Report
Resource Website
10+ mentions
Pavian (RRID:SCR_016679) production service resource, data analysis service, web application, analysis service resource, service resource, software resource Software R package for interactive analysis of metagenomics classification results with a special focus on infectious disease diagnosis. Used for analyzing and visualization of metagenomics classification results from classifiers such as Kraken, Centrifuge and MetaPhlAn. Provides an alignment viewer for validation of matches to a particular genome. interactive, analysis, metagenomics, classification, result, infectious, disease, diagnosis, data, visualization, bio.tools is listed by: Debian
is listed by: bio.tools
is related to: Centrifuge Classifier
NHGRI R01 HG006677;
NIGMS R01 GM083873;
U. S. Army Research Office W911NF1410490
DOI:10.1101/084715 Free, Freely available biotools:pavian https://fbreitwieser.shinyapps.io/pavian/, https://bio.tools/pavian SCR_016679 2026-08-03 09:36:33 22
XYalign
 
Resource Report
Resource Website
1+ mentions
XYalign (RRID:SCR_016661) sequence analysis software, software application, data processing software, data analysis software, software resource Software tool for identifying, understanding, and correcting technical biases on the sex chromosomes in next generation sequencing data. correct, technical, bias, sex, chromosome, next, generation, sequencing, data is listed by: OMICtools NIGMS R35 GM124827 DOI:10.1101/346940 Free, Available for download, Freely available SCR_016661 2026-08-03 09:36:25 1
Centrifuge Classifier
 
Resource Report
Resource Website
1+ mentions
Centrifuge Classifier (RRID:SCR_016665) sequence analysis software, software application, data processing software, data analysis software, software resource Software for rapid and sensitive classification of metagenomic sequences. Used for the classification of DNA sequences from microbial samples and analysis of large metagenomics data sets on conventional desktop computers. classification, large, metagenomic, sequence, DNA, microbial, sample, analysis, data, desktop, computer, bio.tools is listed by: bio.tools
is listed by: Debian
is listed by: OMICtools
is related to: Pavian
has parent organization: Center for Computational Biology at JHU
U. S. Army Research Office W911NF1410490;
NSF ABI1356078;
NHGRI R01 HG006677;
NIGMS R01 GM083873
DOI:10.1101/gr.210641.116 Free, Available for download, Freely available biotools:centrifuge, OMICS_12217 https://github.com/infphilo/centrifuge, https://bio.tools/centrifuge, https://sources.debian.org/src/centrifuge/ SCR_016665 2026-08-03 09:36:55 9
National Biomedical Center for Advanced ESR Technology
 
Resource Report
Resource Website
1+ mentions
National Biomedical Center for Advanced ESR Technology (RRID:SCR_001444) ACERT training resource, biomedical technology research center Biomedical technology research center that develops methods, both experimental and theoretical, of modern electron spin resonance (ESR) for biomedical applications. Center technologies are applicable to the determination of the structure and complex dynamics of proteins. Principal areas of expertise: * Pulsed Fourier Transform and Two Dimensional ESR * High Frequency-High Field (HFHF) ESR * High Resolution ESR Microscopy * Theory and Computational Methods for Modern ESR Activities include: * making resources available to the biomedical community, * publishing results, * running workshops on the new methodologies, * addressing the need to bring these new technologies to other laboratories. electron spin resonance, spectrometer, electron spin resonance spectrometer, structure, dynamics, protein, structural biology technology center has parent organization: Cornell University; New York; USA NIGMS P41GM103521;
NCRR P41RR016292
Free, Freely Available nlx_152669 SCR_001444 ACERT National ESR Center, National Biomedical Center for Advanced Electron Spin Resonance Technology 2026-08-03 09:31:23 1
Laboratory for Fluorescence Dynamics
 
Resource Report
Resource Website
10+ mentions
Laboratory for Fluorescence Dynamics (RRID:SCR_001437) LFD access service resource, training resource, service resource, biomedical technology research center Biomedical technology research center and training resource that develops novel fluorescence technologies, including instrumentation, methods and software applicable to cellular imaging and the elucidation of dynamic processes in cells. The LFD's main activities are: * Services and Resources: the LFD provides a state-of-the-art laboratory for fluorescence measurements, microscopy and spectroscopy, with technical assistance to visiting scientists. * Research and Development: the LFD designs, tests, and implements advances in the technology of hardware, software, and biomedical applications. * Training and Dissemination: the LFD disseminates knowledge of fluorescence spectroscopic principles, instrumentation, and applications to the scientific community. fluorescence, measurement, microscopy, spectroscopy, biochemistry, cell culture, data analysis, biomolecule, membrane, in-vitro, optical spectroscopy, biological process, tissue culture, fluorescence microscopy, optical and laser technology center has parent organization: University of California at Irvine; California; USA NIGMS 8P41GM103540;
NCRR 5P41RR003155
Restricted nlx_152663 SCR_001437 Laboratory for Fluorescence Dynamics (LFD) 2026-08-03 09:31:19 47
NIH Center for Macromolecular Modeling and Bioinformatics
 
Resource Report
Resource Website
10+ mentions
NIH Center for Macromolecular Modeling and Bioinformatics (RRID:SCR_001435) Center for Macromolecular Modeling and Bioinformatics, TCBG training resource, biomedical technology research center Biomedical technology research center focusing on the structure and function of supramolecular systems in the living cell as well as on the development of new algorithms and efficient computing tools for physical biology. They bring the most advanced molecular modeling, bioinformatics, and computational technologies to bear on questions of biomedical relevance. They extend, refine and deliver these technologies in response to experimental progress and emerging needs of the wide biomedical research community. They magnify the impact of their work through direct collaboration with experimental researchers, the distribution of cutting-edge and user-friendly software, and via extensive training, service, and dissemination efforts. The multidisciplinary team is engaged in the modeling of large macromolecular systems in realistic environments, and has produced ground-breaking insights into biomolecular processes coupled with mechanical force, bioelectronic processes in metabolism and vision, and with the function and mechanism of membrane proteins. They are committed and work towards further advancement of * Molecular modeling tools which can integrate structural information with bioinformatics databases and molecular dynamics simulations, and which can be used by a wide audience; * High performance molecular visualization and simulation software, capable of modeling biomolecules in realistic environments of 100,000,000 atoms or more; * Conceptual and methodological foundations of molecular modeling in the fields of quantum biology, mechanobiology, and interactive modeling; * Biomedical science through collaborations between theoretical and experimental researchers; * Support of the entire research process and training through a web-enabled collaborative environment; and * Service, training, and dissemination by leveraging web-based molecular graphics and integrated modeling technologies. supramolecular system, living cell, cell, algorithm, computing, physical biology, software, molecular dynamics, simulation, molecule, visualization, biomolecule, molecular modeling, bioinformatics, computational technology, computing and informatics technology center, model, macromolecule has parent organization: University of Illinois at Urbana-Champaign; Illinois; USA NIGMS P41GM104601 Free, Freely Available nlx_152659 SCR_001435 Resource for Macromolecular Modeling and Bioinformatics, Theoretical and Computational Biophysics Group, NIH Center for Macromolecular Modeling & Bioinformatics 2026-08-03 09:31:22 33
BioCARS
 
Resource Report
Resource Website
50+ mentions
BioCARS (RRID:SCR_001439) BioCARS access service resource, training resource, service resource, biomedical technology research center Biomedical technology research center and training resource that is a state-of-the art, national user facility for synchrotron-based studies of dynamic and static properties of macromolecules by X-ray scattering techniques such as crystallography (specializing in time-resolved), small- and wide-angle X-ray scattering and fiber diffraction. BioCARS operates two X-ray beamlines, embedded in a Biosafety Level 3 (BSL-3) facility unique in the U.S. that permits safe studies of biohazardous materials such as human pathogens., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. synchrotron, macromolecule, x-ray, crystallography, x-ray scattering, fiber diffraction, biological process, time-resolved crystallography, structural biology technology center has parent organization: University of Chicago; Illinois; USA NIGMS P41GM103543;
NCRR P41RR007707
PMID:21685684 THIS RESOURCE IS NO LONGER IN SERVICE nlx_152665 http://cars9.uchicago.edu/biocars/ SCR_001439 BioCARS: A Synchrotron Structural Biology Resource 2026-08-03 09:31:20 64
National Resource for Automated Molecular Microscopy
 
Resource Report
Resource Website
1+ mentions
National Resource for Automated Molecular Microscopy (RRID:SCR_001448) NRAMM training resource, biomedical technology research center Biomedical technology research center that develops, tests and applies technology aimed toward completely automating the processes involved in solving macromolecular structures using cryo-electron microscopy. The goal is to establish a resource that will serve both as a center for high-throughput molecular microscopy as well as for transferring this technique to the research community. Current Core Technology Research and Development is focused on 4 areas: improving grid substrates and specimen preparation; further automation and optimization of image acquisition; development of an integrated single particle analysis and processing pipeline; and the development of automated high throughput EM screening. NRAMM welcomes applications of both collaborative and service projects. macromolecular structure, cryo-electron microscopy, macromolecule, structure, microscopy, automation, high throughput, specimen handling, image acquisition, data processing, data information integration, structural biology technology center NIGMS 9 P41 GM103310;
NCRR 2P41RR017573
THIS RESOURCE IS NO LONGER IN SERVICE nlx_152671 SCR_001448 2026-08-03 09:31:23 2
National Magnetic Resonance Facility at Madison
 
Resource Report
Resource Website
1+ mentions
National Magnetic Resonance Facility at Madison (RRID:SCR_001449) NMRFAM access service resource, service resource, training resource Provides access and developes NMR technology to advance range of applications and improves the efficiency, rigor and reproducibility of NMR data acquisition and analysis. Houses NMR spectrometers equipped with state-of-the-art probe technology and protocols to support acquisition of high-quality data. Spectrometers range from 500 MHz to 1100 MHz. Service is tailored to the needs of individual users and projects. Provides training and advice on experimental design, best practices for data acquisition, and data analysis. Experienced staff support users with training opportunities including workshops, video tutorials and protocols. nmr spectrometer, structure, function, protein, rna, dynamics, complex, membrane protein, paramagnetic protein, metabolomics, analysis, spectroscopy, nucleic acid, automation, data analysis, macromolecule, small angle x-ray scattering, structural biology technology center has parent organization: University of Wisconsin-Madison; Wisconsin; USA NIGMS R24GM141526;
NIGMS P41136463
Free, Freely Available nlx_152672 SCR_001449 2026-08-03 09:31:20 4
Center for Integrative Biomedical Computing
 
Resource Report
Resource Website
1+ mentions
Center for Integrative Biomedical Computing (RRID:SCR_001961) CIBC training resource, biomedical technology research center Biomedical technology research center that produces open-source software tools for biomedical image-based modeling, biomedical simulation and estimation, and the visualization of biomedical data. The Center works closely with software users and collaborators in a range of scientific domains to produce user-optimized tools and provides advice, technical support, workshops, and education to enhance user success. Biological projects and collaborations drive their development efforts, all with a single unifying vision: to develop the role of image-based modeling and analysis in biomedical science and clinical practice. The CIBC has a strong, ongoing emphasis on software simulation of bioelectric fields, with clinically oriented collaborations in cardiac defibrillation and the diagnosis/treatment of epilepsy. In addition, the CIBC has expanded in recent years to include applications of statistical shape analysis and three-dimensional visualization to mouse genetics and neuroimaging and applications of image and geometry processing to cell biology. cardiac defibrillation, epilepsy, software, biomedical, image, modeling, simulation, estimation, visualization, computing, informatics, computing and informatics technology center has parent organization: University of Utah; Utah; USA NIGMS P41GM103545 nif-0000-10535 SCR_001961 NIH/NIGMS Center for Integrative Biomedical Computing 2026-08-03 09:31:39 1
Visual Molecular Dynamics
 
Resource Report
Resource Website
100+ mentions
Visual Molecular Dynamics (RRID:SCR_001820) VMD software resource, source code A molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting. VMD supports computers running MacOS X, Unix, or Windows, is distributed free of charge, and includes source code. standalone software, mac os x, unix, virtual machine, windows, c++ is listed by: OMICtools
has parent organization: University of Illinois at Urbana-Champaign; Illinois; USA
NIGMS PMID:8744570 Free, Freely available OMICS_03804 SCR_001820 2026-08-03 09:31:30 378
National Resource for Network Biology
 
Resource Report
Resource Website
1+ mentions
National Resource for Network Biology (RRID:SCR_004259) NRNB training resource, biomedical technology research center Biomedical technology research center that develops new algorithms, visualizations and conceptual frameworks to study biological networks at multiple levels and scales, from protein-protein and genetic interactions to cell-cell communication and vast social networks. They are developing freely available, open-source suite of software technology that broadly enables network-based visualization, analysis, and biomedical discovery for NIH-funded researchers. This software is enabling researchers to assemble large-scale biological data into models of networks and pathways and to use these networks to better understand how biological systems operate under normal conditions and how they fail in disease. The National Resource for Network Biology is organized around the following key components: Technology Research and Development, Driving Biomedical Projects, Outreach, Training and Dissemination of Tools. The NRNB supports several types of training events, including both virtual and live workshops; tutorials sessions for clinicians, biologists and bioinformaticians; presentations and demonstrations at conferences; online tutorials and webcasts; and annual symposium. protein-protein interaction, interaction, cell, cell communication, network, model, pathway, biological system, disease, visualization, analysis, biomedical, computing and informatics technology center has parent organization: University of California at San Diego; California; USA NIGMS GM103504;
NCRR RR031228
nlx_27231 SCR_004259 2026-08-03 09:32:23 6
Yeast Resource Center
 
Resource Report
Resource Website
1+ mentions
Yeast Resource Center (RRID:SCR_007942) YRC training resource, biomedical technology research center Biomedical technology research center that (1) exploits the budding yeast Saccharomyces cerevisiae to develop novel technologies for investigating and characterizing protein function and protein structure (2) facilitates research and extension of new technologies through collaboration, and (3) actively disseminates data and technology to the research community. Through collaboration, the YRC freely provides resources and expertise in six core technology areas: Protein Tandem Mass Spectrometry, Protein Sequence-Function Relationships, Quantitative Phenotyping, Protein Structure Prediction and Design, Fluorescence Microscopy, Computational Biology. systems biology technology center, protein function, protein structure, mass spectrometry, protein, structure prediction, fluorescence microscopy, computational biology, sequence, function, phenotyping has parent organization: University of Washington; Seattle; USA NCRR ;
NIGMS P41 GM103533
nif-0000-03650 SCR_007942 YRC 2026-08-03 09:33:36 6
Center for Computational Mass Spectrometry
 
Resource Report
Resource Website
1+ mentions
Center for Computational Mass Spectrometry (RRID:SCR_008161) CCMS training resource, biomedical technology research center 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 2026-08-03 09:33:41 7
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 2026-08-03 09:34:01 12
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 training resource, biomedical technology research center 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 2026-08-03 09:34:11 1
Resource for Integrated Glycotechnology
 
Resource Report
Resource Website
Resource for Integrated Glycotechnology (RRID:SCR_009008) Resource for Integrated Glycotechnology training resource, biomedical technology research center 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 2026-08-03 09:34:02 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, training resource, service resource, biomedical technology research center 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 2026-08-03 09:34:11 0
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 training resource, biomedical technology research center 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 2026-08-03 09:34:11 1
SSRL Structural Molecular Biology
 
Resource Report
Resource Website
1+ mentions
SSRL Structural Molecular Biology (RRID:SCR_009000) SSRL SMB training resource, biomedical technology research center 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 2026-08-03 09:34:02 1

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