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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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NGmerge Resource Report Resource Website 10+ mentions |
NGmerge (RRID:SCR_024483) | software resource, software application | Software tool for merging paired-end reads via novel empirically derived models of sequencing errors. Used for merging paired-end reads and removing adapters. Corrects errors and ambiguous bases and assigns quality scores for merged bases that accurately reflect the error rates. | merging paired-end reads, sequencing errors, removing adapters, correct errors, correct ambiguous bases, assign quality scores for merged bases, error rates, | is listed by: SoftCite | PMID:30572828 | Free, Available for download, Freely available | SCR_024483 | 2026-08-12 10:53:08 | 32 | |||||||||
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XMedCon Resource Report Resource Website 1+ mentions |
XMedCon (RRID:SCR_024366) | software resource, software application | Open source software toolkit for medical image conversion. | medical image conversion, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/xmedcon/ | SCR_024366 | xmedcon | 2026-08-12 10:53:07 | 1 | ||||||||
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VMD Resource Report Resource Website 50+ mentions |
VMD (RRID:SCR_024368) | software resource, software application | Software tool as 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. | molecular visualization, displaying, animating, analyzing, large biomolecular systems, . | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/vmd/ | SCR_024368 | vmd | 2026-08-12 10:53:13 | 68 | ||||||||
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DNA Amplicon Resource Report Resource Website 1+ mentions |
DNA Amplicon (RRID:SCR_024481) | software resource, software application | Local Run Manager DNA Amplicon analysis module aligns amplicon reads against reference specified in the manifest file. Variants are called for the targeted regions. | Local Run Manager DNA Amplicon analysis module, align amplicon reads, | Restricted | SCR_024481 | Illumina DNA Amplicon | 2026-08-12 10:53:05 | 1 | ||||||||||
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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 | 2026-08-12 10:48:24 | 2 | ||||||||
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National Magnetic Resonance Facility at Madison Resource Report Resource Website 1+ mentions |
National Magnetic Resonance Facility at Madison (RRID:SCR_001449) | NMRFAM | service resource, access 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 | 2026-08-12 10:48:24 | 4 | |||||||
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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 | 2026-08-12 10:48:24 | 1 | ||||||
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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 | 2026-08-12 10:48:30 | 4 | |||||||
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GenVision Resource Report Resource Website 1+ mentions |
GenVision (RRID:SCR_001166) | GenVision | commercial organization, software resource | A genomic visualization application to support easy generation of publication quality graphics and maps. It produces high quality images of annotated genomes but it can also be customized to accentuate specific areas of interest, such as comparing gene functionality, illustrating gene expression levels, and visualizing the coverage in an assembled contig. | genome, image, visualization, graphic, map, gene expression, contig, genetics |
is listed by: OMICtools works with: Lasergene's SeqMan Pro |
Commercial | OMICS_02135 | SCR_001166 | GenVision - Software for Publication-Quality Illustrations, DNASTAR GenVision | 2026-08-12 10:48:21 | 1 | |||||||
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Laboratory for Fluorescence Dynamics Resource Report Resource Website 50+ mentions |
Laboratory for Fluorescence Dynamics (RRID:SCR_001437) | LFD | service resource, training resource, access 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) | 2026-08-12 10:48:24 | 51 | ||||||
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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 | 2026-08-12 10:48:24 | 39 | ||||||
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BioCARS Resource Report Resource Website 50+ mentions |
BioCARS (RRID:SCR_001439) | BioCARS | service resource, training resource, access 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 | 2026-08-12 10:48:24 | 64 | ||||
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Folic Acid for Vascular Outcome Reduction in Transplantation Resource Report Resource Website 1+ mentions |
Folic Acid for Vascular Outcome Reduction in Transplantation (RRID:SCR_001505) | FAVORIT | resource, clinical trial | Multi-center, randomized, double blind controlled clinical trial to determine whether treatment with a standard multivitamin augmented with high doses of folic acid, vitamin B6 and vitamin B12 reduces the rate of cardiovascular disease outcomes in renal transplant recipients relative to participants receiving a similar multivitamin that contains no folic acid. This study hopes to show that by reducing the level of homocysteine in the body, the risk of heart disease is also reduced among kidney transplant patients. | multivitamin, folic acid, vitamin b6, vitamin b12, outcome, homocysteine, adult human, middle adult human, late adult human, vitamin, bibliography |
is listed by: ClinicalTrials.gov is listed by: NIDDK Information Network (dkNET) has parent organization: University of North Carolina at Chapel Hill; North Carolina; USA |
Cardiovascular disease, Kidney transplant recipient | NIDDK U01DK061700 | PMID:16923411 | Free, Freely available | nlx_152827 | http://www.cscc.unc.edu/favorit/ | http://www.cscc.unc.edu/favorit/favdescrip.htm | SCR_001505 | Folic Acid for Vascular Outcome Reduction in Transplantation (FAVORIT) | 2026-08-12 10:48:24 | 1 | ||
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ADInstruments - Data Acquisition Systems for Life Science Resource Report Resource Website 50+ mentions |
ADInstruments - Data Acquisition Systems for Life Science (RRID:SCR_001620) | material resource, instrument supplier | THIS RESOURCE IS NO LONGER IN SERVICE, documented on May 19, 2018; A provider of computer-based data acquisition and analysis systems for life science. Products enable users to record and analyze life science data quickly and efficiently. ADInstruments product range is based on the PowerLab data acquisition system with LabChart software. The PowerLab system (also MacLab) is used in universities, hospitals, research institutes, pharmaceutical companies, contract research organizations and other private industry research sectors. | acquisition, analysis, biomedical, computer, life science, research, education, pharmaceutical research, transducer, part, signal conditioner, system | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-10146 | SCR_001620 | AD Instruments | 2026-08-12 10:48:26 | 68 | |||||||||
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Ocular Resource Report Resource Website 1+ mentions |
Ocular (RRID:SCR_024467) | data processing software, data acquisition software, software resource, software application | Photometrics acquisition software to capture, save and publish images and movies. Allows users of color and monochrome cameras to capture high quality images and videos from their microscope or lens system. | Teledyne Photometrics, photometrics acquisition, capture control, images and movies capture, microscope, lens system, image, video | Free, Freely available | SCR_024467 | Teledyne Photometrics Ocular | 2026-08-12 10:53:05 | 2 | ||||||||||
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scNTImpute Resource Report Resource Website 1+ mentions |
scNTImpute (RRID:SCR_024395) | data processing software, data analysis software, software resource, software application | Software imputation model for scRNA-seq data. Used to accurately and efficiently identify dropout values and impute them precisely, which helps to improve downstream analyses of single-cell RNA sequencing data. | imputation model, scRNA-seq data, identify dropout values, single-cell RNA sequencing data analysis, | Free, Available for download, Freely available, | SCR_024395 | single-cell Neural Topic Imputation | 2026-08-12 10:53:07 | 1 | ||||||||||
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ChrAccR Resource Report Resource Website 1+ mentions |
ChrAccR (RRID:SCR_024397) | data processing software, data analysis software, software resource, software application | Software R package for comprehensive analysis chromatin accessibility data. Analyzing chromatin accessibility data in R. Used for data quality control, exploratory analyses including unsupervised methods for dimension reduction, clustering and quantifying transcription factor activities, and identification and characterization of differentially accessible regions. Used for analysis of large bulk datasets comprising hundreds of samples as well as for single cell datasets. | analysis chromatin accessibility data, data quality control, identification and characterization of differentially accessible regions, clustering and quantifying transcription factor activities, | Free, Available for download, Freely available | https://greenleaflab.github.io/ChrAccR/ | SCR_024397 | Chromatin Accessibility data in R | 2026-08-12 10:53:13 | 2 | |||||||||
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MapMyCells Resource Report Resource Website 50+ mentions |
MapMyCells (RRID:SCR_024672) | algorithm resource, web application, software resource, software application | MapMyCells maps single cell and spatial transcriptomics data sets to massive, high-quality, and high-resolution cell type taxonomies. It enables speeding up the creation of brain reference atlases by facilitating the integration of datasets from the scientific community with a shared reference. MapMyCells is part of the growing Brain Knowledge Platform. Its key advantage is scale: researchers can provide up to 327 million cell-gene pairs from their own data, a huge leap forward for working with whole-brain datasets. Allen Institute and its collaborators continue to add new reference taxonomies and algorithms to MapMyCells. | mapping of single cell and spatial transcriptomics data, mapping to whole mouse brain taxonomy, mapping to human brain taxonomy, correlation mapping, hierarchical mapping, label transfer |
has parent organization: Allen Institute is organization facet of: BICCN |
NIMH U24MH130918; Paul G. Allen Foundation |
Free, Freely available | https://knowledge.brain-map.org/mapmycells/process/, https://portal.brain-map.org/atlases-and-data/bkp/mapmycells/mapmycells-use-case-single-cell-genomics | SCR_024672 | Map My Cells, Allen MapMyCells | 2026-08-12 10:53:16 | 60 | |||||||
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Efficient and Adaptive Gaussian Smoothing Resource Report Resource Website 1+ mentions |
Efficient and Adaptive Gaussian Smoothing (RRID:SCR_024399) | EAGS | data processing software, data analysis software, software resource, software application | Software tool for high resolved spatial transcriptomics. Smoothing approach for spatial transcriptome data with ultrahigh resolution. Used to determine neighborhood relationship of cells, to calculate smoothing contribution to recalculate the gene expression of each cell. | determine neighborhood cells relationship, calculate cell gene expression, high resolved spatial transcriptomics, spatial transcriptome data, data with ultrahigh resolution, | Free, Available for download, Freely available, | SCR_024399 | 2026-08-12 10:53:03 | 1 | ||||||||||
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Olympus FV10-ASW Viewer Resource Report Resource Website 10+ mentions |
Olympus FV10-ASW Viewer (RRID:SCR_024433) | data processing software, software resource, image processing software, software application | Software for image processing. Reads data captured by FV1200/FV1000/FV500/FV300 microscopes. Images saved with FV file format (OIF, OIB, FV Multi-Tiff) can be read. | FV1200/FV1000/FV500/FV300 microscopes image processing, FV1200/FV1000/FV500/FV300 microscopes data processing, FV file format, | Free, Available for download, Freely available | https://www.olympus-lifescience.com/ | SCR_024433 | FV10-ASW Viewer software v4.2b | 2026-08-12 10:53:14 | 39 |
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