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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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DecGPU Resource Report Resource Website 1+ mentions |
DecGPU (RRID:SCR_000585) | software resource | Software tool as parallel and distributed error correction algorithm for high-throughput short reads using CUDA and MPI parallel programming models. | k-mer based corrector, k-mer spectrum, illumina short read, multistage workflow, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:21447171 | Free, Available for download, Freely available | biotools:decgpu, OMICS_01101, SCR_011850, OMICS_01060 | http://musket.sourceforge.net/homepage.htm#latest, https://bio.tools/decgpu | SCR_000585 | Distributed short read Error Correction on GPUs | 2026-08-12 10:48:14 | 5 | ||||||
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sweed Resource Report Resource Website 1+ mentions |
sweed (RRID:SCR_024357) | software resource, software application | Software tool for likelihood based detection of selective sweeps in thousands of genomes. Software parallel and checkpointable tool that implements composite likelihood ratio test for detecting selective sweeps. | likelihood based detection of selective sweeps, parallel and checkpointable tool, composite likelihood ratio test, detecting selective sweeps, genomes, | is listed by: Debian | PMID:23777627 | Free, Available for download, Freely available, | OMICS_08598 | https://sources.debian.org/src/sweed/ | SCR_024357 | 2026-08-12 10:53:02 | 4 | |||||||
|
snpomatic Resource Report Resource Website |
snpomatic (RRID:SCR_024348) | software resource, software application | Short read mapping software. Read mapping tool offering variety of analytical output functions, with emphasis on genotyping, | Short read mapping, analytical output functions, genotyping, | is listed by: Debian | PMID:19574284 | Free, Available for download, Freely available, | OMICS_15114 | https://sources.debian.org/src/snpomatic/ | SCR_024348 | SNP-o-matic | 2026-08-12 10:53:06 | 0 | ||||||
|
WinNonlin Resource Report Resource Website 1000+ mentions |
WinNonlin (RRID:SCR_024504) | software resource, software application | Software to automate repetitive analysis steps and is widely considered the industry standard for NCA, TK, and PK/PD modeling. Used as non-compartmental analysis (NCA), pharmacokinetic/pharmacodynamic (PK/PD), and toxicokinetic (TK) modeling tool. | automate repetitive analysis steps, NCA, TK, PK/PD modeling, non-compartmental analysis, pharmacokinetic/pharmacodynamic, toxicokinetic, modeling tool, | is listed by: SoftCite | SCR_024504 | Phoenix WinNonlin | 2026-08-12 10:53:06 | 2013 | ||||||||||
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PaintShop Pro Resource Report Resource Website 1+ mentions |
PaintShop Pro (RRID:SCR_000338) | PaintShop Pro | commercial organization, software resource | Photo-editing software including editing features, fast brushes, creative tools and color selection that will help turn snapshots into beautiful, gallery-worthy images. | photo, edit | Restricted | SciRes_000165 | SCR_000338 | 2026-08-12 10:48:12 | 9 | |||||||||
|
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 | |||||||||
|
Workrave Resource Report Resource Website |
Workrave (RRID:SCR_024364) | software resource, software application | Software tool to assist in recovery and prevention of Repetitive Strain Injury. Monitors keyboard and mouse usage and using this information, it frequently alerts you to take microbreaks, rest breaks and restricts you to your daily computer usage. | recovery and prevention of Repetitive Strain Injury, monitor keyboard and mouse usage, microbreaks, rest breaks, daily computer usage restriction, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/workrave/ | SCR_024364 | workrave | 2026-08-12 10:53:13 | 0 | ||||||||
|
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 | ||||||||
|
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 | ||||||||||
|
PKD Foundation Resource Report Resource Website |
PKD Foundation (RRID:SCR_000209) | funding resource, nonprofit organization | Organization and funder of polycystic kidney disease research to find treatments. The organization also raises awareness for the disease through education, advocacy and support. | funding, polycystic kidney disease, advocacy, awareness, support, education | is related to: Kidney Health Initiative | Polycystic Kidney Disease | Public | nlx_157910 | SCR_000209 | Polycystic Kidney Disease Foundation | 2026-08-12 10:48:11 | 0 | |||||||
|
BioCurrents Research Center Resource Report Resource Website |
BioCurrents Research Center (RRID:SCR_002020) | BRC | material resource, instrument supplier | The BioCurrents Research Center (BRC) is an integrated technology resource of the NIH:NCRR. The activities of the Center focus on molecular physiology as it relates to the cell function and disease. Our particular interest is how the dynamics of cell responses are reflected in the chemical profiles of microdomains surrounding single living cells. In order to measure complex cellular boundary layers, the BRC has specialized in the development of extremely sensitive signal acquisition and processing methods along with miniaturized electrochemical sensor designs. The technique is non-invasive and termed self-referencing. Since its establishment in 1996, the BRC has directed its technological research and development to the design and application of ultra-microelectrodes (tip diameters of less than 10m) tailored for the detection of specific chemicals. These have been successfully applied to the boundary layer profiles of many different cell types, with thematic strength in diabetes research, reproductive health and development (see collaborative profiles). More recently, it is changing its focus to technical developments, enhancing the integrative approach to cell function. To understand a cell as a dynamic and integrated whole, BRC must be able to examine responses from different domains as near to real time and as synchronously as possible. To this end, it is developing imaging capabilities to work in parallel with electrochemistry and conventional electrophysiological techniques. Imaging includes a spinning disc confocal, as well as a low light/luminescent imager designed and built within the BRC. The technologies developed or under development are in high demand within the biomedical community. Over 40 investigators work with the Center each year in a collaborative or service capacity. Over 80 of our visitor pool is NIH funded, representing approximately 25 NIH divisions and institutes. As part of our training and dissemination program we host occasional workshops at major national and international meetings, train a significant number of new investigators each year and host graduate students undertaking portions of their thesis dissertation using our technologies. In dissemination we advise on, and install, electrochemical systems in off campus research endeavors, both academic and industrial. | electrochemical, electrochemistry, electrophysiological, function, cell, cellular, chemical, confocal, development, diabetes, disease, health, imager, light, microdomain, microelectrode, physiology, reproductive, research, technique, technology |
has parent organization: Marine Biological Laboratory is parent organization of: Pharmabase - an open content cheminformatics resource linking physiology with pharmacology |
NCRR P41RR001395 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-24482 | SCR_002020 | 2026-08-12 10:48:31 | 0 | |||||||
|
hivebench Resource Report Resource Website |
hivebench (RRID:SCR_000915) | commercial organization, software resource | A commercial software laboratory notebook. | protocol sharing tool | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_158032 | SCR_000915 | 2026-08-12 10:48:18 | 0 | ||||||||||
|
Adobe FormsCentral Resource Report Resource Website |
Adobe FormsCentral (RRID:SCR_001729) | FormsCentral | commercial organization, service resource | Service to create PDF and web forms. | pdf, form, template | is listed by: FORCE11 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_156027 | SCR_001729 | Adobe Forms Central | 2026-08-12 10:48:27 | 0 | |||||||
|
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 | ||||||||
|
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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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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Wyss Institute Imaging Core Resource Report Resource Website |
Wyss Institute Imaging Core (RRID:SCR_000898) | material resource, instrument supplier | A core facility with access to imaging equipment and analysis software such as wide-field light microscopy, Total Internal Reflection Fluorescence microscopy (TIRF), confocal microscopy, Atomic Force Microscopy (AFM), Transmission Electron Microscopy (TEM), small animal imaging, spectroscopy, and flow cytometry. | wide field light microscopy, total internal reflection fluorescence microscopy, tirf, confocal microscopy, atomic force microscopy, afm, transmission electron microscopy, tem, small animal imaging, spectroscopy, flow cytometry, imaging, analysis |
is listed by: Eagle I has parent organization: Harvard University; Cambridge; United States |
nlx_156690 | http://harvard.eagle-i.net/i/00000133-a87a-55d3-809a-235280000000 | SCR_000898 | 2026-08-12 10:48:18 | 0 |
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