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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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SMART JUNIOR Resource Report Resource Website 1+ mentions |
SMART JUNIOR (RRID:SCR_012154) | Smart JUNIOR | commercial organization, software resource | Monitor-recognition software | rid_000087 | SCR_012154 | Smart Junior software | 2026-08-04 09:42:54 | 5 | ||||||||||
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Openlab Resource Report Resource Website 1000+ mentions |
Openlab (RRID:SCR_012158) | Openlab | commercial organization, software resource | A software package for performing 2D microscope image processing and integrating and controlling a diverse array of instrumentation in a laboratory environment. The software suite has four basic areas of operation acquisition, image presentation, and storage, analysis, and automation., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | fluorescence imaging, cell biology | is listed by: SoftCite | THIS RESOURCE IS NO LONGER IN SERVICE | rid_000096 | SCR_012158 | 2026-08-04 09:42:54 | 1133 | ||||||||
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CMA Resource Report Resource Website 10+ mentions |
CMA (RRID:SCR_012779) | CMA | commercial organization, software resource | A software package to do meta-analysis which works in a spreadsheet interface and also provides forest plots, which are useful for visualizing between-study heterogeneity. | is listed by: OMICtools | Commercial license | OMICS_00233 | SCR_012779 | Comprehensive Meta-analysis | 2026-08-04 09:43:05 | 22 | ||||||||
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Chromas Resource Report Resource Website 10+ mentions |
Chromas (RRID:SCR_000598) | Chromas | commercial organization, software resource | Software ideal for the most basic of sequencing projects, where assembly of multiple sequences is not required., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | sequencing, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01016, biotools:chromas | https://bio.tools/chromas | SCR_000598 | 2026-08-04 09:40:10 | 16 | |||||||
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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 | 2026-08-04 09:40:06 | 8 | |||||||||
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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 | biomedical technology research center, training resource | 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 | 2026-08-04 09:40:23 | 2 | ||||||||
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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 | biomedical technology research center, training resource | 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 | 2026-08-04 09:40:23 | 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 | biomedical technology research center, training resource | 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 | 2026-08-04 09:40:31 | 1 | |||||||
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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 | 2026-08-04 09:40:19 | 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 | biomedical technology research center, training resource | 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 | 2026-08-04 09:40:23 | 33 | ||||||
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BD FACSDiva Software Resource Report Resource Website 5000+ mentions |
BD FACSDiva Software (RRID:SCR_001456) | BD FACSDiva Software | commercial organization, software resource | A collection of tools for flow cytometer and application setup, data acquisition, and data analysis that help streamline flow cytometry workflows. It provides features to help users integrate flow systems into new application areas, including index sorting for stem cell and single-cell applications, as well as automation protocols for high-throughput and robotic laboratories. | flow cytometry, windows |
is used by: BD Biosciences: LSRFortessa X-20 Cell Analyzer has parent organization: BD Biosciences |
Free, Freely Available | SciRes_000115 | http://www.bdbiosciences.com/instruments/software/facsdiva/index.jsp | SCR_001456 | 2026-08-04 09:40:23 | 8286 | |||||||
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CodonCodes TraceViewer Resource Report Resource Website 1+ mentions |
CodonCodes TraceViewer (RRID:SCR_002304) | TraceViewer | commercial organization, software resource | A Java program that allows you to see, print, and edit DNA sequencing traces. | windows, dna sequencing trace, dna, sequencing, trace | is listed by: OMICtools | Free for academic use | OMICS_01822 | SCR_002304 | CodonCode''s TraceViewer | 2026-08-04 09:40:37 | 1 | |||||||
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Amorphium Resource Report Resource Website 1+ mentions |
Amorphium (RRID:SCR_002062) | Amorphium | commercial organization, software resource | Graphics software for a real-time approach to creating 3D graphics that offers a variety of intuitive, powerful design tools to create your 3D masterpiece. The graphics engine allows for a completely interactive environment, where all operations occur on solid objects in real time. A rendering engine allows you to produce stunning 3D imagery at virtually any resolution for Web, print, digital video, and film. Advanced capabilities include Radiosity rendering for photo-realistic scenes, Raytracing for true-to-life surface reflections and refractions, as well as variable smoke and lighting effects. | 3d software, graphics software, graphics, modeling, painting, animation, rendering, design, vector-based 3d | THIS RESOURCE IS NO LONGER IN SERVICE | SciRes_000164 | http://download.cnet.com/Amorphium-3-0/3000-6677_4-33263.html | SCR_002062 | Amorphium 3, Amorphium 3.0 | 2026-08-04 09:40:33 | 1 | |||||||
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Laser Microbeam and Medical Program Resource Report Resource Website 1+ mentions |
Laser Microbeam and Medical Program (RRID:SCR_001409) | LAMMP | biomedical technology research center, training resource | Biomedical technology research center dedicated to the use of lasers and optics in biology and medicine with activities in technological research and development, collaborative research, service, training, and dissemination. One of the primary goals of LAMMP is to facilitate translational research by rapidly moving basic science and technology discoveries from blackboard to benchtop to bedside. This is accomplished by combining state of the art optical technologies with specialized resource facilities for cell and tissue engineering, histopathology, pre-clinical animal models, and clinical care. The resource center has been organized into 3 cores: * Microscopy and Microbeam Technologies (MMT) for high-resolution functional imaging and manipulation of living cells and tissues * Medical Translational Technologies (MTT) for non- and minimally-invasive monitoring, treating, and imaging pre-clinical animal models and human subjects, and * Virtual Photonics Technologies (VPT) for developing computational models and methods that advance the performance of biophotonic technologies, and enhance the information content derived from optical measurements. LAMMP cores contain complementary technologies that are capable of quantitatively characterizing, imaging, and perturbing structure and biochemical function in cells and tissues with scalable resolution and depth sensitivity ranging from micrometers to centimeters. | laser, optics, biology, medicine, imaging, microscopy, microbeam, photonics, computational model, cell, tissue | has parent organization: University of California at Irvine; California; USA | NIBIB P41EB015890 | Free, Freely Available | nlx_152631 | http://lammp.bli.uci.edu/ | SCR_001409 | 2026-08-04 09:40:22 | 4 | ||||||
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Center for In Vivo Microscopy Resource Report Resource Website 10+ mentions |
Center for In Vivo Microscopy (RRID:SCR_001426) | CIVM | biomedical technology research center, training resource | Biomedical technology research center dedicated to the development of novel imaging methods for the basic scientist and the application of the methods to important biomedical questions. The CIVM has played a major role in the development of magnetic resonance microscopy with specialized MR imaging systems capable of imaging at more than 500,000x higher resolution than is common in the clinical domain. The CIVM was the first to demonstrate MR images using hyperpolarized 3He which has been moved from mouse to man with recent clinical trials performed at Duke in collaboration with GE. More recently the CIVM has developed the molecular imaging workbench---a system dedicated to multimodality cardiopulmonary imaging in the rodent. Their collaborators are employing these unique imaging systems in an extraordinary range of mouse and rat models of neurologic disease, cardiopulmonary disease and cancer to illuminate the underlying biology and explore new therapies. | imaging, magnetic resonance microscopy, magnetic resonance imaging, clinical, mri, ct, x-ray, ultrasound, confocal, optical, spect | has parent organization: Duke University; North Carolina; USA | Cardiopulmonary disease, Cancer, Neurological disease | NIBIB 4P41EB015897-27 | Free, Freely Available | nlx_152650 | SCR_001426 | Duke Center for In Vivo Microscopy | 2026-08-04 09:40:23 | 10 | |||||
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RESBIO Resource Report Resource Website 1+ mentions |
RESBIO (RRID:SCR_001424) | RESBIO | biomedical technology research center, training resource | Biomedical technology research center that works to develop integrated tools and technologies that advance the discovery of polymeric biomaterials for regenerative medicine, the delivery of biological agents, and the next generation of medical implants. To achieve its mission, RESBIO's research is focused on the development of combinatorial and computational approaches to biomaterials design and optimization. Within this framework, RESBIO employs and uses: * Advanced multi-photon confocal laser microscopy to explore, understand, and control the response of cells in contact with artificial surfaces * Electron microscopy techniques to study the effect of nano-scale surface morphological features on cell behavior RESBIO research emphasizes the integration of a strong synthetic effort to create new biomaterial candidates with the development of rapid screening techniques for key material and biological properties relevant to the performance of a biomaterial in a given medical application. | polymeric biomaterial, regenerative medicine, biological agent, medical implant, biomaterial, design, optimization, delivery, confocal laser microscopy, electron microscopy, cell | has parent organization: Rutgers University; New Jersey; USA | NIBIB 4P41EB001046-14 | Free, Freely Available | nlx_152646 | http://www.njbiomaterials.org/web/index.php?p=resbio | SCR_001424 | Polymeric Biomaterials Resource, Integrated Technologies for Polymeric Biomaterials | 2026-08-04 09:40:23 | 1 | |||||
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Center for Magnetic Resonance and Optical Imaging Resource Report Resource Website 1+ mentions |
Center for Magnetic Resonance and Optical Imaging (RRID:SCR_001428) | CMROI | biomedical technology research center, training resource | Biomedical technology research center dedicated to the development and application of innovative, novel magnetic resonance and optical imaging techniques. The facility's core sections provide research and computing resources for numerous user, collaborative, and training projects. The focus of this resource is on developing instrumentation, methodologies, and data analysis techniques for the quantitative assessment of functional, structural, and metabolic parameters in humans with the use of multinuclear magnetic resonance, novel spectral, perfusion, functional, and optical imaging techniques. These technological developments are driven by collaboration with scientists from within and outside University of Pennsylvania, the primary institution. Specifically, the Resource is focused on the development of quantitative, noninvasive MR and optical imaging based biomarkers for studying tissue metabolism and function, with an eye towards clinical translation through early diagnosis. The Center also provides support in the development and evaluation of new therapies in a variety of diseases. | magnetic resonance imaging, optical imaging, multinuclear magnetic resonance | has parent organization: University of Pennsylvania Perelman School of Medicine; Pennsylvania; USA | NIBIB P41 EB015893 | Free, Freely Available | nlx_152652 | http://cmroi.med.upenn.edu/ | SCR_001428 | 2026-08-04 09:40:23 | 1 | ||||||
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National Center for Image-Guided Therapy Resource Report Resource Website 1+ mentions |
National Center for Image-Guided Therapy (RRID:SCR_001419) | NCIGT | biomedical technology research center, training resource | Biomedical Technology Resource Center that serves as a national resource for all aspects of research into medical procedures that are enhanced by imaging. Its common goal is to provide more effective patient care. The center is focused on the multidisciplinary development of innovative image-guided intervention technologies to enable effective, less invasive clinical treatments that are not only more economical, but also produce better results for patients. The NCIGT is helping to implement this vision by serving as a proving ground for some of the next generation of medical therapies. | clinical, patient care, imaging, medical procedure | has parent organization: Harvard Medical School; Massachusetts; USA | NIBIB P41EB015898 | Free, Freely Available | nlx_152641 | SCR_001419 | National Center for Image Guided Therapy | 2026-08-04 09:40:22 | 2 | ||||||
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FEATURE Resource Report Resource Website 10+ mentions |
FEATURE (RRID:SCR_002648) | modeling software, d visualization software | A suite of automated tools that examine biological molecules and produces useful representations of the key biophysical and biochemical features of these structures that are critical for understanding function. The utility of this system extends from medical / pharmaceutical applications (model-based drug design, comparing pharmacological activities) to industrial applications (understanding structural stability, protein engineering). The FEATURE code is made available, without too much support, to any interested scientists. Audience: Researchers interested in identifying functional sites in protein structures. Long Term Goals and Related Uses: Enable improved functional site prediction. | functional site, function annotation, calcium binding site, protein microenvironment, structural bioinformatics, structure, protein classification, bayesian inference, support vector machine, model |
is listed by: Biositemaps has parent organization: Simtk.org |
Free, Available for download, Freely available | nif-0000-23304 | SCR_002648 | 2026-08-04 09:40:43 | 35 | |||||||||
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Omicsoft Sequence Aligner Resource Report Resource Website 1+ mentions |
Omicsoft Sequence Aligner (RRID:SCR_005270) | OSA | commercial organization, software resource | A fast and accurate alignment tool for RNA-Seq data. | alignment, rna-seq | is listed by: OMICtools | Free for academic use, Commercial use requires license | OMICS_01262 | SCR_005270 | OSA: a super-fast and accurate alignment tool for RNA-Seq data | 2026-08-04 09:41:19 | 4 |
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