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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 Website Status Alternate IDs Alternate URLs Old URLs Parent Organization Resource ID Synonyms Record Last Update Mentions Count
University of Delaware BioImaging Center Core Facility
 
Resource Report
Resource Website
1+ mentions
University of Delaware BioImaging Center Core Facility (RRID:SCR_017814) core facility, access service resource, service resource Microscopy facility that houses equipment including confocal microscopes: LSM780 confocal microscope (Located at CBBI),LSM880 confocal microscope (Located at DBI 117),electron microscopes and their accessory instrumentation:Thermo Scientific Apreo VS SEM microscope,Hitachi S-4700, Leica EM ACE600 and Tousimis Autosamdri-815B,CX7 high content analysis system. Our staff has technical expertise across different microscopy platforms and methodologies. Microscopy, bioimaging, confocal, electron, microscope, analysis, service, core is listed by: ABRF CoreMarketplace
has parent organization: University of Delaware; Delaware; USA
NIGMS P20 GM103446;
NSF IIA 1301765;
State of Delaware ;
NCRR S10 RR027273;
NIH Office of the Director S10 OD016361;
NIH Office of the Director S10 OD025165;
NIGMS P20 GM113125
Open ABRF_537 https://coremarketplace.org/?FacilityID=537&citation=1 SCR_017814 Delaware University BioImaging Center Core Facility, University of Delaware Bio-Imaging Center 2026-02-14 02:08:04 1
University of New England COBRE Histology and Imaging Core Facility
 
Resource Report
Resource Website
University of New England COBRE Histology and Imaging Core Facility (RRID:SCR_017885) core facility, access service resource, service resource Core provides access to expertise, training and specialized instrumentation related to tissue processing, sectioning, staining, immunohistochemistry and microscopy. Offers services and training related to image analysis and image analysis software to guide investigators in choosing best methods for presenting their data.Services include Trimming of wet tissues,Tissue processing into paraffin, OCT and paraffin embedding, Sectioning of paraffin-embedded/frozen tissues, Routine and special histochemical staining, Immunohistochemistry/Immunofluorescence, Antibody optimization, Brightfield/ widefield/ confocal microscopy, Image capture and image analysis.Core has cryostats, microtomes and microscopes available for reservation. Instrumentation, tissue, processing, sectioning, staining, immunochemistry, microscopy, training, expertise, image, analysis, data, trimming, wet, tissue, processing, paraffin, embedding, immunofluorescence, antibody, optimization, microscopy, cryostat, microtome, service, core is listed by: ABRF CoreMarketplace NIGMS P20 GM103643 Open ABRF_748 https://coremarketplace.org/?FacilityID=748&citation=1 SCR_017885 Histology and Imaging Core 2026-02-14 02:08:43 0
Megadepth
 
Resource Report
Resource Website
1+ mentions
Megadepth (RRID:SCR_022779) data analysis software, software resource, data processing software, software application Software tool for quantifying alignments and coverage for BigWig and BAM/CRAM input files.Quantifies number of RNA-seq reads assigned to gene in BAM file, successor of bamcounts. quantifying alignments, BigWig and BAM/CRAM input files, RNA-seq reads assigned to gene in BAM file quantification, NIGMS R01GM118568;
NIGMS R01GM121459;
UK Medical Research Council
PMID:33693500 Free, Available for download, Freely available https://bioconductor.org/packages/megadepth SCR_022779 2026-02-14 02:04:58 2
ECO
 
Resource Report
Resource Website
10+ mentions
ECO (RRID:SCR_002477) ECO data or information resource, ontology, controlled vocabulary A controlled vocabulary that describes types of scientific evidence within the realm of biological research that can arise from laboratory experiments, computational methods, manual literature curation, and other means. Researchers can use these types of evidence to support assertions about research subjects that result from scientific research, such as scientific conclusions, gene annotations, or other statements of fact. ECO comprises two high-level classes, evidence and assertion method, where evidence is defined as a type of information that is used to support an assertion, and assertion method is defined as a means by which a statement is made about an entity. Together evidence and assertion method can be combined to describe both the support for an assertion and whether that assertion was made by a human being or a computer. However, ECO can not be used to make the assertion itself; for that, one would use another ontology, free text description, or other means. ECO was originally created around the year 2000 to support gene product annotation by the Gene Ontology. Today ECO is used by many groups concerned with provenance in scientific research. ECO is used in AmiGO 2 evidence, assertion, assertion method, gene product, obo, evidence code, experiment, similarity, provenance is listed by: BioPortal
is related to: AmiGO
is related to: Gene Ontology
has parent organization: University of Maryland School of Medicine; Maryland; USA
has parent organization: Google Code
NIGMS GM089636 Free, Available for download, Freely available nlx_155860 http://code.google.com/p/evidenceontology/
http://bioportal.bioontology.org/ontologies/ECO
SCR_002477 Evidence Codes Ontology, Evidence Ontology, evidenceontology, The Evidence Ontology 2026-02-14 02:05:01 19
SViCT
 
Resource Report
Resource Website
1+ mentions
SViCT (RRID:SCR_023656) data analysis software, software resource, data processing software, software application Software tool for detecting structural variations from cell free DNA containing low dilutions of circulating tumor DNA. detecting structural variations, cell free DNA, cfDNA, circulating tumor DNA low dilutions, ctDNA Natural Sciences and Engineering Research Council Discovery Grant ;
Terry Fox Research Institute New Frontiers Program Project Grant ;
Natural Sciences and Engineering Research Council Discovery Frontiers Program ;
National Science Foundation ;
NIGMS GM108348;
Indiana University Grant Challenges Program ;
Precision Health Initiative
PMID:30759232 Free, Available for download, Freely available SCR_023656 Structural Variant detection in Circulating Tumor DNA 2026-02-14 02:05:08 1
miRanda
 
Resource Report
Resource Website
100+ mentions
miRanda (RRID:SCR_017496) data or information resource, service resource, database Comprehensive resource of microRNA target predictions and expression profiles. Used for whole genome prediction of miRNA target genes. For each miRNA, target genes are selected on basis of sequence complementarity using position weighted local alignment algorithm, free energies of RNA-RNA duplexes, and conservation of target sites in related genomes. Provides information about set of genes potentially regulated by particular microRNA, co-occurrence of predicted target sites for multiple microRNAs in mRNA and microRNA expression profiles in tissues. Users are allowed to customize algorithm, numerical parameters, and position-specific rules., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. Whole, genome, prediction, miRNA, target, gene, expression, profile, data, FASEB list is listed by: SoftCite NIGMS ;
Atlantic Philanthropies ;
Alfred W. Bressler Scholars Endowment Fund
PMID:18158296 THIS RESOURCE IS NO LONGER IN SERVICE http://www.microrna.org/microrna/home.do SCR_017496 MicroRNA.org. microrna.org 2026-02-14 02:06:48 210
Viral Integrated Structural Evolution Dynamic Database
 
Resource Report
Resource Website
1+ mentions
Viral Integrated Structural Evolution Dynamic Database (RRID:SCR_018793) VIStEDD data or information resource, database Database of SARS-CoV-2 and other viruses. Integrates structural and dynamic insights with viral evolution for proteins coded by virus. Each virus within database has workflow performed on each protein. Workflow consists of protein modeling, molecular dynamic simulations, evolutionary analysis, and mapping of protein-protein interactions. On page for each protein is link to individual protein data folder system, video of protein rotating with conservation, details of protein function, widget to purchase 3D print of protein at cost of production, amino acid movement from molecular dynamic simulations, and table of data for each amino acid of protein. Virus, SARS-CoV-2, COVID-19, proteins coded by virus, viral evolution, protein, data, amino acid, protein modeling, molecular dynamic simulation, evolutionary analysis, protein-protein interaction, protein- protein interaction mapping, protein data folder system, rotating protein video, protein function, molecular dynamic simulation has parent organization: Michigan State University; Michigan; USA COVID-19 NIGMS R01 GM108618;
NIEHS K01 ES025435
PMID:32511397 Free, Freely available SCR_018793 Viral Integrated Structural Evolution Dynamic Database, SARS-CoV-2 dynamicome database 2026-02-14 02:06:33 3
CIS-BP
 
Resource Report
Resource Website
100+ mentions
CIS-BP (RRID:SCR_017236) web service, data or information resource, data access protocol, software resource, database Software tool as catalog of inferred sequence binding preferences. Online library of transcription factors and their DNA binding motifs. catalog, inferred, sequence, binding, preference, transcription, factor, DNA, motif, FASEB list Canadian Institutes of Health Research ;
Canadian Institute for Advanced Research Junior Fellows Genetic Networks Program ;
NICHD P01 HD39691;
NIGMS GM082971;
EU Marie Curie International Outgoing Fellowship ;
NSF MCB-1024999;
Howard Hughes Medical Institute ;
Gordon and Betty Moore Foundation ;
Millennium Nucleus for Fungal Integrative and Synthetic Biology ;
Fondo Nacional de Desarrollo Científico y Tecnológico
PMID:25215497 Free, Freely available r3d100013971 https://doi.org/10.17616/R31NJN9V SCR_017236 Catalog of Inferred Sequence Binding Preferences 2026-02-14 02:06:31 104
SRMAtlas
 
Resource Report
Resource Website
1+ mentions
SRMAtlas (RRID:SCR_016996) SRM Atlas, SRMatlas data or information resource, atlas, database Resource of targeted proteomics assays to detect and quantify proteins in complex proteome digests by mass spectrometry. Used to quantify the complete human proteome. collection, proteomic, assay, detect, quantify, protein, mass, spectrometry, peptide American Recovery and Reinvestment Act ;
NHGRI RC2 HG005805;
NIGMS R01 GM087221;
NCRR S10 RR027584;
NIGMS P50 GM076547;
Luxembourg Centre for Systems Biomedicine University Luxembourg ;
European Research Council ;
Swiss National Science Foundation
PMID:27453469 Publicly available, Registration required SCR_016996 2026-02-14 02:06:47 3
NIGMS Computing Life
 
Resource Report
Resource Website
NIGMS Computing Life (RRID:SCR_005850) Computing Life data or information resource, narrative resource An NIGMS magazine that showcases the exciting ways that scientists are using the power of computers to expand our knowledge of biology and medicine. From text messaging friends to navigating city streets with GPS technology, we''re all living the computing life. But as we''ve upgraded from snail mail and compasses, so too have scientists. Computer advances now let researchers quickly search through DNA sequences to find gene variations that could lead to disease, simulate how flu might spread through your school and design three-dimensional animations of molecules that rival any video game. By teaming computers and biology, scientists can answer new and old questions that could offer insights into the fundamental processes that keep us alive and make us sick. This booklet introduces you to just some of the ways that physicists, biologists and even artists are computing life. Each section focuses on a different research problem, offers examples of current scientific projects and acquaints you with the people conducting the work. You can follow the links for online extras and other opportunities to learn aboutand get involved inthis exciting new interdisciplinary field. computer, biology, medicine, human, health has parent organization: National Institute of General Medical Sciences NIGMS nlx_149381 SCR_005850 2026-02-14 02:07:07 0
MORGAN
 
Resource Report
Resource Website
100+ mentions
MORGAN (RRID:SCR_006906) MORGAN software resource, software application Software programs for segregation and linkage analysis, using a variety of Markov chain Monte Carlo (MCMC) methods. Includes MCMC methods for multilocus gene identity by descent (including homozygosity mapping) and Monte Carlo Lod scores. Also, other programs for EM analysis of quantitative traits. gene, genetic, genomic, c, unix, compaq-alpha, solaris, linux, linkage disequilibrium, gl_lods, ibd_haplo, identity by descent, segregation, linkage analysis, markov chain monte carlo is listed by: OMICtools
is listed by: Genetic Analysis Software
has parent organization: University of Washington; Seattle; USA
NIGMS GM-46255 PMID:22298700 nlx_154201, OMICS_00205 SCR_006906 MOnte caRlo Genetic ANalysis PANGAEA 2026-02-14 02:07:09 305
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 2026-02-14 02:07:18 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 2026-02-14 02:07:45 4
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 2026-02-14 02:07:27 1
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 2026-02-14 02:07:50 1
Laboratory for Fluorescence Dynamics
 
Resource Report
Resource Website
10+ mentions
Laboratory for Fluorescence Dynamics (RRID:SCR_001437) LFD biomedical technology research center, service resource, access service resource, training resource 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) 2026-02-14 02:07:27 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 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 2026-02-14 02:07:45 33
BioCARS
 
Resource Report
Resource Website
50+ mentions
BioCARS (RRID:SCR_001439) BioCARS biomedical technology research center, service resource, access service resource, training resource 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 2026-02-14 02:07:49 64
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 2026-02-14 02:07:46 378
National Resource for Network Biology
 
Resource Report
Resource Website
1+ mentions
National Resource for Network Biology (RRID:SCR_004259) NRNB biomedical technology research center, training resource 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 2026-02-14 02:07:54 6

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