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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.
| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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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 | ||||||
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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 | ||||||
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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 | ||||||||
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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 | |||||
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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 | ||||||||
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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 | ||||||
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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 | |||||
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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 | ||||||
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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 | ||||||||
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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 | ||||||||
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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 | ||||||
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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 | 2026-02-14 02:07:18 | 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 | 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 | |||||||
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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 | 2026-02-14 02:07:27 | 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 | 2026-02-14 02:07:50 | 1 | |||||||
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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 | ||||||
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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 | 2026-02-14 02:07:45 | 33 | ||||||
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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 | ||||
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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 | ||||||
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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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