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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 Specification URL Alternate IDs Alternate URLs Old URLs Parent Organization Resource ID Authority Synonyms Record Last Update Mentions Count
NCBI Genome
 
Resource Report
Resource Website
500+ mentions
NCBI Genome (RRID:SCR_002474) Genome data or information resource, data repository, database, service resource, storage service resource Database that organizes information on genomes including sequences, maps, chromosomes, assemblies, and annotations in six major organism groups: Archaea, Bacteria, Eukaryotes, Viruses, Viroids, and Plasmids. Genomes of over 1,200 organisms can be found in this database, representing both completely sequenced organisms and those for which sequencing is in progress. Users can browse by organism, and view genome maps and protein clusters. Links to other prokaryotic and archaeal genome projects, as well as BLAST tools and access to the rest of the NCBI online resources are available. chromosome, organelle, plasmid, viroid, virus, genome, sequence, map, assembly, annotation, gene mapping, dna, blast, protein cluster, gold standard is listed by: re3data.org
is related to: MapViewer
is related to: UniProt Proteomes
is related to: CaspBase
has parent organization: NCBI
works with: nTrackAnnotator
Free, Freely avaialble nif-0000-02802, r3d100010785 http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Genome, https://doi.org/10.17616/R3R89S SCR_002474 SciCrunch Registry Entrez Genomes, Entrez Genome, NCBI, Genome, Genome Database, Genome: Information by genome sequence 2026-11-07 11:54:50 618
Genomes Online Database
 
Resource Report
Resource Website
100+ mentions
Genomes Online Database (RRID:SCR_002817) GOLD data or information resource, data repository, database, service resource, storage service resource Database of information regarding genome and metagenome sequencing projects, and their associated metadata, around the world. It also provides information related to organism properties such as phenotype, ecotype and disease. Both complete and ongoing projects, along with their associated metadata, can be accessed. Users can also register, annotate and publish genome and metagenome data. genome, genetics, metagenome, biosample, phenotype, ecotype, disease, sequencing, FASEB list is listed by: re3data.org
has parent organization: DOE Joint Genome Institute
PMID:22135293
PMID:19914934
PMID:17981842
PMID:16381880
PMID:11125068
PMID:10498782
Free, Freely available, Available for download r3d100010808, nif-0000-02918 https://doi.org/10.17616/R39310 SCR_002817 SciCrunch Registry Genomes On Line Database (GOLD), GOLD:Genomes Online Database 2026-11-07 11:54:47 161
RNA Abundance Database
 
Resource Report
Resource Website
1+ mentions
RNA Abundance Database (RRID:SCR_002771) RAD data or information resource, data repository, database, resource, service resource, storage service resource THIS RESOURCE IS NO LONGER IN SERVICE, Documented on March 24, 2014. A resource for gene expression studies, storing highly curated MIAME-compliant studies (i.e. experiments) employing a variety of technologies such as filter arrays, 2-channel microarrays, Affymetrix chips, SAGE, MPSS and RT-PCR. Data were available for querying and downloading based on the MGED ontology, publications or genes. Both public and private studies (the latter viewable only by users having appropriate logins and permissions) were available from this website. Specific details on protocols, biomaterials, study designs, etc., are collected through a user-friendly suite of web annotation forms. Software has been developed to generate MAGE-ML documents to enable easy export of studies stored in RAD to any other database accepting data in this format. RAD is part of a more general Genomics Unified Schema (http://gusdb.org), which includes a richly annotated gene index (http://allgenes.org), thus providing a platform that integrates genomic and transcriptomic data from multiple organisms. NOTE: Due to changes in technology and funding, the RAD website is no longer available. RAD as a schema is still very much active and incorporated in the GUS (Genomics Unified Schema) database system used by CBIL (EuPathDB, Beta Cell Genomics) and others. The schema for RAD can be viewed along with the other GUS namespaces through our Schema Browser. gene expression, gene, affymetrix, biomaterial, genomics, microarray, mpss, ontology, rna, rt-pcr, sage, functional genomics, transcript abundance is listed by: OMICtools
is related to: MIAME
is related to: MGED Ontology
is related to: MicroArray and Gene Expression Markup Language
has parent organization: University of Pennsylvania; Philadelphia; USA
NIH ;
NHGRI RO1-HG-01539;
NIDDK U01DK56947;
NHGRI K25-HG-02296;
NHGRI K25-HG-00052
THIS RESOURCE IS NO LONGER IN SERVICE OMICS_00869, nif-0000-00133, r3d100000017 https://doi.org/10.17616/R3QP4Q SCR_002771 SciCrunch Registry RNA Abundance Database 2026-11-07 11:54:46 4
NCBI database of Genotypes and Phenotypes (dbGap)
 
Resource Report
Resource Website
500+ mentions
NCBI database of Genotypes and Phenotypes (dbGap) (RRID:SCR_002709) dbGaP data or information resource, data repository, database, service resource, storage service resource Database developed to archive and distribute clinical data and results from studies that have investigated interaction of genotype and phenotype in humans. Database to archive and distribute results of studies including genome-wide association studies, medical sequencing, molecular diagnostic assays, and association between genotype and non-clinical traits. clinical, trial, genotype, interaction, homology, cell, morphology, interaction, phenotype, molecular diagnosis, genetic recombination, gold standard, bio.tools is used by: International Genomics of Alzheimers Project
is used by: NIDDK Inflammatory Bowel Disease Genetics Consortium
is used by: NIH Heal Project
is used by: Genomic Data Commons Data Portal (GDC Data Portal)
is recommended by: National Library of Medicine
is recommended by: NIDDK Information Network (dkNET)
is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases
is listed by: OMICtools
is listed by: re3data.org
is listed by: NIDDK Information Network (dkNET)
is listed by: bio.tools
is listed by: Debian
is related to: NIDDK Central Repository
is related to: eMERGE Network: electronic Medical Records and Genomics
is related to: Framingham Heart Study
is related to: PhenoExplorer
is related to: Chronic Renal Insufficiency Cohort Study
is related to: DbGaP Cleaner
is related to: Psychiatric Genomics Consortium
is related to: ISCA Consortium
is related to: Allen Institute for Brain Science
has parent organization: NCBI
is parent organization of: Resource for Genetic Epidemiology Research on Adult Health and Aging
NLM PMID:24297256
PMID:17898773
Restricted nif-0000-23342, OMICS_00263, biotools:dbgap, r3d100010788 http://www.ncbi.nlm.nih.gov/sites/entrez?db=gap, https://bio.tools/dbgap, https://doi.org/10.17616/R3GS4K SCR_002709 SciCrunch Registry database of Genotypes and Phenotypes (dbGaP), dbGaP, NCBI, Database of Genotypes and Phenotypes 2026-11-07 11:54:45 736
Fungal C-values Database
 
Resource Report
Resource Website
10+ mentions
Fungal C-values Database (RRID:SCR_002726) data or information resource, data repository, database, service resource, storage service resource Database for scientists interested in fungal genomics. Multiple species are included, and the database provides information on DNA C-values and genomic size. It also gives information derived from electrophoresis experiments and genome sequencing projects. The database accepts data submissions. We appreciate receiving published offprints, preprints, and personal communications providing C-value estimates for fungi. fungal c-value, fungal genome, fungus, c-value has parent organization: Estonian University of Life Sciences; Tartu; Estonia PMID:17090588 Free, Freely available nif-0000-02857 SCR_002726 SciCrunch Registry Fungal Genome Size Database 2026-11-07 11:54:45 14
Lowes Syndrome Mutation Database
 
Resource Report
Resource Website
1+ mentions
Lowes Syndrome Mutation Database (RRID:SCR_002907) data or information resource, data repository, database, service resource, storage service resource The Lowe Syndrome Mutation Database is now being maintained by the National Center for Biotechnology Information (NCBI) at the National Institutes of Health. A database of mutations causing Lowe syndrome. Information on new mutations may be submitted online. Lowe oculocerebrorenal syndrome is an X-linked disorder caused by mutations in the OCRL1 gene, which encodes a 105-kDa Golgi protein with phosphatidylinositol (4,5) bisphosphate 5-phosphatase activity. genetics mutation has parent organization: NCBI Lowe syndrome NHGRI THIS RESOURCE IS NO LONGER IN SERVICE nif-0000-00155 http://research.nhgri.nih.gov/lowe/ SCR_002907 SciCrunch Registry Lowe Syndrome Mutation Database 2026-11-07 11:54:47 1
Clinical Trials Registry - India
 
Resource Report
Resource Website
10+ mentions
Clinical Trials Registry - India (RRID:SCR_000679) CTRI clinical trial, data or information resource, data repository, database, service resource, storage service resource Free, online public record system for registration of clinical trials being conducted in India. Initiated as a voluntary measure, trial registration in the CTRI has been made mandatory by the Drugs Controller General (India) (DCGI) (http://www.cdsco.nic.in/). Moreover, Editors of Biomedical Journals of 11 major journals of India declared that only registered trials would be considered for publication. Today, any researcher who plans to conduct a trial involving human participants, of any intervention such as drugs, surgical procedures, preventive measures, lifestyle modifications, devices, educational or behavioral treatment, rehabilitation strategies as well as trials being conducted in the purview of the Department of AYUSH (http://indianmedicine.nic.in/) is expected to register the trial in the CTRI before enrollment of the first participant. Trial registration involves public declaration and identification of trial investigators, sponsors, interventions, patient population etc before the enrollment of the first patient. Submission of Ethics approval and DCGI approval (if applicable) is essential for trial registration in the CTRI. Multi-country trials, where India is a participating country, which have been registered in an international registry, are also expected to be registered in the CTRI. In the CTRI, details of Indian investigators, trial sites, Indian target sample size and date of enrollment are captured. After a trial is registered, trialists are expected to regularly update the trial status or other aspects as the case may be. After a trial is registered, all updates and changes will be recorded and available for public display. The CTRI is working with the WHO ICTRP to ensure that results of all trials registered with the CTRI are adequately reported and publicly available. clinical trial, registry, registration, trial, clinical, randomized, non-randomized, india is listed by: WHO International Clinical Trials Registry Platform
has parent organization: National Institute of Medical Statistics; New Delhi; India
PMID:18630235 THIS RESOURCE IS NO LONGER IN SERVICE r3d100010980, nlx_151507 https://doi.org/10.17616/R3C61N SCR_000679 SciCrunch Registry Clinical Trials Registry-India (CTRI), Clinical Trials Registry-India, Clinical Trials Registry - India (CTRI) 2026-11-07 11:54:06 13
NeuroMouse Database
 
Resource Report
Resource Website
NeuroMouse Database (RRID:SCR_001143) NeuroMouse atlas, data or information resource, data repository, database, service resource, storage service resource THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 17, 2023.Toolbook(tm) based, interactive graphical database which provides structural, molecular, and genetic information on the adult murine nervous system; and its relevance to human neurobiology. This resource is primarily designed as a platform for users to interact, each sharing knowledge on their own area of expertise, which is compiled to a master database. This hypertext atlas presently comprises more than 1000 pages and is designed to provide a flexible integrated resource for the description and discussion of all forms mammalian neurologic data. Version 4.0 of the NeuroMouse program extends the program's basic framework to include a number of areas in modern molecular neurobiology. This system provides an integrated resource for the characterization and description of mammalian neurological data. Major divisions include: Neural Atlas, Molecular Atlas, Genetics/Surgical Lesion Atlas. Neuromouse has been integrated into our strain-specific three dimensional MRI and surgical atlases of the murine CNS. Database contents: Neural Atlas: - Rotational representation of the murine brain. - Neural structures: visual and alphabetic point and click index of neural structures, pathways and systems. - Brain atlas:photographic serial sections in the coronal, sagittal, and horizontal planes (average plate distance - 300 um). Physical brain distances are also provided as are meta-index grids to allow rapid movement between different planes and regions. # Catalog of primary and immortalized neural cells indexed to relevant neural structures. Molecular Atlas: - Index of neurotransmitters: Acetylcholine, GABA, Glutamate, Aspartate, Glycine, Dopamine, Norepinephrine, Epinephrine, Serotonin (synthesis, distribution, degradation, molecular modules, receptors, subunits, agonists, antagonists, gene structure, localization, physical properties and transgenics are indicated for each item). - Index of neurotrophins / neurokines: NGF, BDNF, NT-3, NT-4/5, CNTF, LIF, Onostain M, IL-6, GDNF, FGF's, S100b (ligand, receptors, expression pattern, physical properties, homologous factors, transgenics/knockouts, chromosomal location, effects of agent, and effects of factors on agent are indicated for each item). - Index of additional neural agents: Bcl-2, TNF/Fas, TGF-beta, P53/Rb, PDGF, EGF family (ligand, receptor, expression patterns, physical properties, homologous factors, transgenics/ knockouts, chromosomal location, effects of agent, effects of factors on agent are indicated for each item). - Molecular biology: Molecular biology of important neural genes with integrated l links, plus selected neural topics (ex. programmed cell death, inducible gene systems, protein motifs, neural gene elements, and selected signal transduction pathways). Genetics Atlas: - Lesion paradigms: Index of common neuronal structural and chemical lesion paradigms. - Selected procedures: description of common neurosurgical, cell tracing, culturing and laboratory procedures. - Neurologic syndromes: Index of important human neurologic syndromes and appropriate animals models. - Neural mutant database: Index and description of naturally occurring and genetically modified murine neurologic mutations; including pages on double knockout animals. Interactive maps of each murine chromosome and human syntenic maps. epinephrine, gaba, acetylcholine, agonist, antagonist, aspartate, dopamine, glutamate, glycine, human, molecular biology, murine chromosome, mutant, neural, neural factor, neurokine, neurological, neurotransmitter, n eurotrophin, norepinephrine, serotonin, molecular neuroanatomy resource, nervous system, adult, murine THIS RESOURCE IS NO LONGER IN SERVICE nif-0000-11000 SCR_001143 SciCrunch Registry 2026-11-07 11:54:15 0
Human Genetics Laboratory: WFS1 Gene Mutation and Polymorphism Database
 
Resource Report
Resource Website
1+ mentions
Human Genetics Laboratory: WFS1 Gene Mutation and Polymorphism Database (RRID:SCR_001113) data or information resource, data repository, database, service resource, storage service resource This web site lists the disease causing mutations and polymorphisms found in the Wolfram syndrome (WFS1) gene. Sponsors: This resource is supported by the University of Michigan at Ann Arbor. frequency, gene, auditory, disease, hearing, neuropathy, polymorphism, research, wolfram syndrome has parent organization: University of Michigan; Ann Arbor; USA nif-0000-10276 SCR_001113 SciCrunch Registry WFS1 2026-11-07 12:00:44 3
Open Source Brain
 
Resource Report
Resource Website
10+ mentions
Open Source Brain (RRID:SCR_001393) OSB data or information resource, data repository, database, service resource, storage service resource A resource for sharing and collaboratively developing computational models of neural systems. While models can be submitted and developed in any format, the use of open standards such as NeuroML and PyNN is encouraged, to ensure transparency, modularity, accessibility and cross simulator portability. OSB will provide advanced facilities to analyze, visualize and transform models in these formats, and to connect researchers interested in models of specific neurons, brain regions and disease states. Research themes include: Basal ganglia modelling, Cerebellar Granule cell modelling, Cerebellar modelling, Hippocampal modelling, Neocortical modelling, Whole brain models. Additional themes are welcome. model, neuroml, pynn, computational model, neural system, neuron, disease, data analysis service, visualization, 3d explorer, network, ion channel distribution, ion channel, microcircuit uses: PyNN
uses: NeuroML
is used by: NIF Data Federation
is listed by: Integrated Models
is related to: neuroConstruct
is related to: NWB Explorer
is related to: Allen Institute for Brain Science
has parent organization: University College London; London; United Kingdom
Wellcome Trust Free, Freely Available nlx_152590 SCR_001393 SciCrunch Registry OpenSourceBrain 2026-11-07 12:00:27 27
BioPlex
 
Resource Report
Resource Website
1000+ mentions
BioPlex (RRID:SCR_016144) data or information resource, data repository, database, service resource, storage service resource Database of cell lines with each expressing a tagged version of a protein from the ORFeome collection. The overarching project goal is to determine protein interactions for every member of the collection. cell, line, protein, immunopurification, mass, spectrometry, interaction, bio.tools, FASEB list is listed by: bio.tools
is listed by: Debian
has parent organization: Harvard Medical School; Massachusetts; USA
Canadian Institutes for Health Research ;
NHGRI U41HG006673;
NIDDK K01 DK098285
PMID:28514442 biotools:bioplex_2.0 https://bio.tools/bioplex_2.0 SCR_016144 SciCrunch Registry BioPlex (biophysical interactions of ORFeome-based complexes), Harvard BioPlex, Biophysical Interactions of Orfeome-based comPLEXes (BioPLEX) 2026-11-07 11:58:11 1378
Antibody Validation Database
 
Resource Report
Resource Website
10+ mentions
Antibody Validation Database (RRID:SCR_011996) Antibody Validation Database data or information resource, data repository, database, service resource, storage service resource The aim of this site is to collect and to share experimental results on antibodies that would otherwise remain in laboratories, thus aiding researchers in selection and validation of antibodies. is listed by: OMICtools NHGRI U01 HG004258;
NHGRI U01 HG004270;
OER U01 ES017166
The community can contribute to this resource OMICS_01769 SCR_011996 SciCrunch Registry 2026-11-07 11:57:31 15
MitoBreak
 
Resource Report
Resource Website
10+ mentions
MitoBreak (RRID:SCR_012949) MitoBreak data or information resource, data repository, database, service resource, storage service resource Database with curated datasets of mitochondrial DNA (mtDNA) rearrangements. Users may submit new mtDNA rearrangements. mitochondrial dna rearrangement, mitochondrial dna, deletion, duplication, linear, bio.tools is listed by: OMICtools
is listed by: Debian
is listed by: bio.tools
PMID:24170808 Free, The community can contribute to this resource biotools:mitobreak, OMICS_01640 https://bio.tools/mitobreak SCR_012949 SciCrunch Registry 2026-11-07 11:57:55 11
GenomeRNAi
 
Resource Report
Resource Website
100+ mentions
GenomeRNAi (RRID:SCR_013088) data or information resource, data repository, database, service resource, storage service resource GenomeRNAi is a database of phenotypes from systematic RNA interference (RNAi) screens in cultured Drosophila cells. The phenotype database can be searched by keywords, RNAi identifiers or Drosophila gene sequences. Searches with homologous sequences from human or C. elegans are also possible. Integrated tools evaluate the specificity of long double-stranded RNAs (RNAi probes) by similarity searches against all predicted Drosophila transcripts. This site can also be used to identify pre-designed RNAi probes from available Drosophila RNAi libraries. Caenorhabditis elegans genome, human genome drosophila genome, caenorhabditis elegans, caenorhabditis elegans genome, c. elegans, drosophila, drosophila cells, human genome, rnai is recommended by: NIDDK Information Network (dkNET)
is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases
has parent organization: German Cancer Research Center
nif-0000-02901, r3d100011089 https://www.ncbi.nlm.nih.gov/gap SCR_013088 SciCrunch Registry GenomeRNAi, Genome RNAi 2026-11-07 11:58:00 385
Mizutani Lab 3D Structure Portal
 
Resource Report
Resource Website
1+ mentions
Mizutani Lab 3D Structure Portal (RRID:SCR_016529) data or information resource, data repository, laboratory portal, organization portal, portal, service resource, storage service resource Departamental portal of Applied Biochemistry, School of Engineering, Tokai University, Japan. Used for computed tomography (CT) and visualizing 3D structures of biological soft tissues represented with Cartesian coordinates. computed, tomography, visualize, 3D structure, biological, soft, tissue, imaging, sectioning, Free, Available for download, Freely available, DVDs commercially available SCR_016529 SciCrunch Registry 2026-11-07 12:00:51 2
BatchTINT
 
Resource Report
Resource Website
1+ mentions
BatchTINT (RRID:SCR_014804) BatchTINTV2, BatchTINTV3 data analysis software, data processing software, software application, software repository, software resource GUI created by the Taub Institute in order to create an end-user friendly batch processing solution to complement Axona's new command line modification of TINT. This GUI allows the user to define a directory. Within this directory it will be continuously (unless closed) searching for new files to analyze via TINT. python, gui, batch processing, tint, axona, directory Alzheimer’s Association 2015NIRG341570;
NIA R01 AG050425
DOI:10.5281/zenodo.200977 Open access, Available for download, Operates on Windows https://doi.org/10.5281/zenodo.200977 https://github.com/GeoffBarrett/BatchTINTV2/tree/2.0.0 SCR_014804 SciCrunch Registry BatchTINTV2, BatchTINTV3 2026-11-07 11:58:18 3
Illuminating the Druggable Genome
 
Resource Report
Resource Website
50+ mentions
Illuminating the Druggable Genome (RRID:SCR_016924) IDG consortium, data or information resource, data repository, organization portal, portal, service resource, storage service resource Program to improve understanding of properties and functions of proteins that are currently unannotated within three most commonly drug protein families: targeted G-protein coupled receptors, ion channels, and protein kinases. Includes Data and Resource Generating Centers (DRGC), Knowledge Management Center (KMC), and Resource Dissemination and Outreach Center (RDOC). understudied, target, protein, G protein, coupled, receptor, ion, channel, kinase, bio.tools is recommended by: National Library of Medicine
is listed by: NIDDK Information Network (dkNET)
is listed by: bio.tools
is listed by: Debian
NIH Common Fund biotools:pharos https://pharos.nih.gov/, https://bio.tools/pharos, https://darkmatter.ucsf.edu/about https://druggablegenome.net SCR_016924 SciCrunch Registry Pharos, Illuminating the Druggable Genome, IDG, Illuminating Druggable Genome 2026-11-07 11:58:42 64
Integrative Prediction Strategy
 
Resource Report
Resource Website
1+ mentions
Integrative Prediction Strategy (RRID:SCR_027608) data analysis software, data processing software, software application, software repository, software resource, source code Software with approach that leverages machine learning and network biology to predict brain gene expression from blood-derived features. predict brain gene expression, blood-derived features, Free, Available for download, Freely available https://doi.org/10.5281/zenodo.17477450 SCR_027608 SciCrunch Registry Integrative Prediction Strategy (IPS) 2026-11-07 12:07:03 1
University Health Network Princess Margaret Cancer Biobank Core Facility
 
Resource Report
Resource Website
University Health Network Princess Margaret Cancer Biobank Core Facility (RRID:SCR_027522) access service resource, biobank, core facility, material storage repository, service resource, storage service resource Core offers biobanking services and diverse inventory of biospecimens in the field of Oncology. Offers prospective protocol specific banking tailored to your research needs, including patient eligibility, screening, consenting, biospecimen procurement, handling, and processing, clinical data annotation, short and long-term sample storage, and shipping. ABRF, biobanking services, inventory of biospecimens, oncology, protocols, biospecimen procurement, handling, and processing, clinical data annotation, sample storage, shipping is listed by: ABRF CoreMarketplace
has parent organization: University Health Network
ABRF_5427 https://coremarketplace.org/RRID:SCR_027522/?citation=1 SCR_027522 SciCrunch Registry Princess Margaret Cancer Biobank 2026-11-07 12:07:01 0
MetGENE
 
Resource Report
Resource Website
1+ mentions
MetGENE (RRID:SCR_023402) data access protocol, software resource, web service Web tool identifies associations between genes and metabolites that are biosynthesized, metabolized, or transported by proteins coded by genes. Gene centric metabolomics information retrieval tool. Knowledge based, gene centric data aggregator that hierarchically retrieves information about genes, their related pathways, reactions,metabolites, and metabolomic studies from standard data repositories under one dashboard to enable ease of access through centralization of relevant information. Information can be contextualized by filtering along species, anatomy tissue and disease or phenotype. Gene centric metabolomics information retrieval, genes and metabolites associations identification, gene centric data aggregator, has parent organization: University of California at San Diego; California; USA NIH Common Funds Free, Freely available https://bdcw.org/MW/docs/MetGENETutorial.pdf SCR_023402 SciCrunch Registry 2026-11-07 12:01:06 1

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