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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
Parseq
 
Resource Report
Resource Website
1+ mentions
Parseq (RRID:SCR_003464) Parseq software resource Statistical software for transcription landscape reconstruction at a basepair resolution from RNA Seq read counts. It is based on a state-space model which describes, in terms of abrupt shifts and more progressive drifts, the transcription level dynamics along the genome. Alongside variations of transcription level, it incorporates a component of short-range variation to pull apart local artifacts causing correlated dispersion. Reconstruction of the transcription level relies on a conditional sequential Monte Carlo approach that is combined with parameter estimation in a Markov chain Monte Carlo algorithm known as particle Gibbs. The method allows to estimate the local transcription level, to call transcribed regions, and to identify the transcript borders. rna-seq, genome, transcription, bio.tools is listed by: OMICtools
is listed by: Debian
is listed by: bio.tools
has parent organization: Sorbonne University; Paris; France
PMID:24470570 Free, Available for download, Freely available biotools:parseq, OMICS_02302 https://bio.tools/parseq SCR_003464 2026-02-07 02:06:03 2
Wellcome Trust Case Control Consortium
 
Resource Report
Resource Website
100+ mentions
Wellcome Trust Case Control Consortium (RRID:SCR_001973) WTCCC data or information resource Consortium of 50 research groups across the UK to harness the power of newly-available genotyping technologies to improve our understanding of the aetiological basis of several major causes of global disease. The consortium has gathered genotype data for up to 500,000 sites of genome sequence variation (single nucleotide polymorphisms or SNPs) in samples ascertained for the disease phenotypes. Analysis of the genome-wide association data generated has lead to the identification of many SNPs and genes showing evidence of association with disease susceptibility, some of which will be followed up in future studies. In addition, the Consortium has gained important insights into the technical, analytical, methodological and biological aspects of genome-wide association analysis. The core of the study comprised an analysis of 2,000 samples from each of seven diseases (type 1 diabetes, type 2 diabetes, coronary heart disease, hypertension, bipolar disorder, rheumatoid arthritis and Crohn's disease). For each disease, the case samples have been ascertained from sites widely distributed across Great Britain, allowing us to obtain considerable efficiencies by comparing each of these case populations to a common set of 3,000 nationally-ascertained controls also from England, Scotland and Wales. These controls come from two sources: 1,500 are representative samples from the 1958 British Birth Cohort and 1,500 are blood donors recruited by the three national UK Blood Services. One of the questions that the WTCCC study has addressed relates to the relative merits of these alternative strategies for the generation of representative population cohorts. Genotyping for this main Case Control study was conducted by Affymetrix using the (commercial) Affymetrix 500K chip. As part of this study a total of 17,000 samples were typed for 500,000 SNPs. There are two additional components to the study. First, the WTCCC award is part-funding a study of host resistance to infectious diseases in African populations. The same approach has been used to type 2,000 cases of tuberculosis (TB) and 2,000 cases of malaria, as well as 2,000 shared controls. As well as addressing diseases of major global significance, and extending WTCCC coverage into the area of infectious disease, the inclusion of samples of African origin has obvious benefits with respect to methodological aspects of genome-wide association analysis. Second, the WTCCC has, for four additional diseases (autoimmune thyroid disease, breast cancer, ankylosing spondylitis, multiple sclerosis), completed an analysis of 15,000 SNPs designed to represent a large proportion of the known non-synonymous coding SNPs across the genome. This analysis has been performed at the WTSI using a custom Infinium chip (Illumina). Data release The genotypic data of the control samples (1958 British Birth Cohort and UK Blood Service) and from seven diseases analyzed in the main study are now available to qualified researchers. Summary genotype statistics for these collections are available directly from the website. Access to the individual-level genotype data and summary genotype statistics is by application to the Consortium Data Access Committee (CDAC) and approval subject to a Data Access Agreement. WTCCC2: A further round of GWA studies were funded in April 2008. These include 15 WTCCC-collaborative studies and 12 independent studies be supported totaling approximately 120,000 samples. Many of the studies represent major international collaborative networks that have together assembled large sample collections. WTCCC2 will perform genome-wide association studies in 13 disease conditions: Ankylosing spondylitis, Barrett's oesophagus and oesophageal adenocarcinoma, glaucoma, ischaemic stroke, multiple sclerosis, pre-eclampsia, Parkinson's disease, psychosis endophenotypes, psoriasis, schizophrenia, ulcerative colitis and visceral leishmaniasis. WTCCC2 will also investigate the genetics of reading and mathematics abilities in children and the pharmacogenomics of statin response. Over 60,000 samples will be analyzed using either the Affymetrix v6.0 chip or the Illumina 660K chip. The WTCCC2 will also genotype 3,000 controls each from the 1958 British Birth cohort and the UK Blood Service control group, and the 6,000 controls will be genotyped on both the Affymetrix v6.0 and Illumina 1.2M chips. WTCCC3: The Wellcome Trust has provided support for a further round of GWA studies in January 2009. These include 5 WTCCC-collaborative studies to be carried out in WTCCC3 and 5 independent studies, across a range of diseases. Many of the studies represent major international collaborative networks that have together assembled large sample collections. WTCCC3 will perform genome-wide association studies in the following 4 disease conditions: primary biliary cirrhosis, anorexia nervosa, pre-eclampsia in UK subjects, and the interactions between donor and recipient DNA related to early and late renal transplant dysfunction. The WTCCC3 will also carry out a pilot in a study of the genetics of host control of HIV-1 infection. Over 40,000 samples will be analyzed using the Illumina 660K chip. The WTCCC3 will utilize the 6,000 control genotypes generated by the WTCCC2. gene, genomic, genetics, microarray, genome-wide association study, snp, genome-wide association, blood, dna, genotype, variation, genome, sequence variant, copy number variation, genetic variation, phenotype, disease is related to: Psychiatric Genomics Consortium
has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom
Bipolar disorder, Coronary artery disease, Crohn's disease, Rheumatoid arthritis, Type 1 diabetes, Type 2 diabetes, Hypertension, Control, Multiple sclerosis, Breast cancer, Ankylosing spondylitis, Autoimmune thyroid disease, Malaria, Tuberculosis, Inflammatory bowel disease, Barrett's esophagus, Esophageal adenocarcinoma, Glaucoma, Ischemic stroke, Pre-eclampsia, Parkinson's disease, Psychosis endophenotypes, Psoriasis, Schizophrenia, Ulcerative colitis, Visceral leishmaniasis, Primary biliary cirrhosis, Anorexia nervosa, Human immunodeficiency virus, Renal transplant dysfunction, Diabetes Wellcome Trust ;
Bill and Melinda Gates Foundation ;
Wellcome Trust Sanger Institute; Hinxton; United Kingdom
PMID:17554300 Access to summary data and individual-level genotype data is available by application to the Wellcome Trust Case Control Consortium Data Access Committee. Access to data will be granted to qualified investigators for appropriate use. nif-0000-10551 SCR_001973 Wellcome Trust Case-Control Consortium (WTCCC) 2026-02-07 02:05:38 212
tbrowse
 
Resource Report
Resource Website
tbrowse (RRID:SCR_001918) tbrowse software resource Software providing a HTML5/javascript based browser for visualizing RNA-seq results in the familiar track layout of common genome browser. But given the quantitative nature of RNA-seq data, in addition to visualizing sequence coverage, the browser quantitates transcript abundance across regions of interest. The HTML5 functionality is made of use to render all the tracks using the canvas drawing element. This greatly reduces the load on servers and allows for rich interactive graphics without the need for third-party plugins. Furthermore, this framework completely segregates data from visualization, making development much easier. The browser is designed to run on all modern browsers: Firefox, Safari, Chrome, Opera and Internet Explorer (though not recommended). genome, browser, transcriptome, html5, canvas, extjs, visualization, rna-seq is listed by: OMICtools
has parent organization: Google Code
THIS RESOURCE IS NO LONGER IN SERVICE OMICS_01935 SCR_001918 tbrowse - HTML5 Transcriptome Browser 2026-02-07 02:05:38 0
Genoscope
 
Resource Report
Resource Website
100+ mentions
Genoscope (RRID:SCR_002172) Genoscope institution French national sequencing center with the following resources: * Sequencing ** Genoscope Projects * Environmental genomics ** Microbial diversity in wastewater ** Metabolic genomics * Bioinformatics ** Atelier for comparative genomics ** Computational Systems Biology ** Servers resources *** GGB for Generic Genome Browser: graphic interface for various databases (sequence, annotation, syntenies...) for a given organism. *** MaGe for Magnifying Microbial Genomes: annotation system for microbial genomes. environmental genomics, biocatalysis, environment, genomics, sequencing, bioinformatics, biodiversity, blast, blat, ggb, mage, metabolic, whole genome shotgun, chromosome 3, cdna, chromosome 14, alternative splicing, o��kopleura dioica, mutation, enzymatic cloning, screening, synteny, data set, genome, sequence, annotation, genome browser, FASEB list has parent organization: CEA; Gif sur Yvette; France Free, Freely available ISNI: 0000 0004 0641 2997, Wikidata: Q3100800, grid.434728.e, nif-0000-20957 https://ror.org/028pnqf58 SCR_002172 Genoscope - Centre National de S�quen�age, Genoscope - French National Sequencing Center, French National Sequencing Center, Genoscope - Centre National de Sequencage 2026-02-07 02:05:51 157
ARACHNE
 
Resource Report
Resource Website
1+ mentions
ARACHNE (RRID:SCR_000351) ARACHNE software resource A software for genome assembly, and is specifically designed to analyze long Sanger-chemistry reads. genome, sequencing, analysis, sanger, chemistry, bio.tools is listed by: OMICtools
is listed by: bio.tools
is listed by: Debian
has parent organization: Broad Institute
PMID:11779843 THIS RESOURCE IS NO LONGER IN SERVICE OMICS_01812, biotools:arachne https://bio.tools/arachne SCR_000351 ARACHNE: a whole-genome shotgun assembler, ARACHNE (Unsupported) 2026-02-07 02:05:19 3
HudsonAlpha Genomics Services Lab
 
Resource Report
Resource Website
HudsonAlpha Genomics Services Lab (RRID:SCR_000353) HudsonAlpha Genomics Services Lab service resource A lab that offers genetic research tools such as RNA sequencing and a variety of arrays. genome, sequencing, assembly, rna, microarray, exome is listed by: ScienceExchange THIS RESOURCE IS NO LONGER IN SERVICE SciEx_221 SCR_000353 HudsonAlpha Institute for Biotechnology Genomics Services Lab, Genomics Services Lab 2026-02-07 02:05:21 0
Pindel
 
Resource Report
Resource Website
10+ mentions
Pindel (RRID:SCR_000560) Pindel software resource Software to detect breakpoints of large deletions, medium sized insertions, inversions, tandem duplications and other structural variants at single-based resolution from next-gen sequence data. It uses a pattern growth approach to identify the breakpoints of these variants from paired-end short reads., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. deletion, insertion, nucleotide, genome, read, inversion, tandem duplication, structural variant, next-generation sequencing, pattern growth, indel, breakpoint, bio.tools is listed by: OMICtools
is listed by: bio.tools
is listed by: Debian
has parent organization: Washington University School of Medicine in St. Louis; Missouri; USA
works with: cgpPindel
PMID:19561018 THIS RESOURCE IS NO LONGER IN SERVICE biotools:pindel, OMICS_00321 https://bio.tools/pindel SCR_000560 2026-02-07 02:05:24 22
FPSAC
 
Resource Report
Resource Website
1+ mentions
FPSAC (RRID:SCR_000555) FPSAC software resource Sogftware for fast Phylogenetic Scaffolding of Ancient Contigs. genome, scaffolding, bio.tools is listed by: OMICtools
is listed by: bio.tools
is listed by: Debian
has parent organization: Simon Fraser University; British Columbia; Canada
PMID:24068034 biotools:fpsac, OMICS_00041 https://bio.tools/fpsac SCR_000555 Fast Phylogenetic Scaffolding of Ancient Contigs (FPSAC) and application to the medieval Black Death agent, Fast Phylogenetic Scaffolding of Ancient Contigs, FPSAC: fast phylogenetic scaffolding of ancient contigs 2026-02-07 02:05:21 1
Genome BioInformatics Research Lab - gff2ps
 
Resource Report
Resource Website
1+ mentions
Genome BioInformatics Research Lab - gff2ps (RRID:SCR_000462) software resource THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Software program for visualizing annotations of genomic sequences. The program has features such as the ability to create comprehensive plots, customizable parameters, and flexibility in file format. genome, sequence, visualization, parameters, bioinformatics, bio.tools is listed by: Debian
is listed by: bio.tools
is listed by: OMICtools
PMID:11099262
DOI:10.1093/bioinformatics/16.8.743
Free, Available for download, Freely available OMICS_17140, biotools:gff2ps, nif-0000-30611 https://bio.tools/gff2ps
https://sources.debian.org/src/gff2ps/
SCR_000462 gff2ps 2026-02-07 02:05:22 1
HapCompass
 
Resource Report
Resource Website
1+ mentions
HapCompass (RRID:SCR_000942) algorithm Software that utilizes a fast cycle basis algorithm for the accurate haplotype assembly of sequence data. It is able to create pairwise SNP phasings. algorithm, haplotype, sequence, genome, dna, rna, snp is listed by: OMICtools
has parent organization: Brown University; Rhode Island; USA
NSF 1048831;
NSF 1321000
THIS RESOURCE IS NO LONGER IN SERVICE OMICS_00197 SCR_000942 2026-02-07 02:05:24 1
QuadGT
 
Resource Report
Resource Website
1+ mentions
QuadGT (RRID:SCR_000073) QuadGT software resource Software package for calling single-nucleotide variants in four sequenced genomes comprising a normal-tumor pair and the two parents. Genotypes are inferred using a joint model of parental variant frequencies, de novo germline mutations, and somatic mutations. The model quantifies the descent-by-modification relationships between the unknown genotypes by using a set of parameters in a Bayesian inference setting. Note that you can use it on any subset of the four related genomes, including parent-offspring trios, and normal-tumor pairs without parental samples. single-nucleotide variant, sequenced genome, genotype, genome is listed by: OMICtools
has parent organization: University of Montreal; Quebec; Canada
Normal, Tumor, Cancer Terry Fox Research Institute ;
Canadian Institutes for Health Research ;
Canada National Sciences and Engineering Research Council
PMID:23734724 Free, Available for download, Freely available OMICS_02108 SCR_000073 2026-02-07 02:05:16 1
SOAPfuse
 
Resource Report
Resource Website
1+ mentions
SOAPfuse (RRID:SCR_000078) SOAPfuse software resource THIS RESOURCE IS NO LONGER IN SERVICE.Documented on August 23,2022. An open source tool developed for genome-wide detection of fusion transcripts from human being paired-end RNA-Seq data. This tool is a part of a larger set of tools to efficiently align oligonucleotides onto reference sequences . software, resource, open license, DNA sequencing, genome, transcripts, RNA, oligonucleotide is listed by: OMICtools
is listed by: SourceForge
is listed by: SOAP
PMID:23409703 THIS RESOURCE IS NO LONGER IN SERVICE OMICS_01357 SCR_000078 2026-02-07 02:05:19 7
EdgeBio
 
Resource Report
Resource Website
EdgeBio (RRID:SCR_000183) EdgeBio commercial organization THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. A contract research organization that provides genomics services such as sequencing, bioinformatics, NGS data analysis and whole exome sequencing. EdgeBio is a CLIA-approved service provider. contract research organization, CRO, genomics, genome, sequencing, bioinformatics, NGS data analysis, whole exome sequencing, research, Illumina NGS is listed by: ScienceExchange THIS RESOURCE IS NO LONGER IN SERVICE SciEx_203 https://www.edgebio.com/ SCR_000183 Edge Bio, EdgeBio.com 2026-02-07 02:05:18 0
GenomeCloud
 
Resource Report
Resource Website
GenomeCloud (RRID:SCR_011886) GenomeCloud storage service resource, service resource, data repository THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 29, 2019. A cloud platform for next-generation sequencing analysis and storage. Services include: * g-Analysis: Automated genome analysis pipelines at your fingertips * g-Cluster: Easy-of-use and cost-effective genome research infrastructure * g-Storage: A simple way to store, share and protect data * g-Insight: Accurate analysis and interpretation of biological meaning of genome data genome is listed by: OMICtools THIS RESOURCE IS NO LONGER IN SERVICE OMICS_01219 SCR_011886 2026-02-11 10:58:25 0
RAST Server
 
Resource Report
Resource Website
500+ mentions
RAST Server (RRID:SCR_014606) RAST service resource, production service resource A SEED-quality automated service that annotates complete or nearly complete bacterial and archaeal genomes across the entire phylogenetic tree. RAST can also be used to analyze draft genomes. microbiome, seed, annotate, genome, bacteria, archaea, service, bio.tools is listed by: Human Microbiome Project
is listed by: Debian
is listed by: bio.tools
National Science Foundation 0850546;
NIAID contract HHSN272200900040C
PMID:18261238 Free for the scientific community, Login required biotools:theseed https://bio.tools/theseed SCR_014606 Rapid Annotation using Subsystem Technology, Rapid Annotation using Subsystem Technology Server 2026-02-11 10:58:57 907
ESTHER
 
Resource Report
Resource Website
100+ mentions
ESTHER (RRID:SCR_002621) ESTHER data or information resource, database Database and tools for analysis of protein and nucleic acid sequences belonging to superfamily of alpha/beta hydrolases homologous to cholinesterases. Covers multiple species, including human, mouse caenorhabditis and drosophila., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. alpha hydrolase, beta hydrolase, cholinesterase, protein, protein superfamily, blast, gene, protein binding, protein-protein interaction, nucleotide, nucleotide sequence, enzyme, genetics, genome, genomics, mutation, disease, gene expression, peptide, chromosome is listed by: re3data.org
is related to: UniProtKB
is related to: AceDB
has parent organization: INRA - French National Institute for Agricultural Research; Paris; France
PMID:23193256 Free, Available for download, Freely available nif-0000-30526, SCR_008479, nif-0000-02817, r3d100010542 https://doi.org/10.17616/R33K77 SCR_002621 ESTerases and alpha/beta-Hydrolase Enzymes and Relatives, ESTHER Database, ESTerases and alpha / beta-hydrolase Enzymes and Relatives 2026-02-11 10:56:35 134
FlyMine
 
Resource Report
Resource Website
100+ mentions
FlyMine (RRID:SCR_002694) FlyMine data or information resource, database THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 14,2026. Integrated database of genomic, expression and protein data for Drosophila, Anopheles, C. elegans and other organisms. You can run flexible queries, export results and analyze lists of data. FlyMine presents data in categories, with each providing information on a particular type of data (for example Gene Expression or Protein Interactions). Template queries, as well as the QueryBuilder itself, allow you to perform searches that span data from more than one category. Advanced users can use a flexible query interface to construct their own data mining queries across the multiple integrated data sources, to modify existing template queries or to create your own template queries. Access our FlyMine data via our Application Programming Interface (API). We provide client libraries in the following languages: Perl, Python, Ruby and & Java API anopheles, genome, c. elegans, drosophila, gene, chromosomal location, genomics, proteomics, gene expression, interaction, homology, function, regulation, protein, phenotype, pathway, disease, publication, FASEB list is related to: FlyBase
is related to: UniProt
is related to: Ensembl
is related to: InterPro
is related to: Biological General Repository for Interaction Datasets (BioGRID)
is related to: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB)
is related to: Tree families database
is related to: IntAct
is related to: Gene Ontology
is related to: GOA
is related to: ArrayExpress
is related to: REDfly Regulatory Element Database for Drosophilia
is related to: KEGG
is related to: Reactome
has parent organization: University of Cambridge; Cambridge; United Kingdom
Wellcome Trust 067205;
NHGRI
PMID:17615057 THIS RESOURCE IS NO LONGER IN SERVICE nif-0000-02845 SCR_002694 2026-02-11 10:56:31 104
Scripps Wellderly Genome Reference
 
Resource Report
Resource Website
Scripps Wellderly Genome Reference (RRID:SCR_010250) SWGR data or information resource, data set Whole genome sequencing data for 454 unrelated Scripps Wellderly Study participants with European ancestry from a project that is studying the genetic architecture of exceptional healthspan from a cohort comprised of more than 1300 healthy individuals over the age of 80 years. SWGR_v1.0 includes chromosome-specific VCF4.1 bgzipped and tabix indexed files. Annotations for each variant can be found at Scripps Genome ADVISER (SG-ADVISER, http://genomics.scripps.edu/) Additional data releases are expected. genomics, genomic sequence, genome, female, male, late adult human has parent organization: Scripps Translational Science Institute Healthy aging, Aging, Healthy Scripps Health; California; USA ;
NCATS ScienceUL1 TR00114
Free, Public, Acknowledgement required nlx_156888 SCR_010250 2026-02-11 10:58:14 0
Fungal Genome Initiative
 
Resource Report
Resource Website
10+ mentions
Fungal Genome Initiative (RRID:SCR_003169) FGI data or information resource, data set Produces and analyzes sequence data from fungal organisms that are important to medicine, agriculture and industry. The FGI is a partnership between the Broad Institute and the wider fungal research community, with the selection of target genomes governed by a steering committee of fungal scientists. Organisms are selected for sequencing as part of a cohesive strategy that considers the value of data from each organism, given their role in basic research, health, agriculture and industry, as well as their value in comparative genomics. sequence, fungi, gene annotation, genome is listed by: 3DVC
has parent organization: Broad Institute
NHGRI ;
NSF ;
NIAID ;
USDA
Free, Freely available nif-0000-30591 SCR_003169 2026-02-11 10:56:41 18
1000 Genomes Project and AWS
 
Resource Report
Resource Website
5000+ mentions
1000 Genomes Project and AWS (RRID:SCR_008801) 1000 Genomes Project and AWS data or information resource, data set A dataset containing the full genomic sequence of 1,700 individuals, freely available for research use. The 1000 Genomes Project is an international research effort coordinated by a consortium of 75 companies and organizations to establish the most detailed catalogue of human genetic variation. The project has grown to 200 terabytes of genomic data including DNA sequenced from more than 1,700 individuals that researchers can now access on AWS for use in disease research free of charge. The dataset containing the full genomic sequence of 1,700 individuals is now available to all via Amazon S3. The data can be found at: http://s3.amazonaws.com/1000genomes The 1000 Genomes Project aims to include the genomes of more than 2,662 individuals from 26 populations around the world, and the NIH will continue to add the remaining genome samples to the data collection this year. Public Data Sets on AWS provide a centralized repository of public data hosted on Amazon Simple Storage Service (Amazon S3). The data can be seamlessly accessed from AWS services such Amazon Elastic Compute Cloud (Amazon EC2) and Amazon Elastic MapReduce (Amazon EMR), which provide organizations with the highly scalable compute resources needed to take advantage of these large data collections. AWS is storing the public data sets at no charge to the community. Researchers pay only for the additional AWS resources they need for further processing or analysis of the data. All 200 TB of the latest 1000 Genomes Project data is available in a publicly available Amazon S3 bucket. You can access the data via simple HTTP requests, or take advantage of the AWS SDKs in languages such as Ruby, Java, Python, .NET and PHP. Researchers can use the Amazon EC2 utility computing service to dive into this data without the usual capital investment required to work with data at this scale. AWS also provides a number of orchestration and automation services to help teams make their research available to others to remix and reuse. Making the data available via a bucket in Amazon S3 also means that customers can crunch the information using Hadoop via Amazon Elastic MapReduce, and take advantage of the growing collection of tools for running bioinformatics job flows, such as CloudBurst and Crossbow. genomic data, genome, cloud computing, cloud, human, gene, genetic variation, research, dna is used by: HmtVar
has parent organization: Amazon Web Services
nlx_144340 SCR_008801 1000 Genomes Project and Amazon Web Services, 000 Genomes Project Amazon Web Services, 1000 Genomes Project AWS 2026-02-11 10:57:55 7075

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