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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 Synonyms Record Last Update Mentions Count
Pig Genome Database
 
Resource Report
Resource Website
Pig Genome Database (RRID:SCR_006367) PGD data analysis service, analysis service resource, production service resource, service resource, database, data or information resource Database facilitating information integration and mining within the pig and across species of all genomics / genetics research results accumulated over the years including pig gene expression, quantitative trait loci (QTL), candidate gene, and whole genome association study (WGAS) results. The key functions developed so far include pig gene pages (a centralized gene search tool), a local copy of Biomart (for customizable genome information queries), genome feature alignment tools (Pig QTLdb and Gbrowse), integrated gene expression information (ANEXDB and ESTdb), a dedicated pig genome and gene set BLAST server, and virtual comparative map database and tools (VCmap). By developing the PGD, it is our aim to collaboratively utilize existing databases and tools via networked functions, such as web services, database API, etc., to maximize the potential of all related databases through the PGD implementation. gene expression, quantitative trait loci, candidate gene, whole genome association study, genome, chromosome, dna, trait, marker has parent organization: NAGRP Bioinformatics Coordination Program United States Department of Agriculture nlx_152113 SCR_006367 2026-08-04 09:41:35 0
Proteome Commons
 
Resource Report
Resource Website
10+ mentions
Proteome Commons (RRID:SCR_006234) Proteome Commons portal, storage service resource, software resource, community building portal, data repository, service resource, database, data or information resource THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 17, 2013. A public resource for sharing general proteomics information including data (Tranche repository), tools, and news. Joining or creating a group/project provides tools and standards for collaboration, project management, data annotation, permissions, permanent storage, and publication. proteomics, protein, peptide, data sharing, data, tool, news, annotation, proteome, genome is listed by: re3data.org
has parent organization: University of Michigan; Ann Arbor; USA
is parent organization of: Proteome Commons Tranche repository
NCI ;
Clinical Proteomics Technologies for Cancer ;
NCRR P41-RR018627
PMID:20356086 THIS RESOURCE IS NO LONGER IN SERVICE nlx_151800 SCR_006234 ProteomeCommons.org, ProteomeCommons 2026-08-04 09:41:33 12
TCGAbiolinks
 
Resource Report
Resource Website
50+ mentions
TCGAbiolinks (RRID:SCR_017683) data processing software, software application, software resource, data analysis software Software R Bioconductor package for integrative analysis with TCGA data.TCGAbiolinks is able to access National Cancer Institute Genomic Data Commons thorough its GDC Application Programming Interface to search, download and prepare relevant data for analysis in R. Integrative, analysis, TCGA data, cancer, genome, atlas, genomic, analysis, expression, methylated, region, survival plot, phenotype, tumor, epigenomic, alteration, clinical, molecular, retrival BridgeIRIS ;
INNOVIRIS ;
Region de Bruxelles Capitale ;
Brussels ;
Belgium ;
GENGISCAN ;
São Paulo Research Foundation
PMID:26704973
DOI:10.12688/f1000research.8923.2
Free, Available for download, Freely available https://github.com/BioinformaticsFMRP/TCGAbiolinks SCR_017683 Cancer Genome Atlas (TCGA) biolinks 2026-08-04 09:44:11 93
CRISPy-web
 
Resource Report
Resource Website
10+ mentions
CRISPy-web (RRID:SCR_017970) data access protocol, software resource, web service Web tool to design sgRNAs for CRISPR applications. Web tool based on CRISPy to design sgRNAs for any user-provided microbial genome. Implemented as standalone web application for Cas9 target prediction. Design, sgRNA, CRISP, microbial, genome, Cas9, target, prediction, data, guide, single, editing, bio.tools is listed by: bio.tools
is listed by: Debian
Novo Nordisk Foundation PMID:29062934 Free, Freely available biotools:crispy https://bio.tools/crispy SCR_017970 single guide RNA desing 2026-08-04 09:44:16 25
PAFScaff
 
Resource Report
Resource Website
1+ mentions
PAFScaff (RRID:SCR_017976) data processing software, data analysis software, software resource, sequence analysis software, software application Software as Pairwise mApping Format reference based Scaffold anchoring and super scaffolding tool. Dsigned for mapping genome assembly scaffolds to closely related chromosome level reference genome assembly. Pairwise, mapping, reference, scaffold, genomics, scaffolding, assembly, genome, chromosome, bio.tools is listed by: Debian
is listed by: bio.tools
Free, Freely available biotools:PAFScaff https://github.com/slimsuite/pafscaff/blob/master/PAFScaff.md, https://slimsuite.github.io/pafscaff/, https://bio.tools/PAFScaff SCR_017976 Pairwise mApping Format reference-based Scaffold 2026-08-04 09:44:15 4
Codon Usage Analyzer
 
Resource Report
Resource Website
Codon Usage Analyzer (RRID:SCR_018500) Bio::CUA, Bio-CUA data processing software, software application, software resource, data analysis software Software tool as flexible and comprehensive codon usage analyzer. Used to analyze codon usage bias (CUB) and relevant problems. Codon usage analyzer, codon, codon usage bias, genome, gene, codon, sequence has parent organization: University of Rochester; New York; USA David and Lucile Packard Foundation ;
University of Rochester
DOI:10.1101/022814 Free, Freely available https://metacpan.org/release/Bio-CUA SCR_018500 2026-08-04 09:44:21 0
rVista
 
Resource Report
Resource Website
10+ mentions
rVista (RRID:SCR_018707) analysis service resource, web service, software resource, data access protocol, production service resource, service resource Web tool for analyzing regulatory potential of noncoding sequences. rVISTA web server is interconnected with TRANSFAC database, allowing users to either search for matrices present in TRANSFAC library collection or search for user defined consensus sequences. rVISTA 2.0 web server is used for high throughput discovery of cis-regulatory elements. Can process alignments generated by zPicture and blastz alignment programs or use pre-computed pairwise alignments of several vertebrate genomes available from ECR Browser and GALA database. Evolutionary analysis of transcription factor binding sites. Noncoding sequence, regulatory potential analysis, matrices search, TRANSFAC library collection, cis regulatory element, process alignment, zPicture, blastz, pairwise alignment, genome, analysis, transcription factor binding site, bio.tools is listed by: Debian
is listed by: bio.tools
works with: TRANSFAC
PMID:15215384 Free, Freely available biotools:rvista https://bio.tools/rvista SCR_018707 rVista 2.0 2026-08-04 09:44:26 30
FunCoup
 
Resource Report
Resource Website
1+ mentions
FunCoup (RRID:SCR_018711) web service, software resource, data access protocol, service resource, database, data or information resource Database of genome wide functional coupling networks. Provides tools to explore predicted networks and to retrieve detailed information about data underlying each prediction. Web service for functional coupling search. Genome, genome functional coupling network, coupling network, functional coupling, functional couplings search, gene identifier, genome data has parent organization: Karolinska Institute; Stockholm; Sweden Swedish Research Council ;
Stockholm University
PMID:24185702 Free, Freely available SCR_018711 2026-08-04 09:44:23 3
Preseq
 
Resource Report
Resource Website
10+ mentions
Preseq (RRID:SCR_018664) data processing software, data analysis software, software resource, software application, software toolkit Software package for predicting library complexity and genome coverage in high throughput sequencing. Aimed at predicting yield of distinct reads from genomic library from initial sequencing experiment. Predicting molecular complexity of sequencing libraries. Genome, high throughput sequencing, predicting library complexity, distinct yield prediction, genomic library, initial sequencing experiment, molecular complexity prediction, sequencing libraryb, bio.tools is listed by: bio.tools
is listed by: Debian
has parent organization: Stanford University; Stanford; California
PMID:23435259 Free, Freely available biotools:preseq https://github.com/smithlabcode/preseq, https://bio.tools/preseq SCR_018664 2026-08-04 09:44:22 19
Mugsy
 
Resource Report
Resource Website
50+ mentions
Mugsy (RRID:SCR_001414) data processing software, data analysis software, software resource, sequence analysis software, software application Software resource for multiple whole genome alignment. It uses Nucmer, a custom graph-based segmentation procedure, for pairwise alignment, and the Seqan:TCoffee's multiple alignment strategy. software, genome, genome alignment, segmentation, pairwise alignment, sequence analysis software is listed by: OMICtools
is listed by: Debian
has parent organization: SourceForge
PMID:21148543
DOI:10.1093/bioinformatics/btq665
Free, Available for download, Freely available OMICS_03606 https://sources.debian.org/src/mugsy/ SCR_001414 2026-08-04 09:40:22 71
Ensembl Variation
 
Resource Report
Resource Website
1+ mentions
Ensembl Variation (RRID:SCR_001630) Ensembl Variation data analysis service, analysis service resource, production service resource, service resource, database, data or information resource Public database that stores areas of genome that differ between individual genomes (variants) and, where available, associated disease and phenotype information. Different types of variants for several species: single nucleotide polymorphisms (SNPs), short nucleotide insertions and/or deletions, and longer variants classified as structural variants (including CNVs). Effects of variants on the Ensembl transcripts and regulatory features for each species are predicted. You can run same analysis on your own data using Variant Effect Predictor. These data are integrated with other data sources in Ensembl, and can be accessed using the API or website. For several different species in Ensembl, they import variation data (SNPs, CNVs, allele frequencies, genotypes, etc) from a variety of sources (e.g. dbSNP). Imported variants and alleles are subjected to quality control process to flag suspect data. In human, they calculate linkage disequilibrium for each variant, by population. genome, disease, phenotype, genomic variant, single nucleotide polymorphism nucleotide, insertion, deletion, structural variant, copy number variation, inversion, translocation, somatic variant, allele frequency, genotype, disease phenotype, inherited disease is used by: MONARCH Initiative
is related to: dbSNP
is related to: Database of Genomic Variants Archive (DGVa)
is related to: PubMed
is related to: Animal QTLdb
is related to: OMIA - Online Mendelian Inheritance in Animals
has parent organization: Ensembl
PMID:23203987
PMID:20562413
PMID:20459810
PMID:20459805
Free, Available for download, Freely available nlx_153897 SCR_001630 ensembl variation 2026-08-04 09:40:26 4
Ancora
 
Resource Report
Resource Website
10+ mentions
Ancora (RRID:SCR_001623) Ancora data analysis service, analysis service resource, production service resource, service resource, database, data or information resource Web resource that provides data and tools for exploring genomic organization of highly conserved noncoding elements (HCNEs) for multiple genomes. It includes a genome browser that shows HCNE locations and features novel HCNE density plots as a powerful tool to discover developmental regulatory genes and distinguish their regulatory elements and domains. They identify HCNEs as non-exonic regions of high similarity between genome sequences from distantly related organisms, such as human and fish, and provide tools for studying the distribution of HCNEs along chromosomes. Major peaks of HCNE density along chromosomes most often coincide with developmental regulatory genes. Their aim with this site is to aid discovery of developmental regulatory genes, their regulatory domains and their fundamental regulatory elements. genome, highly conserved noncoding element, noncoding element, regulatory gene, regulatory domain, regulatory element, developmental regulatory gene, evolution, enhancer is related to: MONARCH Initiative
has parent organization: University of Bergen; Bergen; Norway
Research Council of Norway ;
Bergen Research Foundation ;
Sars Centre
PMID:18279518 Free, Freely available nlx_153891 SCR_001623 Atlas of Noncoding Conserved Regions in Animals 2026-08-04 09:40:26 19
Animal QTLdb
 
Resource Report
Resource Website
50+ mentions
Animal QTLdb (RRID:SCR_001748) Animal QTLdb storage service resource, data repository, service resource, database, data or information resource Database of trait mapping data, i.e. QTL (phenotype / expression, eQTL), candidate gene and association data (GWAS) and copy number variations (CNV) mapped to livestock animal genomes, to facilitate locating and comparing discoveries within and between species. New data and database tools are continually developed to align various trait mapping data to map-based genome features, such as annotated genes. QTLdb is open to house QTL/association date from other animal species where feasible. Most scientific journals require that any original QTL/association data be deposited into public databases before paper may be accepted for publication. User curator accounts are provided for direct data deposit. Users can download QTLdb data from each species or individual chromosome. chromosome, comparative genomics, dna sequence, genome, livestock, quantitative trait locus, non-human animal, structural genomics, single-nucleotide polymorphism, gene association, genomics, trait, copy number variation, trait, phenotype, expression, eqtl, genome wide association study, candidate gene, genotype uses: Entrez Gene
uses: Ensembl
is used by: NIF Data Federation
is used by: MONARCH Initiative
is listed by: re3data.org
is related to: Ensembl Variation
is related to: Vertebrate Trait Ontology
has parent organization: Iowa State University; Iowa; USA
has parent organization: NAGRP Bioinformatics Coordination Program
USDA NRSP-8;
USDA 2007-04187
PMID:23180796
PMID:17245610
Free, Freely available nif-0000-02550, r3d100010744 http://www.animalgenome.org/QTLdb/ SCR_001748 Animal QTL database, Animal Quantitative Trait Loci database, AnimalQTLdb, Animal Quantitative Trait Loci (QTL) database 2026-08-04 09:40:28 50
Sea Urchin Genome Project
 
Resource Report
Resource Website
1+ mentions
Sea Urchin Genome Project (RRID:SCR_001735) portal, project portal, data or information resource Provides informationa about Genome of California Purple Sea Urchin, one species (Strongylocentrotus purpuratus) of which has been sequenced and annotated by Sea Urchin Genome Sequencing Consortium led by HGSC. Reports sequence and analysis of genome of sea urchin Strongylocentrotus purpuratus, a model for developmental and systems biology. echinoderm, evolutionary, fragile urchin, gene, genome, allocentrotus fragilis, bacterial artificial chromosome (bac), biology, chromosome, clone, core facility, deuterostome, developmental biology, heterozygosity, metabase, model, sea urchin, sequence, shotgun, strongylocentrotus franciscanus, strongylocentrotus purpuratus, systems biology, vertebrate has parent organization: Baylor University; Texas; USA Free, Freely Available nif-0000-25606, SCR_002841, nif-0000-10253 http://www.hgsc.bcm.tmc.edu/project-species-o-Strongylocentrotus%20purpuratus.hgsc?pageLocation=Strongylocentrotus%20purpuratus SCR_001735 Sea Urchin, HGSC Sea Urchin Genome Project 2026-08-04 09:40:27 1
MEME Suite - Motif-based sequence analysis tools
 
Resource Report
Resource Website
1000+ mentions
MEME Suite - Motif-based sequence analysis tools (RRID:SCR_001783) MEME Suite data analysis service, data processing software, source code, analysis service resource, data analysis software, software resource, software application, production service resource, service resource, database, data or information resource Suite of motif-based sequence analysis tools to discover motifs using MEME, DREME (DNA only) or GLAM2 on groups of related DNA or protein sequences; search sequence databases with motifs using MAST, FIMO, MCAST or GLAM2SCAN; compare a motif to all motifs in a database of motifs; associate motifs with Gene Ontology terms via their putative target genes, and analyze motif enrichment using SpaMo or CentriMo. Source code, binaries and a web server are freely available for noncommercial use. gene ontology, motif, comparative genomics, dna regulatory motif, dna sequence, dna, gene, transcription factor, genome, protein, analysis, function analysis, comparison, cluster, enrichment analysis, sequence analysis, bio.tools, FASEB list lists: DREME
is listed by: OMICtools
is listed by: bio.tools
is listed by: Debian
is related to: Gene Ontology
is related to: Glam2
is related to: ANNOgesic
is related to: memesuite-lite
has parent organization: National Biomedical Computation Resource
is parent organization of: GOMO - Gene Ontology for Motifs
NCRR R01 RR021692 PMID:19458158
DOI:10.1093/nar/gkl198
Free, Freely available nif-0000-10298, biotools:meme_suite, OMICS_08103 https://bio.tools/meme_suite http://meme.sdsc.edu/meme4_6_1/intro.html, http://meme.nbcr.net/meme/, https://sources.debian.org/src/meme/ SCR_001783 The MEME Suite 2026-08-04 09:40:28 2091
AStalavista
 
Resource Report
Resource Website
50+ mentions
AStalavista (RRID:SCR_001815) AStalavista data analysis service, analysis service resource, software resource, production service resource, service resource Tool that extracts and displays alternative splicing (AS) events from a given genomic annotation of exon-intron gene coordinates. By comparing all given transcripts, it detects the variations in their splicing structure and identifies all AS events (like exon skipping, alternate donor, etc) by assigning to each of them an AS code. It provides a visual summary of the AS landscape in the analyzed dataset, the possibility to browse the results on the UCSC website or to download them in GTF or ASTA format. You can use AStalavista for any genome by providing your own annotation set, the identifier of your gene(s) of interest, or analyze the AS landscape of reference annotation datasets like Gencode, RefSeq, Ensembl, FlyBase, etc. alternative splicing event, alternative splicing, visualization, genome, transcript is listed by: OMICtools
is listed by: SoftCite
has parent organization: Center for Genomic Regulation; Barcelona; Spain
PMID:17485470 THIS RESOURCE IS NO LONGER IN SERVICE OMICS_01943 http://genome.imim.es/astalavista, http://genome.crg.es/astalavista/ SCR_001815 Alternative Splicing transcriptional landscape visualization tool 2026-08-04 09:40:28 83
ASPGD
 
Resource Report
Resource Website
100+ mentions
ASPGD (RRID:SCR_002047) ASPGD, ASPGD LOCUS, ASPGD REF storage service resource, data repository, service resource, database, data or information resource Database of genetic and molecular biological information about the filamentous fungi of the genus Aspergillus including information about genes and proteins of Aspergillus nidulans and Aspergillus fumigatus; descriptions and classifications of their biological roles, molecular functions, and subcellular localizations; gene, protein, and chromosome sequence information; tools for analysis and comparison of sequences; and links to literature information; as well as a multispecies comparative genomics browser tool (Sybil) for exploration of orthology and synteny across multiple sequenced Sgenus species. Also available are Gene Ontology (GO) and community resources. Based on the Candida Genome Database, the Aspergillus Genome Database is a resource for genomic sequence data and gene and protein information for Aspergilli. Among its many species, the genus contains an excellent model organism (A. nidulans, or its teleomorph Emericella nidulans), an important pathogen of the immunocompromised (A. fumigatus), an agriculturally important toxin producer (A. flavus), and two species used in industrial processes (A. niger and A. oryzae). Search options allow you to: *Search AspGD database using keywords. *Find chromosomal features that match specific properties or annotations. *Find AspGD web pages using keywords located on the page. *Find information on one gene from many databases. *Search for keywords related to a phenotype (e.g., conidiation), an allele (such as veA1), or an experimental condition (e.g., light). Analysis and Tools allow you to: *Find similarities between a sequence of interest and Aspergillus DNA or protein sequences. *Display and analyze an Aspergillus sequence (or other sequence) in many ways. *Navigate the chromosomes set. View nucleotide and protein sequence. *Find short DNA/protein sequence matches in Aspergillus. *Design sequencing and PCR primers for Aspergillus or other input sequences. *Display the restriction map for a Aspergillus or other input sequence. *Find similarities between a sequence of interest and fungal nucleotide or protein sequences. AspGD welcomes data submissions. function, gene, gene name, annotation, aspergillus, aspergillus nidulans, chromosome, community, dna, genome, genomic, localization, orthology, phenotype, protein, protein-coding genes, s. cerevisiae, sequence, allele, data analysis service, bio.tools, FASEB list is used by: NIF Data Federation
is listed by: bio.tools
is listed by: Debian
is related to: Candida Genome Database
is related to: AmiGO
has parent organization: Stanford University School of Medicine; California; USA
has parent organization: Broad Institute
NIAID R01 AI077599 PMID:19773420 THIS RESOURCE IS NO LONGER IN SERVICE nif-0000-12244, biotools:aspgd http://www.aspergillusgenome.org/, https://bio.tools/aspgd SCR_002047 Aspergillus Genome Database, ASPGD REF, ASPGD LOCUS 2026-08-04 09:40:32 212
South African National Bioinformatics Institute: Resources
 
Resource Report
Resource Website
South African National Bioinformatics Institute: Resources (RRID:SCR_001867) data processing software, portal, data analysis software, software resource, software application, organization portal, database, data or information resource THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23, 2022. The South African National Bioinformatics Institute delivers biomedical discovery appropriate to both international and African context. Researchers at SANBI perform the highest level of research and provide excellence in education. Research at SANBI has set well recognized milestones in the field of computational biology. The tools and techniques used have not only been developed but also implemented across heterogeneous domains of advanced research. Local and international efforts have driven our discoveries. Until recently, the core of SANBIs research has focused upon gene expression biology. Methods developed and applied at SANBI revolve around a greater understanding of the underlying causes of diseases. SANBI approaches the problem by comparison of genes, genomes and transcriptomes. It uses computational gene expression biology to create novel biological insights and to provide biomarkers for experimental validation. It also performs analysis of human genome variation, transcriptional diversity on both the expression and splicing level and the unravelling of transcriptional regulatory networks. Resources - Hinv, STACKdb, Malaria resources and Trypanosome databases are available for on-line seaching. - SANBI offers WCD, STACKdb, stackPACK and eVOC and the eVOKE viewer as tools that can be downloaded. Sponsors: SANBI receives funding and support from a range of organisations in South Africa and Internationally. Organisations currently supporting SANBI include: South Africa * South African Medical Research Council * South African AIDS Vaccine Initiative * National Bioinformatics Network * National Research Foundation * Claude Leon Foundation * International Business Machines Inc. Europe * European Unions 6th Framework Programme * World Health Organization USA * US National Institutes of Health * Fogarty International Centre * Ludwig Institute for Cancer Research expression, gene, gene expression, bioinformatics, biological, biology, biomaker, biomedical, computational biology, disease, genome, heterogeneous domain, human, splicing, transcriptional diversity, transcriptional regulatory network, transcriptome, variation THIS RESOURCE IS NO LONGER IN SERVICE nif-0000-10432 SCR_001867 SANBI 2026-08-04 09:40:29 0
University of California at Los Angeles - Department of Energy Institute for Genomics and Proteomics
 
Resource Report
Resource Website
1+ mentions
University of California at Los Angeles - Department of Energy Institute for Genomics and Proteomics (RRID:SCR_001921) portal, data computation service, organization portal, database, data or information resource The UCLA-DOE Institute for Genomics and Proteomics carries out research in bioenergy, structural biology, genomics and proteomics, consistent with the research mission of the United States Department of Energy. Major interests of the 12 Principal Investigators and 9 Associate Members include systems approaches to organisms, structural biology, bioinformatics, and bioenergetic systems. The Institute sponsors 5 Core Technology Centers, for X-ray and NMR structural determination, bioinformatics and computation, protein expression and purification, and biochemical instrumentation. Services offered by this Institute: - Databases: * DIP (The Database of Interacting Proteins): The DIPTM database catalogs experimentally determined interactions between proteins. It combines information from a variety of sources to create a single, consistent set of protein-protein interactions. * ProLinks Database of Functional Linkages: The Prolinks database is a collection of inference methods used to predict functional linkages between proteins. These methods include the Phylogenetic Profile method which uses the presence and absence of proteins across multiple genomes to detect functional linkages; the Gene Cluster method, which uses genome proximity to predict functional linkage; Rosetta Stone, which uses a gene fusion event in a second organism to infer functional relatedness; and the Gene Neighbor method, which uses both gene proximity and phylogenetic distribution to infer linkage. - Data-to-Structure Servers: * SAVEs Structure Verification Server * Merohedral Twinning Test Server * SER Surface Entropy Reduction Server * VERIFY3D Structure Verification Server * ERRAT Structure Verification Server - Structure-to-Function Servers: * ProKnow Protein Functionator * Hot Patch Functional Site Locator expression, functional linkage, gene, biochemical instrumentation, bioenergetic system, bioenergy, bioinformatic, computation, genome, genomic, nmr, organism, protein, protein-protein interaction, proteomic, purification, structural biology, x-ray nif-0000-10491 SCR_001921 UCLA-DOE 2026-08-04 09:40:30 4
Stanford Genomic Resourses
 
Resource Report
Resource Website
Stanford Genomic Resourses (RRID:SCR_001874) topical portal, portal, data or information resource This resource hyperlinks to systematic analysis projects, resources, laboratories, and departments at Stanford University. gene, genes, aspergillus, candida, genome, genomics, human, mouse THIS RESOURCE IS NO LONGER IN SERVICE nif-0000-10436 SCR_001874 Genomic Databases 2026-08-04 09:40:29 0

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