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SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.

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Resource Name Proper Citation Abbreviations Resource Type Description Keywords Resource Relationships Related Condition Funding Defining Citation Availability Website Status Alternate IDs Alternate URLs Old URLs Parent Organization Resource ID Synonyms Record Last Update Mentions Count
FusionMap
 
Resource Report
Resource Website
50+ mentions
FusionMap (RRID:SCR_005242) FusionMap software resource An efficient fusion aligner which aligns reads spanning fusion junctions directly to the genome without prior knowledge of potential fusion regions. It detects and characterizes fusion junctions at base-pair resolution. FusionMap can be applied to detect fusion junctions in both single- and paired-end dataset from either gDNA-Seq or RNA-Seq studies. FusionMap runs under both Windows and Linux (requiring MONO) environments. Although it can run on 32 bit machine, it is recommended to run on 64-bit machine with 8GB RAM or more. If you have an ArrayStudio License, you can run the fusion detection easily through its GUI. windows, linux, c#, fusion gene, next-generation sequencing, gene, reference indexing, read filtering, fusion alignment, reporting, alignment, bio.tools is listed by: OMICtools
is listed by: Debian
is listed by: bio.tools
PMID:21593131 Free, Non-commercial biotools:fusionmap, OMICS_00316 https://bio.tools/fusionmap SCR_005242 2026-02-14 02:01:05 88
COVA
 
Resource Report
Resource Website
50+ mentions
COVA (RRID:SCR_005175) COVA software resource A variant annotation and comparison tool for next-generation sequencing. It annotates the effects of variants on genes and compares those among multiple samples, which helps to pinpoint causal variation(s) relating to phenotype. next-generation sequencing, variant annotation, variant, annotation, gene, genetic variation, phenotype is listed by: OMICtools
has parent organization: SourceForge
OMICS_00171 SCR_005175 COVA - Comparison of variants and functional annotation, Comparison of variants and functional annotation 2026-02-14 02:01:03 58
VARIANT
 
Resource Report
Resource Website
1000+ mentions
VARIANT (RRID:SCR_005194) VARIANT data processing software, data analysis service, analysis service resource, data analysis software, production service resource, service resource, software application, software resource Analysis tool that can report the functional properties of any variant in all the human, mouse or rat genes (and soon new model organisms will be added) and the corresponding neighborhoods. Also other non-coding extra-genic regions, such as miRNAs are included in the analysis. It not only reports the obvious functional effects in the coding regions but also analyzes noncoding SNVs situated both within the gene and in the neighborhood that could affect different regulatory motifs, splicing signals, and other structural elements. These include: Jaspar regulatory motifs, miRNA targets, splice sites, exonic splicing silencers, calculations of selective pressures on the particular polymorphic positions, etc. Software analysis pipelines used in the analysis of NGS data are highly modular, heterogeneous, and rapidly evolving. VARIANT can easily be incorporated into a NGS resequencing pipeline either as a CLI or invoked a webservice. It inputs data directly from the most widely used programs for SNV detection., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. functional property, variant, gene, non-coding region, mirna, function, single nucleotide variant, next generation sequencing, command line is listed by: OMICtools
has parent organization: Principe Felipe Research Centre; Valencia; Spain
Spanish Ministry of Science and Innovation BIO2011-27069 PMID:22693211 THIS RESOURCE IS NO LONGER IN SERVICE OMICS_00193 SCR_005194 Variant effect, VARIant ANalysis Tool 2026-02-14 02:00:50 1366
NGS-SNP
 
Resource Report
Resource Website
10+ mentions
NGS-SNP (RRID:SCR_005182) NGS-SNP software resource A collection of command-line scripts for providing rich annotations for SNPs identified by the sequencing of transcripts or whole genomes from organisms with reference sequences in Ensembl. Included among the annotations, several of which are not available from any existing SNP annotation tools, are the results of detailed comparisons with orthologous sequences. These comparisons allow, for example, SNPs to be sorted or filtered based on how drastically the SNP changes the score of a protein alignment. Other fields indicate the names of overlapping protein domains or features, and the conservation of both the SNP site and flanking regions. NCBI, Ensembl, and Uniprot IDs are provided for genes, transcripts, and proteins when applicable, along with Gene Ontology terms, a gene description, phenotypes linked to the gene, and an indication of whether the SNP is novel or known. A ?Model_Annotations? field provides several annotations obtained by transferring in silico the SNP to an orthologous gene, typically in a well-characterized species. annotation, snp, sequencing, transcript, genome, reference sequence, indel, annotate, reference chromosome, reference transcript, gene, command-line is listed by: OMICtools
is related to: Ensembl
has parent organization: University of Alberta; Alberta; Canada
OMICS_00177 SCR_005182 2026-02-14 02:00:50 32
MRC Mammalian Genetics Unit
 
Resource Report
Resource Website
100+ mentions
MRC Mammalian Genetics Unit (RRID:SCR_005378) MGU data or information resource, portal, topical portal It is now widely known that animals share many genes with humans and can suffer from the same diseases, for example diabetes or deafness. Investigating these diseases in animals can provide vital leads to understanding both their causes and ways to treat them in humans. This approach to medical research lies at the heart of work at the MRC Mammalian Genetics Unit (MGU) at Harwell in Oxfordshire. In 1995 the MRC Radiobiology Unit was reconstituted to form two new units, the Radiation and Genome Stability Unit and the MGU. These opened in January 1996, together with the UK Mouse Genome Centre which is now part of MGU, making MRC Harwell a unique campus for multi-disciplinary genetics research. Since MGU's Director Steve Brown took the reins in 1996, the unit has dramatically expanded its scientific scope and increased its personnel from 40 to over 100. It now has 13 research programs encompassing molecular genetics, genomics, genetic manipulation and data analysis at all levels, from single genes to the whole genome. With a combination of cutting-edge facilities and expertise unrivaled in Europe, MGU Harwell has become firmly established as one of the world's leading academic centres for mouse genetics. mouse, genetics, gene is parent organization of: European Mouse Phenotyping Resource of Standardised Screens
is parent organization of: Europhenome Mouse Phenotyping Resource
is parent organization of: International Mouse Strain Resource
nlx_144449 http://www.mrc.ac.uk/Ourresearch/Unitscentresinstitutes/Profiles/MGU/index.htm SCR_005378 Medical Research Council Mammalian Genetics Unit, MGU Harwell, MRC MGU 2026-02-14 02:00:55 236
KGGSeq
 
Resource Report
Resource Website
50+ mentions
KGGSeq (RRID:SCR_005311) KGGSeq software resource A biological Knowledge-based mining platform for Genomic and Genetic studies using Sequence data. The software platform, constituted of bioinformatics and statistical genetics functions, makes use of valuable biologic resources and knowledge for sequencing-based genetic mapping of variants / genes responsible for human diseases / traits. It facilitates geneticists to fish for the genetic determinants of human diseases / traits in the big sea of DNA sequences. KGGSeq has paid attention to downstream analysis of genetic mapping. The framework was implemented to filter and prioritize genetic variants from whole exome sequencing data. genomic, genetic, sequence, mutation, exome sequencing, disease, gene, variant, bio.tools is listed by: OMICtools
is listed by: bio.tools
is listed by: Debian
Monogenic disorder, Cancer PMID:22241780 biotools:kggseq, OMICS_02260 https://bio.tools/kggseq SCR_005311 KGGSeq: A biological Knowledge-based mining platform for Genomic and Genetic studies using Sequence data 2026-02-14 02:00:52 53
MuGeX
 
Resource Report
Resource Website
MuGeX (RRID:SCR_005306) MuGeX service resource Service that automatically extracts mutation-gene pairs from MEDLINE abstracts for a given disease. disease, gene, mutation is listed by: OMICtools
is related to: MEDLINE
has parent organization: Sabanci University; Istanbul; Turkey
PMID:18172928 Acknowledgement requested OMICS_01189 SCR_005306 MuGeX - Mutation Gene Extractor, Mutation Gene Extractor 2026-02-14 02:00:52 0
Synergizer
 
Resource Report
Resource Website
1+ mentions
Synergizer (RRID:SCR_005308) Synergizer web service, data analysis service, analysis service resource, production service resource, service resource, data access protocol, software resource The Synergizer database is a growing repository of gene and protein identifier synonym relationships. This tool facilitates the conversion of identifiers from one naming scheme (a.k.a namespace) to another. The Synergizer is a service for translating between sets of biological identifiers. It can, for example, translate Ensembl Gene IDs to Entrez Gene IDs, or IPI IDs to HGNC gene symbols, and much more. Unlike some other tools for this purpose, The Synergizer is simple and easy to learn. The Synergizer works via a web interface (for users who are not programmers) or through a web service (for programmatic access). gene, protein, json has parent organization: University of Toronto; Ontario; Canada nlx_144380 SCR_005308 The Synergizer 2026-02-14 02:00:54 9
CoPub
 
Resource Report
Resource Website
1+ mentions
CoPub (RRID:SCR_005327) CoPub data access protocol, software resource, web service, service resource Text mining tool that detects co-occuring biomedical concepts in abstracts from the MedLine literature database. It allows batch input of multiple human, mouse or rat genes and produces lists of keywords from several biomedical thesauri that are significantly correlated with the set of input genes. These lists link to Medline abstracts in which the co-occurring input genes and correlated keywords are highlighted. Furthermore, CoPub can graphically visualize differentially expressed genes and over-represented keywords in a network, providing detailed insight in the relationships between genes and keywords, and revealing the most influential genes as highly connected hubs. microarray, gene, literature, enrich, annotate, network, database, differential expression, bio.tools uses: MEDLINE
uses: Gene Ontology
is listed by: OMICtools
is listed by: Debian
is listed by: bio.tools
has parent organization: Netherlands Bioinformatics Centre
Netherlands Bioinformatics Centre PMID:18442992 Free, Public, Acknowledgement requested OMICS_01178, biotools:copub https://bio.tools/copub http://services.nbic.nl/cgi-bin/copub/CoPub.pl SCR_005327 2026-02-14 02:00:52 5
PAZAR
 
Resource Report
Resource Website
10+ mentions
PAZAR (RRID:SCR_005410) PAZAR data repository, storage service resource, data or information resource, service resource, software resource, database Database that unites independently created and maintained data collections of transcription factor and regulatory sequence annotation. The flexible PAZAR schema permits the representation of diverse information derived from experiments ranging from biochemical protein-DNA binding to cellular reporter gene assays. Data collections can be made available to the public, or restricted to specific system users. The data ''boutiques'' within the shopping-mall-inspired system facilitate the analysis of genomics data and the creation of predictive models of gene regulation., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. transcription factor, target gene, regulatory sequence, transcription factor profile, annotation, sequence, profile, transcription factor binding profile, chip, chip-seq, gene, cis-regulatory element, bio.tools is listed by: OMICtools
is listed by: bio.tools
is listed by: Debian
has parent organization: University of British Columbia; British Columbia; Canada
has parent organization: SourceForge
PMID:18971253 THIS RESOURCE IS NO LONGER IN SERVICE OMICS_00540, biotools:pazar https://bio.tools/pazar SCR_005410 2026-02-14 02:01:06 32
Genetic Testing Registry
 
Resource Report
Resource Website
10+ mentions
Genetic Testing Registry (RRID:SCR_005565) GTR data repository, storage service resource, data or information resource, service resource, database Central location for voluntary submission of genetic test information by providers including the test''s purpose, methodology, validity, evidence of the test''s usefulness, and laboratory contacts and credentials. GTR aims to advance the public health and research into the genetic basis of health and disease. GTR is accepting registration of clinical tests for Mendelian disorders, complex tests and arrays, and pharmacogenetic tests. These tests may include multiple methods and may include multiple major method categories such as biochemical, cytogenetic, and molecular tests. GTR is not currently accepting registration of tests for somatic disorders, research tests or direct-to-consumer tests. genetic, gene, clinical, genetic test, condition, phenotype, disease name, trait, drug, protein, analyte, disease, laboratory, molecular, clinical, genetics, people lists: MedGen
is listed by: OMICtools
has parent organization: NCBI
The community can contribute to this resource nlx_144654, OMICS_01541 SCR_005565 NIH Genetic Testing Registry, GTR: Genetic Testing Registry 2026-02-14 02:00:55 35
TRANSPATH
 
Resource Report
Resource Website
1+ mentions
TRANSPATH (RRID:SCR_005640) TRANSPATH data analysis service, analysis service resource, data or information resource, production service resource, service resource, database Database on eukaryotic transcription factors, their experimentally-proven binding sites, consensus binding sequences (positional weight matrices) and regulated genes. Its broad compilation of binding sites allows the derivation of positional weight matrices. It can either be used as an encyclopedia, for both specific and general information on signal transduction, or can serve as a network analyzer. Cross-references to important sequence and signature databases such as EMBL/GenBank UniProt/Swiss-Prot InterPro or Ensembl EntrezGene RefSeq are provided. The database is equipped with the tools for data visualization and analysis. It has three modules: the first one is the data, which have been manually extracted, mostly from the primary literature; the second is PathwayBuilder, which provides several different types of network visualization and hence facilitates understanding; the third is ArrayAnalyzer, which is particularly suited to gene expression array interpretation, and is able to identify key molecules within signalling networks (potential drug targets). These key molecules could be responsible for the coordinated regulation of downstream events. Manual data extraction focuses on direct reactions between signalling molecules and the experimental evidence for them, including species of genes/proteins used in individual experiments, experimental systems, materials and methods. This combination of materials and methods is used in TRANSPATH to assign a quality value to each experimentally proven reaction, which reflects the probability that this reaction would happen under physiological conditions. Another important feature in TRANSPATH is the inclusion of transcription factor-gene relations, which are transferred from TRANSFAC, a database focused on transcription regulation and transcription factors. Since interactions between molecules are mainly direct, this allows a complete and stepwise pathway reconstruction from ligands to regulated genes. signal transduction, network analyzer, transcriptional regulator, transcription factor, metabolic pathway, signaling pathway, protein-protein interaction, gene-regulatory pathway, signal transduction pathway, complex, signaling molecule, reaction, molecule, gene, pathway, gene expression is related to: TRANSFAC
is related to: GeneTrail
has parent organization: BIOBASE Corporation
BMBF 031U210B;
BMBF 0313092;
European Union FP6 contract LSHG-CT-2004-503568;
European Union MRTN-CT-2004-512285
PMID:18629064
PMID:16381929
PMID:12519957
PMID:11724734
Free for academic use, Free for non-profit use, Account required nif-0000-03580 http://transpath.gbf.de, http://www.gene-regulation.com/pub/databases.html, http://www.biobase.de/pages/products/databases.html SCR_005640 2026-02-14 02:01:08 2
Roth Laboratory
 
Resource Report
Resource Website
1+ mentions
Roth Laboratory (RRID:SCR_005711) Roth Lab portal, laboratory portal, data or information resource, organization portal, software resource The Roth Laboratory is designing and interpreting large-scale experiments to understand pathway structure and its relationship to phenotype and human disease. Software for research focused on a specific research goal is available. Current experimental interests: * Exploiting parallel sequencing technology to phenotype all pairwise gene deletion combinations in S. cerevisiae, with initial application to genes involved in transcription. * Generation of S. cerevisiae strains carrying dozens of chosen targeted deletions, with initial application to delete all ABC transporters imparting multidrug resistance. * Targeted insertion of gene sets encoding entire human pathways into S. cerevisiae, with initial application to genes involved in drug metabolism. Current computational interests: * Systematic analysis of genetic interaction to reveal redundant systems and order of action in genetic pathways * Integrating large-scale studies - including phenotype, genetic epistasis, protein-protein and transcription-regulatory interactions and sequence patterns - to quantitatively assign function to genes and guide experimentation and disease association studies. * Alternative splicing and its relationship to protein interaction networks. gene, pathway, phenotype, disease, transcription, drug metabolism, drug, metabolism, protein-protein interaction, transcription-regulatory interaction, protein interaction, protein has parent organization: University of Toronto; Ontario; Canada
has parent organization: Harvard Medical School; Massachusetts; USA
is parent organization of: FuncAssociate: The Gene Set Functionator
nlx_149163 http://llama.med.harvard.edu SCR_005711 2026-02-14 02:00:57 5
netClass
 
Resource Report
Resource Website
netClass (RRID:SCR_005672) netClass software resource An R package for network-based feature (gene) selection for biomarkers discovery via integrating biological information. The package adapts the following 5 algorithms for classifying and predicting gene expression data using prior knowledge: # average gene expression of pathway (aep); # pathway activities classification (PAC); # Hub network classification (hubc); # filter via top ranked genes (FrSVM); # network smoothed t-statistic (stSVM). protein-protein interaction network, biomarker discovery, classification, micoarray, gene expression profile, protein-protein interaction, gene expression, gene, biomarker is listed by: OMICtools
has parent organization: SourceForge
PMID:24443376 Free, Public OMICS_02241 SCR_005672 2026-02-14 02:00:57 0
GUMC Department of Biostatistics Bioinformatics and Biomathematics - Liu Lab
 
Resource Report
Resource Website
GUMC Department of Biostatistics Bioinformatics and Biomathematics - Liu Lab (RRID:SCR_005708) GUMC Liu Lab laboratory portal, data or information resource, organization portal, portal THIS RESOURCE IS NO LONGER IN SERVCE, documented September 2, 2016. microarray, data mining, natural language processing, biomedical, ontology, biomedicine, data analysis, dna microarray, gene THIS RESOURCE IS NO LONGER IN SERVICE nlx_149157 SCR_005708 Georgetown University Medical Center Department of Biostatistics Bioinformatics and Biomathematics - Liu Lab, Georgetown University Medical Center Liu Lab, GUMC Department of Biostatistics Bioinformatics Biomathematics - Liu Lab 2026-02-14 02:00:59 0
GeneMANIA
 
Resource Report
Resource Website
1000+ mentions
GeneMANIA (RRID:SCR_005709) GeneMANIA data analysis service, analysis service resource, data or information resource, production service resource, service resource, software resource, database Data analysis service to predict the function of your favorite genes and gene sets. Indexing 1,421 association networks containing 266,984,699 interactions mapped to 155,238 genes from 7 organisms. GeneMANIA interaction networks are available for download in plain text format. GeneMANIA finds other genes that are related to a set of input genes, using a very large set of functional association data. Association data include protein and genetic interactions, pathways, co-expression, co-localization and protein domain similarity. You can use GeneMANIA to find new members of a pathway or complex, find additional genes you may have missed in your screen or find new genes with a specific function, such as protein kinases. Your question is defined by the set of genes you input. If members of your gene list make up a protein complex, GeneMANIA will return more potential members of the protein complex. If you enter a gene list, GeneMANIA will return connections between your genes, within the selected datasets. GeneMANIA suggests annotations for genes based on Gene Ontology term enrichment of highly interacting genes with the gene of interest. GeneMANIA is also a gene recommendation system. GeneMANIA is also accessible via a Cytoscape plugin, designed for power users. Platform: Online tool, Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible gene, association data, protein interaction, genetic interaction, pathway, co-expression, co-localization, protein, software library, statistical analysis, term enrichment, analysis, browser, gene ontology, gene predicting, gene prioritization, database or data warehouse, other analysis, interaction browser, protein-protein interaction, interaction, FASEB list is listed by: Gene Ontology Tools
is related to: Cytoscape
is related to: Gene Ontology
is related to: PSICQUIC Registry
has parent organization: University of Toronto; Ontario; Canada
Genome Canada ;
Ontario Ministry of Research and Innovation 2007-OGI-TD-05
PMID:20576703
PMID:18613948
PMID:20926419
Open unspecified license, Free for academic use nlx_149159, r3d100013978 https://doi.org/10.17616/R31NJNA2 SCR_005709 2026-02-14 02:01:10 3358
MolGen
 
Resource Report
Resource Website
10+ mentions
MolGen (RRID:SCR_005700) MolGen data or information resource, portal, topical portal The research of the group concentrates on the molecular biology of Gram-positive bacteria, with Bacillus subtilis and Lactococcus lactis as the main model organisms. A number of important (human) pathogens are also investigated: Bacillus cereus, Streptococcus pneumoniae and Enterococcus faecalis. The nature of the research is both fundamental and application-oriented. Transcript- and protein profiling by high-throughput technologies such as DNA microarrays and proteomics tools are being used. The very large data sets generated are analyzed by employing existing and novel bioinformatics tools. Major lines of research are in the field of functional genomics of these organisms, using systems- and synthetic biology approaches. molecular biology, gram-positive bacteria, pathogen, transcript, protein, profile, high-throughput, dna microarray, proteomics, dna, microarray, functional genomics, bioinformatics, genetics, gene has parent organization: University of Groningen; Groningen; Netherlands
is parent organization of: FIVA - Functional Information Viewer and Analyzer
nlx_149166 http://molgen.biol.rug.nl/molgen/index.php SCR_005700 Molecular Genetics 2026-02-14 02:01:10 27
KI Biobank
 
Resource Report
Resource Website
KI Biobank (RRID:SCR_005664) KI Biobank - Gallstone biomaterial supply resource, material resource THIS RESOURCE IS NO LONGER IN SERVICE, documented August 29, 2016. KI Biobank - Gallstone aims at investigating genetics of gallstone disease on Swedish Twins. Types of samples * EDTA whole blood * DNA * Plasma Number of sample donors: 82 gene, genetics is listed by: One Mind Biospecimen Bank Listing
is related to: Swedish Twin Registry
has parent organization: Karolisnka Biobank
Gallstone disease, Twin THIS RESOURCE IS NO LONGER IN SERVICE nlx_151297, nlx_151300, SCR_005796 https://www.researchgate.net/publication/246710484_Gallstone_disease_in_Swedish_twins_is_linked_to_ABCG8_D19H_risk_genotype SCR_005664 KI Biobank - Gallstone, KI Biobank - KTS 2026-02-14 02:00:57 0
Brain Basics
 
Resource Report
Resource Website
Brain Basics (RRID:SCR_005606) Brain Basics data or information resource, narrative resource, training material, video resource Brain Basics provides information on how the brain works, how mental illnesses are disorders of the brain, and ongoing research that helps us better understand and treat disorders. Mental disorders are common. You may have a friend, colleague, or relative with a mental disorder, or perhaps you have experienced one yourself at some point. Such disorders include depression, anxiety disorders, bipolar disorder, attention deficit hyperactivity disorder (ADHD), and many others. Some people who develop a mental illness may recover completely; others may have repeated episodes of illness with relatively stable periods in between. Still others live with symptoms of mental illness every day. They can be moderate, or serious and cause severe disability. Through research, we know that mental disorders are brain disorders. Evidence shows that they can be related to changes in the anatomy, physiology, and chemistry of the nervous system. When the brain cannot effectively coordinate the billions of cells in the body, the results can affect many aspects of life. Scientists are continually learning more about how the brain grows and works in healthy people, and how normal brain development and function can go awry, leading to mental illnesses. Brain Basics will introduce you to some of this science, such as: * How the brain develops * How genes and the environment affect the brain * The basic structure of the brain * How different parts of the brain communicate and work with each other * How changes in the brain can lead to mental disorders, such as depression. brain, depression, anxiety disorder, bipolar disorder, attention deficit-hyperactivity disorder, depressive disorder, mental disease, gene, environment has parent organization: NIMH Educational Resources NIMH nlx_146226 SCR_005606 NIMH Brain Basics 2026-02-14 02:01:08 0
TAIR Keyword Browser
 
Resource Report
Resource Website
10+ mentions
TAIR Keyword Browser (RRID:SCR_005687) TAIR Keyword Browser data analysis service, analysis service resource, data or information resource, production service resource, service resource, database TAIR Keyword Browser searches and browses for Gene Ontology, TAIR Anatomy, and TAIR Developmental stage terms, and allows you to view term details and relationships among terms. It includes links to genes, publications, microarray experiments and annotations associated with the term or any children terms. Platform: Online tool gene ontology, gene, publication, microarray, annotation, cellular component, biological process, molecular function, plant, growth, development, stage, anatomical entity, anatomy, ontology, browser, ontology or annotation browser is listed by: Gene Ontology Tools
is related to: Gene Ontology
has parent organization: TAIR
Free for academic use nlx_149132 http://www.arabidopsis.org/servlets/Search?action=new_search&type=keyword SCR_005687 TAIR Keyword Search and Browse, The Arabidopsis Information Resource Keyword Browser 2026-02-14 02:01:08 37

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