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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
GeneCodis
 
Resource Report
Resource Website
100+ mentions
GeneCodis (RRID:SCR_006943) GeneCodis analysis service resource, data access protocol, software resource, service resource, web service, production service resource, data analysis service Web-based tool for the ontological analysis of large lists of genes. It can be used to determine biological annotations or combinations of annotations that are significantly associated to a list of genes under study with respect to a reference list. As well as single annotations, this tool allows users to simultaneously evaluate annotations from different sources, for example Biological Process and Cellular Component categories of Gene Ontology., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. functional analysis, gene, annotation, statistical analysis, functional genomics, bio.tools is listed by: Gene Ontology Tools
is listed by: OMICtools
is listed by: bio.tools
is listed by: Debian
is related to: Gene Ontology
is related to: KEGG
has parent organization: Spanish National Research Council; Madrid; Spain
Juan de la Cierva research program ;
Spanish Minister of Science and Innovation BIO2010-17527;
Government of Madrid P2010/BMD-2305
PMID:22573175
PMID:19465387
PMID:17204154
THIS RESOURCE IS NO LONGER IN SERVICE OMICS_02221, biotools:genecodis3, nlx_149254 https://bio.tools/genecodis3 SCR_006943 Gene annotations co-ocurrence discovery, GeneCodis - Gene annotations co-ocurrence discovery 2026-02-12 09:44:36 348
MAPPER - Multi-genome Analysis of Positions and Patterns of Elements of Regulation
 
Resource Report
Resource Website
10+ mentions
MAPPER - Multi-genome Analysis of Positions and Patterns of Elements of Regulation (RRID:SCR_003077) MAPPER, MAPPER 2, data or information resource, database, service resource A platform composed of three modules: the Database, the Search Engine, and rSNPs, for the computational identification of transcription factor binding sites (TFBSs) in multiple genomes, that combines TRANSFAC and JASPAR data with the search power of profile hidden Markov models (HMMs). The Database contains putative TFBSs found in the upstream sequences of genes from the human, mouse and D.melanogaster genomes. For each gene, they scanned the region from 10,000 base pairs upstream of the transcript start to 50 base pairs downstream of the coding sequence start against all their models. Therefore, the database contains putative binding sites in the gene promoter and in the initial introns and non-coding exons. Information displayed for each putative binding site includes the transcription factor name, its position (absolute on the chromosome, or relative to the gene), the score of the prediction, and the region of the gene the site belongs to. If the selected gene has homologs in any of the other two organisms, the program optionally displays the putative TFBSs in the homologs. The Search Engine allows the identification, visualization and selection of putative TFBSs occurring in the promoter or other regions of a gene from the human, mouse, D.melanogaster, C.elegans or S.cerevisiae genomes. In addition, it allows the user to upload a sequence to query and to build a model by supplying a multiple sequence alignment of binding sites for a transcription factor of interest. rSNPs MAPPER is designed to identify Single Nucleotide Polymorphisms (SNPs) that may have an effect on the presence of one or more TFBSs. transcription factor binding site, gene promoter, intron, non-coding exon, transcription factor, chromosome, gene, homolog, rsnp, single nucleotide polymorphism, search engine is listed by: OMICtools
has parent organization: University of Florida; Florida; USA
is parent organization of: rSNPs MAPPER
PMID:15608292
PMID:15799782
THIS RESOURCE IS NO LONGER IN SERVICE OMICS_01877, nif-0000-03101 http://bio.chip.org/mapper SCR_003077 Multi-genome Analysis of Positions and Patterns of Elements of Regulation, MAPPER 2 - Multi-genome Analysis of Positions and Patterns of Elements of Regulation, MAPPER database 2026-02-12 09:43:31 11
HomoloGene
 
Resource Report
Resource Website
100+ mentions
HomoloGene (RRID:SCR_002924) HomoloGene data or information resource, database, service resource Automated system for constructing putative homology groups from complete gene sets of wide range of eukaryotic species. Databse that provides system for automatic detection of homologs, including paralogs and orthologs, among annotated genes of sequenced eukaryotic genomes. HomoloGene processing uses proteins from input organisms to compare and sequence homologs, mapping back to corresponding DNA sequences. Reports include homology and phenotype information drawn from Online Mendelian Inheritance in Man, Mouse Genome Informatics, Zebrafish Information Network, Saccharomyces Genome Database and FlyBase. homolog, paralog, ortholog, genome, gene, protein, protein alignment, phenotype, conserved domain, homology, amino acid sequence, cell, dna, gold standard is used by: NIF Data Federation
is used by: Nowomics
is used by: MitoMiner
is listed by: OMICtools
is listed by: re3data.org
is related to: OMIM
is related to: Mouse Genome Informatics (MGI)
is related to: Zebrafish Information Network (ZFIN)
is related to: SGD
is related to: FlyBase
is related to: ProbeMatchDB 2.0
is related to: Biomine
is related to: Consensus CDS
has parent organization: NCBI
PMID:23193264 Free, Freely availalbe nif-0000-02975, r3d100010781, OMICS_01544 http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=homologene
https://doi.org/10.17616/R3889F
SCR_002924 NCBI HomoloGene 2026-02-12 09:43:29 437
FIDEA
 
Resource Report
Resource Website
1+ mentions
FIDEA (RRID:SCR_004187) FIDEA service resource, analysis service resource, production service resource, data analysis service A web server for the functional interpretation of differential expression analysis. It can: * Calculate overrepresentation statistics using KEGG, Interpro, Gene Ontology Molecular Function, Gene Ontology Biological Process, Gene Ontology Cellular Component and GoSlim classifications; * Analyze down-regulated and up-regulated DE genes separately or together as a single set; * Provide interactive graphs and tables that can be modified on the fly according to user defined parameters; the user can set a fold change filter and interactively see the effects on the gene set under examination; * Output publication-ready plot of the graph; * Compare the results of several experiments in any combination. is listed by: OMICtools
has parent organization: Sapienza University of Rome; Rome; Italy
PMID:23754850 Public, Free, Acknowledgement requested OMICS_01539 SCR_004187 Functional Interpretation of Differential Expression Analysis 2026-02-12 09:43:46 9
4D Genome
 
Resource Report
Resource Website
10+ mentions
4D Genome (RRID:SCR_017489) data repository, service resource, storage service resource, database, data or information resource Repository for chromatin interaction data. Records can be queried by genomic regions, gene names, organism, and detection technology. Database is continuously updated by curators. Contributions from scientific community. Repository, chromatic, interaction, data, genomic, region, gene, name, detection, technology, curated has parent organization: University of Pennsylvania; Philadelphia; USA Free, Available for download, Freely available r3d100012282 https://doi.org/10.17616/R3SH37 SCR_017489 2026-02-12 09:46:53 10
InteroPorc
 
Resource Report
Resource Website
1+ mentions
InteroPorc (RRID:SCR_002067) InteroPorc analysis service resource, source code, software resource, service resource, production service resource, database, software application, data analysis service, data analysis software, data processing software, data or information resource Automatic prediction tool to infer protein-protein interaction networks, it is applicable for lots of species using orthology and known interactions. The interoPORC method is based on the interolog concept and combines source interaction datasets from public databases as well as clusters of orthologous proteins (PORC) available on Integr8. Users can use this page to ask InteroPorc for all species present in Integr8. Some results are already computed and users can run InteroPorc to investigate any other species. Currently, the following databases are processed and merged (with datetime of the last available public release for each database used): IntAct, MINT, DIP, and Integr8. orthology, prediction, protein interaction, tool, sequenced genome, proteinprotein interaction, inferred interaction, molecular interaction, interaction, protein, bio.tools is listed by: bio.tools
is listed by: Debian
is related to: Integr8 : Access to complete genomes and proteomes
is related to: IntAct
is related to: MINT
is related to: Database of Interacting Proteins (DIP)
is related to: PSICQUIC Registry
has parent organization: CEA; Gif sur Yvette; France
European Union FELICS 021902 RII3;
Marie Curie Fellowship ;
French National Agency of Research ANR Biosys06_134823 SULFIRHOM;
French Atomic Energy Commission
PMID:18508856 Open unspecified license, Acknowledgement requested nif-0000-20816, biotools:interoporc https://bio.tools/interoporc SCR_002067 InteroPorc: Automatic molecular interaction predictions, Automatic molecular interaction predictions 2026-02-12 09:43:17 6
Cell Centered Database
 
Resource Report
Resource Website
10+ mentions
Cell Centered Database (RRID:SCR_002168) CCDB data repository, service resource, image repository, storage service resource, database, data or information resource THIS RESOURCE IS NO LONGER IN SERVICE, documented June 5, 2017. It has been merged with Cell Image Library. Database for sharing and mining cellular and subcellular high resolution 2D, 3D and 4D data from light and electron microscopy, including correlated imaging that makes unique and valuable datasets available to the scientific community for visualization, reuse and reanalysis. Techniques range from wide field mosaics taken with multiphoton microscopy to 3D reconstructions of cellular ultrastructure using electron tomography. Contributions from the community are welcome. The CCDB was designed around the process of reconstruction from 2D micrographs, capturing key steps in the process from experiment to analysis. The CCDB refers to the set of images taken from microscope the as the Microscopy Product. The microscopy product refers to a set of related 2D images taken by light (epifluorescence, transmitted light, confocal or multiphoton) or electron microscopy (conventional or high voltage transmission electron microscopy). These image sets may comprise a tilt series, optical section series, through focus series, serial sections, mosaics, time series or a set of survey sections taken in a single microscopy session that are not related in any systematic way. A given set of data may be more than one product, for example, it is possible for a set of images to be both a mosaic and a tilt series. The Microscopy Product ID serves as the accession number for the CCDB. All microscopy products must belong to a project and be stored along with key specimen preparation details. Each project receives a unique Project ID that groups together related microscopy products. Many of the datasets come from published literature, but publication is not a prerequisite for inclusion in the CCDB. Any datasets that are of high quality and interest to the scientific community can be included in the CCDB. electron microscope, light microscopy, electron tomography, electron microscopy, image, cell, microscopy, tomography is used by: NIF Data Federation
is used by: Integrated Datasets
is listed by: re3data.org
is related to: Cell Image Library (CIL)
is related to: Cell Image Library (CIL)
is related to: Whole Brain Catalog
is related to: Integrated Manually Extracted Annotation
has parent organization: University of California at San Diego; California; USA
has parent organization: University of California; San Diego;National Center for Microscopy and Imaging Research - NCMIR
is parent organization of: Subcellular Anatomy Ontology
is parent organization of: CCDB Image Converter
is parent organization of: Jinx
is parent organization of: WebImageBrowser
is parent organization of: Image Workflow
is parent organization of: Animal Imaging Database
PMID:18054501
PMID:12160711
Free, Freely available nif-0000-00007 SCR_002168 CCDB, Cell-Centered Database 2026-02-12 09:43:18 31
EGAN: Exploratory Gene Association Networks
 
Resource Report
Resource Website
1+ mentions
EGAN: Exploratory Gene Association Networks (RRID:SCR_008856) EGAN software resource, software application, data analysis software, data processing software Exploratory Gene Association Networks (EGAN) is a software tool that allows a bench biologist to visualize and interpret the results of high-throughput exploratory assays in an interactive hypergraph of genes, relationships (protein-protein interactions, literature co-occurrence, etc.) and meta-data (annotation, signaling pathways, etc.). EGAN provides comprehensive, automated calculation of meta-data coincidence (over-representation, enrichment) for user- and assay-defined gene lists, and provides direct links to web resources and literature (NCBI Entrez Gene, PubMed, KEGG, Gene Ontology, iHOP, Google, etc.). EGAN functions as a module for exploratory investigation of analysis results from multiple high-throughput assay technologies, including but not limited to: * Transcriptomics via expression microarrays or RNA-Seq * Genomics via SNP GWAS or array CGH * Proteomics via MS/MS peptide identifications * Epigenomics via DNA methylation, ChIP-on-Chip or ChIP-Seq * In-silico analysis of sequences or literature EGAN has been built using Cytoscape libraries for graph visualization and layout, and is comparable to DAVID, GSEA, Ingenuity IPA and Ariadne Pathway Studio. There are pre-collated EGAN networks available for human (Homo sapiens), mouse (Mus musculus), rat (Rattus norvegicus), chicken (Gallus gallus), zebrafish (Danio rerio), fruit fly (Drosophila melanogaster), nematode (Caenorhabditis elegans), mouse-ear cress (Arabidopsis thaliana), rice (Oryza sativa) and brewer's yeast (Saccharomyces cerevisiae). There is now an EGAN module available for GenePattern (human-only). Platform: Windows compatible, Mac OS X compatible, Linux compatible gene, gene association, network, protein-protein interaction, pathway, interaction, annotation, signaling pathway, enrichment, cytoscape, visualization is listed by: 3DVC
is listed by: Gene Ontology Tools
is related to: Gene Ontology
is related to: Cytoscape
has parent organization: UCSF Helen Diller Family Comprehensive Cancer Center Biostatistics Core
NCI P30 CA92103 PMID:19933825 Free for academic use nlx_149222 SCR_008856 Exploratory Gene Association Networks, Exploratory Gene Association Networks (EGAN) 2026-02-12 09:44:42 8
BABAM
 
Resource Report
Resource Website
BABAM (RRID:SCR_015632) software resource, data analysis resource, software application, data processing software, data visualization software Graphical user interface for exploring hypotheses of correlations between neural activity in regions of the brain and behavior for Drosophila melanogaster. These correlation hypotheses are the result of our thermogenetic neural activation screen from the Janelia GAL4 collection. drosophila melanogaster, correlation hypothesis, neural activity, thermogenetic neural activation screen uses: MATLAB Free, Available for download SCR_015632 Browsable Atlas of Behavior-Anatomy Maps, Browsable Atlas of Behavior-Anatomy Maps (BABAM) 2026-02-12 09:46:18 0
BrainTrap: Fly Brain Protein Trap Database
 
Resource Report
Resource Website
1+ mentions
BrainTrap: Fly Brain Protein Trap Database (RRID:SCR_003398) BrainTrap data or information resource, database, d spatial image This database contains information on protein expression in the Drosophila melanogaster brain. It consists of a collection of 3D confocal datasets taken from EYFP expressing protein trap Drosophila lines from the Cambridge Protein Trap project. Currently there are 884 brain scans from 535 protein trap lines in the database. Drosophila protein trap strains were generated by the St Johnston Lab and the Russell Lab at the University of Cambridge, UK. The piggyBac insertion method was used to insert constructs containing splice acceptor and donor sites, StrepII and FLAG affinity purification tags, and an EYFP exon (Venus). Brain images were acquired by Seymour Knowles-Barley, in the Armstrong Lab at the University of Edinburgh. Whole brain mounts were imaged by confocal microscopy, with a background immunohistochemical label added to aid the identification of brain structures. Additional immunohistochemical labeling of the EYFP protein using an anti-GFP antibody was also used in most cases. The trapped protein signal (EYFP / anti-GFP), background signal (NC82 label), and the merged signal can be viewed on the website by using the corresponding channel buttons. In all images the trapped protein / EYFP signal appears green and the background / NC82 channel appears magenta. Original .lsm image files are also available for download. brain, exon, expression, 3d confocal, affinity, antibody, dataset, immunohistochemical, microscopy, image, protein, protein-trap, gene has parent organization: University of Edinburgh; Scotland; United Kingdom EPSRC ;
British society for Developmental Biology ;
Society for Experimental Biology ;
Virtual Fly Brain e-Science Institute Theme ;
BBSRC ;
MRC
PMID:20624714 Free, Freely available nif-0000-32989 http://fruitfly.inf.ed.ac.uk/braintrap/ SCR_003398 Fly Brain Protein Trap Database, Brain Trap 2026-02-12 09:43:36 1
dbVar
 
Resource Report
Resource Website
100+ mentions
dbVar (RRID:SCR_003219) dbVar data repository, service resource, storage service resource, database, data or information resource Structural variation database designed to store data on variant DNA > / = 1 bp in size from all organisms. Associations of defined variants with phenotype information is also provided. Users can browse data containing number of variant cells from each study, and filter studies by organism, study type, method and genomic variant. Organisms include human, mouse, cattle and several additional animals. structure, variation, structural variation, genetics, insertion, deletion, copy number variant, inversion, translocation, genomic imbalance, genotype, gene expression, dna, genomics, phenotype, genetic code 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: re3data.org
is related to: Database of Genomic Variants Archive (DGVa)
is related to: Database of Genomic Variants
has parent organization: NCBI
PMID:23193291 Free, Freely available nlx_157217, r3d100010758 https://doi.org/10.17616/R3V610 SCR_003219 dbVar, Database of Genomic Structural Variation, NCBI dbVar 2026-02-12 09:43:33 190
modENCODE
 
Resource Report
Resource Website
100+ mentions
modENCODE (RRID:SCR_006206) modENCODE analysis service resource, service resource, production service resource, data analysis service, data or information resource, data set A comprehensive encyclopedia of genomic functional elements in the model organisms C. elegans and D. melanogaster. modENCODE is run as a Research Network and the consortium is formed by 11 primary projects, divided between worm and fly, spanning the domains of gene structure, mRNA and ncRNA expression profiling, transcription factor binding sites, histone modifications and replacement, chromatin structure, DNA replication initiation and timing, and copy number variation. The raw and interpreted data from this project is vetted by a data coordinating center (DCC) to ensure consistency and completeness. The entire modENCODE data corpus is now available on the Amazon Web Services EC2 cloud. What this means is that virtual machines and virtual compute clusters that you run within the EC2 cloud can mount the modENCODE data set in whole or in part. Your software can run analyses against the data files directly without experiencing the long waits and logistics associated with copying the datasets over to your local hardware. You may also view the data using GBrowse, Dataset Search, or download the data via FTP, as well as download pre-release datasets. epigenomics, epigenetics, genomics, functional element, model organism, genome, copy number variation, gene structure, genome sequence, histone modification, histone replacement, chromatin binding site, expression profiling, replication, transcription factor binding site, transcription factor, binding site, chromatin, rna, expression profiling, regulatory network, mrna, ncrna, dna replication, genotype is related to: ENCODE
is related to: Encode
NHGRI PMID:19536255 Public, With some restrictions on its use for 9 months following publication, Acknowledgement requested nlx_151752 SCR_006206 NHGRI model organism ENCyclopedia Of DNA Elements, National Human Genome Research Institute model organism ENCyclopedia Of DNA Elements, model organism ENCyclopedia Of DNA Elements 2026-02-12 09:44:19 255
Resource Identification Portal
 
Resource Report
Resource Website
10+ mentions
Resource Identification Portal (RRID:SCR_004098) RII Portal data or information resource, portal Portal providing identifiers for Antibodies, Model Organisms, and Tools (software, databases, services) created in support of the Resource Identification Initiative, which aims to promote research resource identification, discovery, and reuse. The portal offers a central location for obtaining and exploring Research Resource Identifiers (RRIDs) - persistent and unique identifiers for referencing a research resource. A critical goal of the RII is the widespread adoption of RRIDs to cite resources in the biomedical literature and other places that reference their generation or use. RRIDs use established community identifiers where they exist, and are cross-referenced in their system where more than one identifier exists for a single resource. antibody, organism, service resource, software resource, database, resource, identifier, citation, biomedical, publication, research resource identifier, rrid, ASWG uses: Antibody Registry
uses: SciCrunch Registry
uses: Mouse Genome Informatics (MGI)
uses: Zebrafish Information Network (ZFIN)
uses: Rat Genome Database (RGD)
uses: WormBase
uses: FlyBase
recommends: SciCrunch Registry
recommends: Mouse Genome Informatics (MGI)
recommends: Zebrafish Information Network (ZFIN)
recommends: Rat Genome Database (RGD)
is recommended by: Neuroscience Information Framework
is recommended by: SciCrunch Registry
is related to: NIF Data Federation
has parent organization: SciCrunch
NIGMS R24 GM144308 The community can contribute to this resource nlx_158572 SCR_004098 Resource Identification Initiative Portal 2026-02-12 09:43:44 19
Information Hyperlinked Over Proteins
 
Resource Report
Resource Website
10+ mentions
Information Hyperlinked Over Proteins (RRID:SCR_004829) iHOP data or information resource, database, service resource Information system that provides a network of concurring genes and proteins extends through the scientific literature touching on phenotypes, pathologies and gene function. It provides this network as a natural way of accessing millions of PubMed abstracts. By using genes and proteins as hyperlinks between sentences and abstracts, the information in PubMed can be converted into one navigable resource, bringing all advantages of the internet to scientific literature research. Moreover, this literature network can be superimposed on experimental interaction data (e.g., yeast-two hybrid data from Drosophila melanogaster and Caenorhabditis elegans) to make possible a simultaneous analysis of new and existing knowledge. The network contains half a million sentences and 30,000 different genes from humans, mice, D. melanogaster, C. elegans, zebrafish, Arabidopsis thaliana, yeast and Escherichia coli. phenotype, gene, protein, interaction, pathology, physiology, gene network, network, literature, gene function, text-mining, bio.tools is listed by: OMICtools
is listed by: Debian
is listed by: bio.tools
is related to: PubMed
has parent organization: Autonomous University of Madrid; Madrid; Spain
European Union IST-2001- 32688;
European Union QLRT-2001-00015
PMID:15226743 Creative Commons Attribution-NoDerivs License, Works v3 biotools:ihop, nif-0000-00232, OMICS_01185 https://bio.tools/ihop SCR_004829 iHOP - Information Hyperlinked over Proteins 2026-02-12 09:43:55 24
FuncAssociate: The Gene Set Functionator
 
Resource Report
Resource Website
10+ mentions
FuncAssociate: The Gene Set Functionator (RRID:SCR_005768) FuncAssociate service resource, analysis service resource, production service resource, data analysis service A web-based tool that accepts as input a list of genes, and returns a list of GO attributes that are over- (or under-) represented among the genes in the input list. Only those over- (or under-) representations that are statistically significant, after correcting for multiple hypotheses testing, are reported. Currently 37 organisms are supported. In addition to the input list of genes, users may specify a) whether this list should be regarded as ordered or unordered; b) the universe of genes to be considered by FuncAssociate; c) whether to report over-, or under-represented attributes, or both; and d) the p-value cutoff. A new version of FuncAssociate supports a wider range of naming schemes for input genes, and uses more frequently updated GO associations. However, some features of the original version, such as sorting by LOD or the option to see the gene-attribute table, are not yet implemented. Platform: Online tool gene, gene ontology, statistical analysis, web service, bio.tools is listed by: Gene Ontology Tools
is listed by: OMICtools
is listed by: bio.tools
is listed by: Debian
is related to: Gene Ontology
has parent organization: Roth Laboratory
NIH ;
Canadian Institute for Advanced Research ;
NINDS NS054052;
NINDS NS035611;
NHLBI HL081341;
NHGRI HG0017115;
NHGRI HG004233;
NHGRI HG003224
PMID:19717575
PMID:14668247
Free for academic use, Acknowledgement requested biotools:funcassociate, OMICS_02264, nlx_149233 http://llama.mshri.on.ca/cgi/func/funcassociate
https://bio.tools/funcassociate
SCR_005768 2026-02-12 09:44:16 36
ADGO
 
Resource Report
Resource Website
1+ mentions
ADGO (RRID:SCR_006343) ADGO service resource, analysis service resource, production service resource, data analysis service A web-based tool that provides composite interpretations for microarray data comparing two sample groups as well as lists of genes from diverse sources of biological information. It provides multiple gene set analysis methods for microarray inputs as well as enrichment analyses for lists of genes. It screens redundant composite annotations when generating and prioritizing them. It also incorporates union and subtracted sets as well as intersection sets. Users can upload their gene sets (e.g. predicted miRNA targets) to generate and analyze new composite sets. microarray, gene, annotation, bio.tools is listed by: OMICtools
is listed by: Debian
is listed by: bio.tools
PMID:21624890 Acknowledgement requested OMICS_02229, biotools:adgo https://bio.tools/adgo SCR_006343 2026-02-12 09:44:31 3

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