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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
Virtual Fly Brain
 
Resource Report
Resource Website
10+ mentions
Virtual Fly Brain (RRID:SCR_004229) VFB data or information resource, atlas, neurons, expression An interactive tool for neurobiologists to explore the detailed neuroanatomy, neuron connectivity and gene expression of the adult Drosophila melanogaster brain. Drosophila, brain, neurons, innervation patterns, gene expression, transgene expression, phenotypes, neuroanatomy, neurobiology uses: Drosophila Gross Anatomy Ontology
uses: Drosophila Development Ontology
is related to: FlyBase
is related to: Flycircuit
is related to: Janelia Research
has parent organization: University of Edinburgh; Scotland; United Kingdom
has parent organization: University of Cambridge; Cambridge; United Kingdom
has parent organization: European Bioinformatics Institute
Wellcome Trust PMID:22180411 nlx_143644 http://www.virtualflybrain.org/site/vfb_site/home.htm SCR_004229 VirtualFlyBrain.org, VFB, Virtual Fly Brain 2026-02-12 09:43:47 45
BestGene
 
Resource Report
Resource Website
500+ mentions
BestGene (RRID:SCR_012605) BestGene core facility, access service resource, service resource, commercial organization We provide high quality Drosophila transgenic service to both research institutions and companies. We offer you partial to full service ranging from DNA preparation, embryo microinjection, screening for white+, yellow+, and/or GFP/RFP phenotypes, to balancing crosses. Most importantly, the cost of our Drosophila embryo injection services is more reasonable compared to that of others. With a large number of facilities and the highly experienced staff, we are able to initiate the process immediately upon receiving your sample. Our friendly web-based database allows you to track your sample status, service history and more. FASEB list is listed by: ScienceExchange SciEx_532 SCR_012605 BestGene Inc., BestGene Inc 2026-02-13 10:56:59 693
Vienna Drosophila Resource Center
 
Resource Report
Resource Website
100+ mentions
Vienna Drosophila Resource Center (RRID:SCR_013805) VDRC biomaterial supply resource, material resource Biomaterial supply resource which collects, maintains, and distributes independent transgenic fly lines. Most of the 38,000 fly lines are RNAi lines, but VDRC also maintains a collection of enhancer-GAL4 driver lines. Nearly all lines are in duplicate. Users can search for the stocks or DNA constructs for the gene of interest by entering CG number, synonym, or Transformant ID. RIN, Resource Information Network, biomaterial supply resource, drosophila, fly lines, RRID Community Authority is listed by: Resource Information Network Free, Public, Must create an account, Acknowledgment required http://www.csf.ac.at/facilities/vienna-drosophila-resource-center/
http://stockcenter.vdrc.at/control/main
SCR_013805 2026-02-13 10:57:11 379
Evolutionary Rate Covariation
 
Resource Report
Resource Website
1+ mentions
Evolutionary Rate Covariation (RRID:SCR_015669) ERC data processing software, web application, data analysis software, software application, software resource Web-based statistical application that measures correlated rates across a phylogeny, allowing for extraction of genes with similar evolutionary histories. It can identify new functional connections between genes. statistical software, correlation, phylogeny, gene extraction, genetic evolutionary history, covariation, group analysis PMID:25679399
PMID:24453993
PMID:22287101
Freely available, Free, Available for download SCR_015669 ERC: Evolutionary Rate Covariation, Evolutionary Rate Covariation (ERC) Analysis, Evolutionary Rate Covariation (ERC) 2026-02-13 10:57:32 1
Janelia Workstation
 
Resource Report
Resource Website
1+ mentions
Janelia Workstation (RRID:SCR_014302) software resource, image analysis software, data processing software, software application A discovery platform used to analyze and annotate imagery for individual projects, while assembling shared data resources. It was originally applied to Drosophila neuronal anatomy and neuroblast lineage analysis and is currently being extended to support mouse whole-brain projection tracing. The Workstation is both a pipeline management system that extracts entities from 3D imagery and a suite of tools that enable scientists to annotate large imagery datasets. A Entity-Attribute-Value (EAV) graph permits any element to be annotated by users with custom ontologies. By allowing any entity to have multiple parents, the graph can be re-arranged by each user without copying the underlying image data. annotate, image analysis software, discovery platform, shared data resource, drosophila, mouse, pipeline management, 3d image, suite, software tools SCR_014302 2026-02-13 10:57:16 3
Drosophila induction-based torque compensator
 
Resource Report
Resource Website
1+ mentions
Drosophila induction-based torque compensator (RRID:SCR_017276) instrument resource Compensator measure rotational force of tethered fly around its vertical body axis (yaw torque). Used as behavioral read-out after sensory stimulation or to control various environmental stimuli in different kinds of behavioral experiments. Measurement device uses measurement principle that is based on magnetic induction and compensates for any movement of fly. compensator, torque, yaw, insect, Diptera, time series, sensory, stimulation, fly, rotational, force, vertical, body, axis, tethered SCR_017276 2026-02-07 02:09:54 1
miRNA
 
Resource Report
Resource Website
10+ mentions
miRNA (RRID:SCR_010849) miRNA data or information resource, data set Data set of 2003 and 2005 miRNA-Target predictions for Drosophila miRNAs. is listed by: OMICtools
has parent organization: European Molecular Biology Laboratory
PMID:16337999
PMID:15723116
PMID:14691535
OMICS_00407 SCR_010849 miRNA - Target Gene Prediction at EMBL 2026-02-11 10:58:18 41
PITA
 
Resource Report
Resource Website
1000+ mentions
PITA (RRID:SCR_010853) PITA data or information resource, data set Catalogs of predicted microRNA targets in worm (based on ce6 genome assembly), fly (dm3), mouse (mm9) and human (hg18). We follow standard seed parameter settings and consider seeds of length 6-8 bases, beginning at position 2 of the microRNA. No mismatches or loops are allowed, but a single G:U wobble is allowed in 7- or 8-mers. In genes missing a 3' UTR annotation, 500 bp (fly), 800 bp (human and mouse) or 300 bp (worm) downstream of the annotated end of the coding sequence were used as the predicted UTR. For each organism, a catalog with zero flank and with a flank of 3 and 15 bases upstream and downstream. is listed by: OMICtools OMICS_00412 SCR_010853 2026-02-11 10:58:22 1047
Target genes of Wnt/beta-catenin signaling
 
Resource Report
Resource Website
10+ mentions
Target genes of Wnt/beta-catenin signaling (RRID:SCR_007022) Target genes of Wnt/beta-catenin signaling data or information resource, data set A list of target genes of Wnt/beta-catenin signaling. Suggestions for additions are welcome. Direct targets are defined as those with Tcf binding sites and demonstrating that these sites are important. target gene, wnt/beta-catenin signaling, wnt, beta-catenin, signaling, gene has parent organization: Stanford University; Stanford; California Colon cancer, Tumor, Adenocarcinoma, Melanoma, Cancer The community can contribute to this resource nlx_156867 SCR_007022 2026-02-11 10:57:28 24
Unified Human Interactome
 
Resource Report
Resource Website
10+ mentions
Unified Human Interactome (RRID:SCR_005805) UniHI data or information resource, database A database of human molecular interaction networks that integrates human protein-protein and transcriptional regulatory interactions from 15 distinct resources and aims to give direct and easy access to the integrated data set and to enable users to perform network-based investigations. The database includes tools (i) to search for molecular interaction partners of query genes or proteins in the integrated dataset, (ii) to inspect the origin, evidence and functional annotation of retrieved proteins and interactions, (iii) to visualize and adjust the resulting interaction network, (iv) to filter interactions based on method of derivation, evidence and type of experiment as well as based on gene expression data or gene lists and (v) to analyze the functional composition of interaction networks. molecular interaction network, interactome, protein, protein interaction network, protein interaction, pathway, function, visualization, protein-protein interaction, transcriptional regulatory interaction, network is listed by: OMICtools
has parent organization: University of Algarve; Faro; Portugal
PMID:24214987
PMID:22218860
PMID:18984619
PMID:17158159
Public, Non-commercial OMICS_01911, nif-0000-03609 http://www.mdc-berlin.de/unihi SCR_005805 2026-02-11 10:57:14 19
DroID - Drosophila Interactions Database
 
Resource Report
Resource Website
10+ mentions
DroID - Drosophila Interactions Database (RRID:SCR_006634) DroID data or information resource, database A gene and protein interactions database designed specifically for the model organism Drosophila including protein-protein, transcription factor-gene, microRNA-gene, and genetic interactions. For advanced searches and dynamic graphing capabilities the IM Browser and a DroID Cytoscape plugin are available. interaction, gene, protein, protein interaction, annotation, transcription factor, rna, protein-protein interaction, interactome, gene expression, phenotype, interolog, ortholog is listed by: OMICtools
is related to: Cytoscape
has parent organization: Wayne State University School of Medicine; Michigan; USA
PMID:21036869
PMID:18840285
Free, Public, Acknowledgement requested nif-0000-02767, OMICS_01908 SCR_006634 DroID - The Drosophila Interactions Database 2026-02-11 10:57:26 35
Drosophila polymorphism database
 
Resource Report
Resource Website
1+ mentions
Drosophila polymorphism database (RRID:SCR_007629) DPDB data or information resource, database Database providing a collection of all the existing polymorphic sequences in the Drosophila genus. It allows users to search for any polymorphic set according to different parameter values of nucleotide diversity. For data collection, diversity measures and updating they use PDA, a pipeline made of a set of Perl modules that automates the process of sequence retrieving, grouping, aligning and estimating diversity parameters from GenBank sequences. Diversity measures, including polymorphism estimates in synonymous and non-synonymous sites, linkage disequilibrium and codon bias, are calculated for each polymorphic set in different functional regions. The database also includes the primary information retrieved from different external sources: the Drosophila publicly available nucleotide sequences (excluding ESTs, STSs, GSSs, working draft and patents) with their annotations and references from GenBank (see the NCBI's Disclaimer and Copyright), additional information of genes and aberrations (from FlyBase), and the cross-references to the PopSet database (from NCBI). The database content is updated daily and records are assigned unique and permanent DPDB identification numbers to facilitate cross-database referencing. polymorphism has parent organization: Autonomous University of Barcelona; Barcelona; Spain nif-0000-02769 SCR_007629 2026-02-11 10:57:36 1
Assembly/Alignment/Annotation of 12 Related Drosophila Species
 
Resource Report
Resource Website
10+ mentions
Assembly/Alignment/Annotation of 12 Related Drosophila Species (RRID:SCR_002921) organism-related portal, portal, data set, data or information resource, topical portal A single source for sequences, assemblies, annotations and analyses of the genomes of members of the fruitfly genus Drosophlia. It is meant as resource for Drosophilists and other researchers interested in comparative analysis of these species and their genomes. There are pages for each species, as well as pages for different types of multi-species resources (e.g. alignments). If you have a public resource that will help this project, please consider making it available through this page by emailing multiple_at_fruitfly.org. sequence, annotation, analysis, genome, fruitfly, drosophila, research, comparative, alignment, assembly has parent organization: Lawrence Berkeley National Laboratory THIS RESOURCE IS NO LONGER IN SERVICE nif-0000-30021 SCR_002921 AAA: 12 Drosophila Genomes 2026-02-13 10:55:08 35
Flybrain at Stanford
 
Resource Report
Resource Website
1+ mentions
Flybrain at Stanford (RRID:SCR_001877) Flybrain(at)Stanford, FlybrainatStanford data processing software, image collection, data or information resource, software application, software resource, image analysis software Project content including raw image data, neuronal tracings, image registration tools and analysis scripts covering three manuscripts: Comprehensive Maps of DrosophilaHigher Olfactory Centres : Spatially Segregated Fruit and Pheromone Representation which uses single cell labeling and image registration to describe the organization of the higher olfactory centers of Drosophila; Diversity and wiring variability of olfactory local interneurons in the Drosophila antennal lobe which uses single cell labeling to describe the organization of the antennal lobe local interneurons; and Sexual Dimorphism in the Fly Brain which uses clonal analysis and image registration to identify a large number of sex differences in the brain and VNC of Drosophila. Data * Raw Data of Reference Brain (pic, amira) (both seed and average) * Label field of LH and MB calyx and surfaces for these structures * Label field of neuropil of Reference Brain * Traces (before and after registration). Neurolucida, SWC and AmiraMesh lineset. * MB and LH Density Data for different classes of neuron. In R format and as separate amira files. * Registration files for all brains used in the study * MBLH confocal images for all brains actually used in the study (Biorad pic format) * Sample confocal images for antennal lobe of every PN class * Confocal stacks of GABA stained ventral PNs Programs * ImageJ plugins (Biorad reader /writer/Amira reader/writer/IGS raw Reader) * Binary of registration, warp and gregxform (macosx only, others on request) * Simple GUI for registration tools (macosx only at present) * R analysis/visualization functions * Amira Script to show examples of neuronal classes The website is a collaboration between the labs of Greg Jefferis and Liqun Luo and has been built by Chris Potter and Greg Jefferis. The core Image Registration tools were created by Torsten Rohlfing and Calvin Maurer. brain, cell, neuron, neuropil, olfactory, pheromone, confocal image, antennal lobe, axon trace, forum, neuronal tracing, image registration tool, analysis script, single-cell labeling, image registration, mushroom body, lateral horn, olfactory receptor neuron has parent organization: Stanford University; Stanford; California Wellcome Trust WT076726;
Damon Runyon Cancer Research Foundation DRG-1766-03;
NIAAA AA05965;
NIAAA AA13521;
NIDCD R01-DC005982
PMID:17382886 THIS RESOURCE IS NO LONGER IN SERVICE nif-0000-10437 SCR_001877 Flybrain (at) Stanford - A warped brain is a good thing, Flybrain (at) Stanford 2026-02-13 10:54:56 6
NeuroMorpho.Org
 
Resource Report
Resource Website
50+ mentions
NeuroMorpho.Org (RRID:SCR_002145) data repository, storage service resource, data or information resource, service resource, database Centrally curated inventory of digitally reconstructed neurons associated with peer-reviewed publications that contains some of the most complete axonal arborizations digitally available in the community. Each neuron is represented by a unique identifier, general information (metadata), the original and standardized ASCII files of the digital morphological reconstruction, and a set of morphometric features. It contains contributions from over 100 laboratories worldwide and is continuously updated as new morphological reconstructions are collected, published, and shared. Users may browse by species, brain region, cell type or lab name. Users can also download morphological reconstructions for research and analysis. Deposition and distribution of reconstruction files ultimately prevents data loss. Centralized curation and annotation aims at minimizing the effort required by data owners while ensuring a unified format. It also provides a one-stop entry point for all available reconstructions, thus maximizing data visibility and impact. neuron, morphological reconstruction, morphometry, axonal arborization, digital neuronal reconstruction, neuronal reconstruction, neuronal morphology, data sharing, annotation, brain region, neocortex, digital reconstruction, neurogenetics, neurochemistry, neuroscience, neurology, FASEB list is used by: NIF Data Federation
is used by: BICCN
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 listed by: NeuroImaging Tools and Resources Collaboratory (NITRC)
is related to: DONE: Detection of Outlier NEurons
is related to: NIF Literature
is related to: Computational Neurobiology and Imaging Center
is related to: Integrated Manually Extracted Annotation
is related to: xyz2swc
is related to: Allen Institute for Brain Science
has parent organization: George Mason University; Virginia; USA
is parent organization of: NeuroMorpho.Org species ontology
is parent organization of: NeuroMorpho.Org species ontology old
NINDS R01 NS39600;
MURI ONR N000141010198
PMID:17728438
PMID:16552417
PMID:18949582
Free, Available for download, Freely available nif-0000-00006, r3d100010107 http://www.nitrc.org/projects/neuromorpho_org
http://neuromorpho.org/
https://doi.org/10.17616/R3WW2K
SCR_002145 Neuro Morpho, NeuroMorpho.org, NeuroMorpho 2026-02-13 10:54:59 96
Fly EM
 
Resource Report
Resource Website
1+ mentions
Fly EM (RRID:SCR_002242) Fly EM, FlyEM data processing software, portal, data set, data or information resource, software application, segmentation software, software resource, image analysis software, topical portal A project producing datasets, software, and algorithms that is developing the technology to produce connectomes at the electron microscopic level of behaviorally-relevant neural circuits as well as the entire Drosophila nervous system. This technology will enable them to create a map of every neuron and synapse in the Drosophila nervous system, using novel approaches to electron microscopy (EM) as the foundation. In the same way that the fly genome paved the way for larger projects, including sequencing the human genome, Fly EM may ultimately contribute to our understanding of the human brain by establishing a fly "connectome" a map that shows how all neurons in the fly brain are connected to each other. They began their entry into EM reconstruction with the fly's adult visual system, where much is known about cell types from previous EM and histological studies, as well as ongoing studies in the Fly Light Project. In addition to establishing and publishing a fly connectome, Fly EM will make technology and methodology available that is needed to perform large-scale EM reconstructions. Fly EM will generally pursue an open policy with their datasets, software, and algorithms after relevant publications. When an EM reconstruction is published, the derived connectome and reconstructed neuronal skeletons will be made available online. The raw data and annotatations will be made available upon request as logistics dictate. To encourage further collaboration and scientific discovery, a small fraction of their raw data and corresponding segmentation will be made available independent of publication. Their goal is to enable others who wish to approach the many algorithmic challenges, but who do not have access to an EM facility, to have the data they need to support methods development, as well as their results to use as a benchmark. Fly EM emphasizes publication of supporting techniques and software approaches before major EM reconstruction releases to encourage rapid feedback from the community and adoption of their strategies. FlyEM maintains much of its software in the open-source repository GitHub:http://janelia-flyem.github.com. They will provide information on official release versions of these packages on git-hub when it reaches reasonable maturity. neuron, synapse, nervous system, electron microscopy, visual system, connectome, reconstruction, adult, optic lobe, medulla, lobula has parent organization: Janelia Research PMID:30033368 Janelia Farm license, A 3-clause BSD license nlx_155555 SCR_002242 Fly EM Project 2026-02-13 10:55:00 3
Genevestigator
 
Resource Report
Resource Website
100+ mentions
Genevestigator (RRID:SCR_002358) Genevestigator commercial organization, data analysis service, analysis service resource, data or information resource, production service resource, service resource, database A high performance search engine for gene expression that integrates thousands of manually curated public microarray and RNAseq experiments and nicely visualizes gene expression across different biological contexts (diseases, drugs, tissues, cancers, genotypes, etc.). There are two basic analysis approaches: # for a gene of interest, identify which conditions affect its expression. # for condition(s) of interest, identify which genes are specifically expressed in this/these conditions. Genevestigator builds on the deep integration of data, both at the level of data normalization and on the level of sample annotations. This deep integration allows scientists to ask new types of questions that cannot be addressed using conventional tools. gene, genetic, animal, development, disease, meta-analysis, regulation, stage, microarray, rnaseq, visualization, gene expression, disease, drug, tissue, cancer, genotype, pharma, biomedical, conditions, genotype, anatomy, neoplasm, chemical, hormone, infection, model organism, organ, cell type, cell line, target, biomarker, similarity, FASEB list is parent organization of: RefGenes 4 products:, Free, Free for academic use, Account required, Paid subscription, Local installation nif-0000-21172, OMICS_00763 SCR_002358 2026-02-13 10:55:01 396
Clocklab
 
Resource Report
Resource Website
500+ mentions
Clocklab (RRID:SCR_014309) data processing software, data acquisition software, data analysis software, software application, software resource, standalone software Point and click program used to quickly analyse circadian activity data using algorithms and embedded controls to make every graph interactive and useful for data analysis. The analysis program has been used for a variety of species including mice, hamsters, rats, sheep, Drosophila, and humans. This program has three separate applications: one for data collection, one for analysis, and a chamber control program. circadian activity data, interactive, data analysis software, data acquisition software, standalone software is listed by: SoftCite Pay for product, Users can order different components of ClockLab separately SCR_014309 2026-02-13 10:57:17 546
Cscan
 
Resource Report
Resource Website
1+ mentions
Cscan (RRID:SCR_006756) Cscan data analysis service, analysis service resource, data or information resource, production service resource, service resource, database Data resource that includes a large collection of genome-wide ChIP-Seq experiments performed on transcription factors (TFs), histone modifications, RNA polymerases and others. Enriched peak regions from the ChIP-Seq experiments are crossed with the genomic coordinates of a set of input genes, to identify which of the experiments present a statistically significant number of peaks within the input genes' loci. The input can be a cluster of co-expressed genes, or any other set of genes sharing a common regulatory profile. Users can thus single out which TFs are likely to be common regulators of the genes, and their respective correlations. Also, by examining results on promoter activation, transcription, histone modifications, polymerase binding and so on, users can investigate the effect of the TFs (activation or repression of transcription) as well as of the cell or tissue specificity of the genes' regulation and expression. regulator, gene, genome-wide chip-seq, chip-seq, gene, genome is listed by: OMICtools PMID:22669907 Free OMICS_00529 SCR_006756 2026-02-13 10:55:55 4
FlyBase
 
Resource Report
Resource Website
1000+ mentions
FlyBase (RRID:SCR_006549) FB data repository, storage service resource, organism-related portal, portal, data or information resource, service resource, topical portal, database Database of Drosophila genetic and genomic information with information about stock collections and fly genetic tools. Gene Ontology (GO) terms are used to describe three attributes of wild-type gene products: their molecular function, the biological processes in which they play a role, and their subcellular location. Additionally, FlyBase accepts data submissions. FlyBase can be searched for genes, alleles, aberrations and other genetic objects, phenotypes, sequences, stocks, images and movies, controlled terms, and Drosophila researchers using the tools available from the "Tools" drop-down menu in the Navigation bar. RIN, Resource Information Network, mutant, gene, genome, blast, genotype, phenotype, allele, sequence, stock, image, movie, controlled term, video resource, image collection, life-cycle, genome, expression, rna-seq, genetics, drosophilidae, bio.tools, FASEB list, RRID Community Authority is used by: NIF Data Federation
is used by: Resource Identification Portal
is used by: PhenoGO
is used by: Integrated Animals
is used by: Drososhare
is recommended by: NIDDK Information Network (dkNET)
is recommended by: National Library of Medicine
is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases
is listed by: re3data.org
is listed by: OMICtools
is listed by: bio.tools
is listed by: Debian
is listed by: Resource Information Network
is related to: FlyMine
is related to: Virtual Fly Brain
is related to: AmiGO
is related to: Drosophila melanogaster Exon Database
is related to: HomoloGene
is related to: UniParc at the EBI
is related to: UniParc
is related to: Gene Ontology
is related to: NIH Data Sharing Repositories
is related to: GBrowse
is related to: Integrated Manually Extracted Annotation
is related to: PhenoGO
has parent organization: Harvard University; Cambridge; United States
has parent organization: University of Cambridge; Cambridge; United Kingdom
has parent organization: Indiana University; Indiana; USA
has parent organization: University of New Mexico; New Mexico; USA
is parent organization of: Drosophila anatomy and development ontologies
is parent organization of: Fly Taxonomy
is parent organization of: FlyBase Controlled Vocabulary
is parent organization of: Drosophila Development Ontology
MRC ;
Indiana Genomics Initiative ;
NSF ;
NIH Blueprint for Neuroscience Research ;
NIHGRI P41 HG000739
PMID:24234449
PMID:22127867
PMID:18948289
PMID:18641940
PMID:18160408
PMID:17099233
PMID:16381917
PMID:15608223
PMID:12519974
PMID:11752267
PMID:11465064
PMID:9847148
PMID:9399806
PMID:9045212
PMID:8594600
PMID:8578603
PMID:7937045
PMID:7925011
nif-0000-00558, r3d100010591, OMICS_01649, biotools:flybase https://bio.tools/flybase
https://doi.org/10.17616/R3903Q
http://flybase.net SCR_006549 flybase A Drosophila Genomic and Genetic Database, FlyBase: A Database of Drosophila Genes and Genomes, FLYBASE, FlyBase: A Database of Drosophila Genes & Genomes, FB 2026-02-13 10:55:53 4025

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