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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
OpenNeuro
 
Resource Report
Resource Website
100+ mentions
OpenNeuro (RRID:SCR_005031) OpenNeuro, OpenfMRI data or information resource, data repository, database, image repository, service resource, storage service resource Open platform for analyzing and sharing neuroimaging data from human brain imaging research studies. Brain Imaging Data Structure ( BIDS) compliant database. Formerly known as OpenfMRI. Data archives to hold magnetic resonance imaging data. Platform for sharing MRI, MEG, EEG, iEEG, and ECoG data. neuroinformatics, database, storing, dataset, neuroimaging, data, MRI, MEG, EEG, iEEG, ECoG, FASEB list uses: Brain Imaging Data Structure (BIDs)
uses: HED Tags
is used by: studyforrest.org
is used by: DataLad
is used by: NIF Data Federation
is used by: Integrated Datasets
is used by: NIH Heal Project
is used by: Baby Open Brains
is recommended by: National Library of Medicine
is recommended by: BRAIN Initiative
is recommended by: NIDDK Information Network (dkNET)
is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC)
is listed by: re3data.org
is listed by: DataCite
is listed by: FAIRsharing
is affiliated with: NEMAR
is related to: Integrated Manually Extracted Annotation
has parent organization: Stanford University; Stanford; California
has parent organization: Stanford Center for Reproducible Neuroscience
has parent organization: BRAIN Initiative
is provided by: OpenNeuro
BRAIN Initiative ;
Laura and John Arnold Foundation ;
NIDA ;
NIMH ;
NSF OCI1131441;
Squishymedia ;
Stanford
Free, Freely available DOI:10.25504/FAIRsharing.s1r9bw, r3d100010924, nlx_144048, DOI:10.17616/R33047, DOI:10.18112 http://www.nitrc.org/projects/openfmri, https://github.com/OpenNeuroDatasets, https://doi.org/10.17616/R33047, https://doi.org/10.17616/r33047, https://doi.org/10.18112/, https://dx.doi.org/10.18112/, https://fairsharing.org/10.25504/FAIRsharing.s1r9bw, https://doi.org/10.17616/R33047 http://openfmri.org SCR_005031 OpenfMRI, Open fMRI, OpenNeuro 2026-09-05 06:25:28 310
QUEST
 
Resource Report
Resource Website
500+ mentions
QUEST (RRID:SCR_005210) QUEST community building portal, data or information resource, narrative resource, outreach program, podcast, portal, training material, training resource, video resource An award-winning multimedia science and environment series created by KQED, San Francisco, the public media station serving Northern California. Launched in February 2007, by the end of its fourth season (in September 2010), QUEST had reached approximately 36 million viewers and listeners through its traditional TV and radio broadcasts and its growing Web audience. QUEST''s ultimate aim is to raise science literacy in the San Francisco Bay Area and beyond, inspiring audiences to discover and explore science and environment issues for themselves. Every season, KQED''s QUEST produces: * half-hour television episodes episodes that air weekly, exploring the cutting-edge work of Northern California scientists and researchers (QUEST airs Wednesdays 7:30pm on KQED Public Television 9); * weekly radio reports covering urban environmental issues which often include multimedia slide shows, and interactive online maps (QUEST airs Mondays 6:30am and 8:30am on KQED Public Radio 88.5 FM); * Educational resources, for use by formal and informal educators; QUEST also provides professional development for science educators to support multimedia and technology integration in science classrooms and programs; * 20 six-minute stories for its new web only series, Science on the SPOT, which takes a fresh, fast and curious look at science with stories about albino redwoods, the science of fog and banana slugs, to name a few. (launched in 2010); * A daily science blog written by Northern California scientists, QUEST producers and science enthusiasts; * Exclusive web extras, featuring extended interviews with scientists; Flickr photos, and science hikes. Formal and informal Educators who would like to become involved withthe educational outreach program should contact: ScienceEd (at) kqed.org. science, environment, astronomy, biology, chemistry, climate, engineering, environment, geology, health, physics, news, television, radio, digital media is used by: NIF Data Federation
is used by: Integrated Blogs
is parent organization of: QUEST Community Science Blog
NSF ;
Corporation for Public Broadcasting ;
Richard and Rhoda Goldman Fund ;
S. D. Bechtel Jr. Foundation ;
Dirk and Charlene Kabcenell Foundation ;
Vadasz Family Foundation ;
Wyncote Foundation ;
George and Jeanette Stuart Charitable Trust
nlx_144230 SCR_005210 QUEST Northern California, KQED QUEST 2026-09-05 06:25:31 806
Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB)
 
Resource Report
Resource Website
10000+ mentions
Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) (RRID:SCR_012820) RCSB PDB data or information resource, data repository, database, service resource, storage service resource Collection of structural data of biological macromolecules. Database of information about 3D structures of large biological molecules, including proteins and nucleic acids. Users can perform queries on data and analyze and visualize results. 3-dimensional, annotation, molecule, nucleic acid, protein, visualization, sequence, function, macromolecule, ligand, model, dna, x-ray crystallography, ribosome, structure, oncogene, nucleic acids, molecular structure, cryomicroscopy, gold standard, FASEB list is used by: Structural Genomics Consortium
is used by: Ligand Expo
is used by: DARC - Database for Aligned Ribosomal Complexes
is used by: FireDB
is used by: Protein Data Bank Bind Database
is used by: Protein Data Bank Site
is used by: NIF Data Federation
is used by: ChannelPedia
is used by: MobiDB
is used by: BALBES
is used by: Structural Antibody Database
is used by: BioLiP
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 affiliated with: EMDataResource.org
is affiliated with: ConSurf Database
is related to: pdb-data
is related to: PDB2MultiGif
is related to: GlyProt
is related to: pdb-care
is related to: pdb2linucs
is related to: GlyVicinity
is related to: GlyTorsion
is related to: GlySeq
is related to: AffinDB
is related to: StatAlign
is related to: Community Structure-Activity Resource
is related to: Binding MOAD
is related to: ConSurf Database
is related to: glycosciences.de
is related to: DOMINE: Database of Protein Interactions
is related to: Jenalib: Jena Library of Biological Macromolecules
is related to: SynSysNet
is related to: EMDataResource.org
is related to: PDBe - Protein Data Bank in Europe
is related to: TFinDIT
is related to: HOLLOW
is related to: ccPDB - Compilation and Creation of datasets from PDB
is related to: DOMMINO - Database Of MacroMolecular INteractiOns
is related to: InterEvol database
is related to: Polbase
is related to: PoSSuM
is related to: ProtChemSI
is related to: RNA CoSSMos
is related to: PDBsum
is related to: Worldwide Protein Data Bank (wwPDB)
is related to: canSAR
is related to: CAPS Database
is related to: Dockground: Benchmarks, Docoys, Templates, and other knowledge resources for DOCKING
is related to: Combinatorial Extension (CE)
is related to: Metalloprotein Site Database
is related to: PDBj - Protein Data Bank Japan
is related to: Statistical Torsional Angles Potentials of NMR Refinement Database
is related to: Metalloprotein Ligand Interaction Database
is related to: CARP
is related to: PDBTM
is related to: RNA FRABASE - RNA FRAgments search engine and dataBASE
is related to: AmiGO
is related to: ConsensusPathDB
is related to: Biological Magnetic Resonance Data Bank (BMRB)
is related to: DNA DataBank of Japan (DDBJ)
is related to: FlyMine
is related to: NCBI Protein Database
is related to: NCBI Nucleotide
is related to: FunTree
is related to: IndelFR - Indel Flanking Region Database
is related to: NMR Restraints Grid
is related to: Enzyme Structures Database
is related to: Electron Microscopy Data Bank at PDBe (MSD-EBI)
is related to: Worldwide Protein Data Bank (wwPDB)
is related to: DNA DataBank of Japan (DDBJ)
is related to: PDBe - Protein Data Bank in Europe
is related to: MINAS - Metal Ions in Nucleic AcidS
is related to: PDBj - Protein Data Bank Japan
has parent organization: University of California at San Diego; California; USA
has parent organization: Rutgers University; New Jersey; USA
is parent organization of: RCSB PDB Software Tools
is parent organization of: Protein Data Bank Markup Language
is parent organization of: Ligand Expo
works with: CellPhoneDB
DOE ;
NIH ;
NSF DBI-1338415
PMID:12037327 Public, Acknowledgement requested nif-0000-00135, SCR_017379, r3d100010327 http://www.rcsb.org, http://www.pdb.org, http://www.rcsb.org/pdb/ SCR_012820 RCSB, Research Collaboratory for Structural Bioinformatics Protein Data Bank, The Protein Data Bank, PDB, Protein Databank, RCSB Protein Data Bank, Protein Data Bank 2026-09-05 06:27:28 12459
GRASSIUS
 
Resource Report
Resource Website
10+ mentions
GRASSIUS (RRID:SCR_012999) GRASSIUS analysis service resource, data analysis service, data or information resource, data repository, database, production service resource, service resource, storage service resource A public resource composed of a collection of databases, computational and experimental resources that relate to the control of gene expression in the grasses, and their relationship with agronomic traits. As knowledge on the interactions of transcription factors (TFs) and cis-regulatory elements in the promoters of the genes that they regulate continues to accumulate, the information is acquired by GRASSIUS, either through contributions by the community, or by literature analysis. The overarching objective of GRASSIUS is to provide a one-stop resource that will facilitate research and communication within the plant community with regards to genome-wide regulation of gene expression processes. transcription factor, coregulator, promoter sequence, transcription factor orf clone, blast, genome browser is listed by: OMICtools
has parent organization: Ohio State University; Ohio; USA
NSF PMID:18987217 Free OMICS_00555 SCR_012999 Grass Regulatory Information Server 2026-09-05 06:27:30 32
ChromHMM
 
Resource Report
Resource Website
50+ mentions
ChromHMM (RRID:SCR_018141) data analysis software, data processing software, software application, software resource Software tool for chromatin state discovery and characterization. Used for chromatin state discovery and genome annotation of non coding genome using epigenomic information across one or multiple cell types. Combines multiple genome wide epigenomic maps, and uses combinatorial and spatial mark patterns to infer complete annotation for each cell type. Provides automated enrichment analysis of resulting annotations. Chromatin state discovery, chromatin characterization, genome annotation, non coding genome, epigenomic, cell, annotation, analysis, pattern is listed by: Debian
is listed by: OMICtools
Alfred P. Sloan Fellowship ;
CAREER Award ;
NHGRI RC1HG005334;
NHGRI U01 HG007912;
NHGRI U54 HG004570;
NIEHS R01 ES024995;
NIMH U01 MH105578;
NSF 0905968
PMID:29120462
PMID:22373907
Free, Available for download, Freely available OMICS_03490 https://sources.debian.org/src/chromhmm/ SCR_018141 2026-09-05 06:28:31 50
RaptorX
 
Resource Report
Resource Website
100+ mentions
RaptorX (RRID:SCR_018118) data access protocol, simulation software, software application, software resource, web service Software package and web server for protein structure and function prediction. Used for predicting 3D structures for protein sequences without close homologs in Protein Data Bank. Given input sequence, predicts its secondary and tertiary structures, contacts, solvent accessibility, disordered regions and binding sites. Assigns some confidence scores to indicate quality of predicted 3D model. Protein structure predictor, 3D structure, protein sequence, secondary and tertiary structure, binding site, solvent accessibility, disordered region, bio.tools is listed by: bio.tools
is listed by: Debian
has parent organization: University of Chicago; Illinois; USA
NIGMS R01 GM089753;
NSF DBI 0960390
PMID:21987485 Restricted biotools:raptorx https://bio.tools/raptorx SCR_018118 2026-09-05 06:28:31 198
UltraScan
 
Resource Report
Resource Website
10+ mentions
UltraScan (RRID:SCR_018126) data analysis software, data processing software, software application, software resource Software package for hydrodynamic data from analytical ultracentrifugation experiments. Features integrated data editing and analysis environment with portable graphical user interface. Provides resolution for sedimentation velocity experiments using high-performance computing modules for 2-dimensional spectrum analysis, genetic algorithm, and for Monte Carlo analysis. Hydrodynamic data, analytical ultracentrifugation experiment, data editing, analysis, sedimentation velocity experiment, spectrum analysis, genetic algorithm, Monte Carlo analysis Howard Hughes Medical Institute ;
NCRR RR 022200 03S1;
NCRR RR022200;
NIGMS GM120600;
NSF ACI 1339649;
NSF ANI 228927;
NSF DBI 9724273;
NSF DBI 9974819;
NSF OCI 1032742;
NSF TG-MCB 060019T;
NSF TG-MCB 070038;
NSF TG-MCB 070039;
NSF TG-MCB 070040;
Robert J. Kleberg Jr. and Helen C. Kleberg Foundation ;
San Antonio Life Science Institute
Free, Available for download, Freely available SCR_018126 2026-09-05 06:28:31 20
ReproNim/containers
 
Resource Report
Resource Website
1+ mentions
ReproNim/containers (RRID:SCR_018467) data or information resource, knowledge environment resource, narrative resource, portal, software resource, software toolkit, training material, workflow Software containerized environments for reproducible neuroimaging. Part of ReproNim - Center for Reproducible Neuroimaging Computation. DataLad dataset with collection of popular computational tools provided within ready to use containerized environments. Containerized environment, reproducible neuroimaging, ReproNim, neuroimaging, dataset, DataLad, imaging, data is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) German Federal Ministry of Education and Research ;
NIBIB P41 EB019936;
NSF 1429999
Free, Freely available https://github.com/ReproNim/containers SCR_018467 2026-09-05 06:28:37 1
DiANNA
 
Resource Report
Resource Website
50+ mentions
DiANNA (RRID:SCR_018529) analysis service resource, data access protocol, production service resource, service resource, software resource, web service Neural network and web server, which determines cysteine oxidation state and disulfide connectivity of protein, given only its amino acid sequence. Used to predict disulfide connectivity topology. Predicts which half-cystines are covalently bound to which other half-cystines. DiANNA 1.1 is extension of DiANNA web server for ternary cysteine classification. Ternary cysteine classification, cysteine oxidation, disulfide protein connectivity, amino acid sequence, predict disulfide connectivity, connectivity topology, cysteine covalent bound, Boston College ;
NSF DBI 0543506
PMID:16844987
PMID:15980459
Free, Freely available http://bioinformatics.bc.edu/clotelab/DiANNA/ SCR_018529 DiANNA 1.1 2026-09-05 06:28:37 55
CohortMethod
 
Resource Report
Resource Website
10+ mentions
CohortMethod (RRID:SCR_018511) data analysis software, data processing software, data visualization software, software application, software resource Software R package for performing new user cohort studies in observational database in OMOP Common Data Model. Cohort study, observational database, OMOP Common Data Model, data, drugs, diagnosis, procedure, age, comorbidity index, data visualization NSF IIS 1251151 Free, Available for download, Freely available SCR_018511 2026-09-05 06:28:37 11
BioSimulations
 
Resource Report
Resource Website
1+ mentions
BioSimulations (RRID:SCR_018733) software resource, web application Web tool for sharing and re-using biomodels, simulations, and visualizations of simulations results. Supports variety of modeling frameworks including kinetic, constraint based, and logical modeling, model formats including BNGL, CellML, SBML, and simulation tools including COPASI, libRoadRunner/tellurium, NFSim, VCell. Sharing, reusing, biomodel, simulation, visualization, simulation result, modeling framework support, simulation tool support, model format support, bio.tools is listed by: bio.tools
is listed by: Debian
has parent organization: Icahn School of Medicine at Mount Sinai; New York; USA
has parent organization: University of Connecticut; Connecticut; USA
NIBIB P41 EB023912;
NIGMS ;
NSF
Restricted biotools:biosimulations https://bio.tools/biosimulations SCR_018733 2026-09-05 06:28:41 1
BpForms
 
Resource Report
Resource Website
BpForms (RRID:SCR_018653) data access protocol, software resource, software toolkit, web service Software toolkit for unambiguously describing molecular structure of DNA, RNA, and proteins, including non-canonical monomeric forms, crosslinks, nicks, and circular topologies. Aims to help epigenomics, transcriptomics, proteomics, systems biology, and synthetic biology researchers share and integrate information about DNA modification, post-transcriptional modification, post-translational modification, expanded genetic codes, and synthetic parts. Molecular structure description, DNA, RNA, protein, modification, epigenetics, transcriptomics, post transcriptional modification, post translational modification, bio.tools uses: BcForms
is used by: ObjTables
is used by: Datanator
is listed by: Debian
is listed by: bio.tools
is related to: BcForms
is related to: ObjTables
NIBIB P41 EB023912;
NIGMS R35 GM119771;
NSF 1649014
PMID:32423472 Free, Freely available biotools:bpforms https://bio.tools/bpforms SCR_018653 2026-09-05 06:28:40 0
ObjTables
 
Resource Report
Resource Website
ObjTables (RRID:SCR_018652) data management software, data processing software, software application, software resource, software toolkit Software toolkit for creating reusable datasets that are both human and machine readable, combining spreadsheets with schemas including classes, their attributes, type of each attribute, and possible relationships between instances of classes.Consists of format for describing schemas for spreadsheets, numerous data types for science, syntax for indicating class and attribute represented by each table and column in workbook, and software for using schemas to rigorously validate, merge, split, compare, and revision datasets. Used for supplementary materials of journal article, as well as for emerging domains which need to quickly build new formats for new types of data and associated software with minimal effort. Creating reusable dataset, combining spreadsheet with schema, spreadsheet, table, supplementary material, schema, object relational map, validation, bio.tools uses: BpForms
uses: BcForms
is listed by: bio.tools
is listed by: Debian
is related to: BpForms
NIBIB P41 EB023912;
NIGMS R35 GM119771;
NSF 1649014
Free, Freely available biotools:objtables https://bio.tools/objtables SCR_018652 2026-09-05 06:28:40 0
DoubletFinder
 
Resource Report
Resource Website
1000+ mentions
DoubletFinder (RRID:SCR_018771) data analysis software, data processing software, software application, software resource Software R package that predicts doublets in single cell RNA sequencing data. Doublet detection in single cell RNA sequencing data using artificial nearest neighbors. Identifies doublets using only gene expression data. Doublet detection in single cell RNA, single cell RNA, doublet detection, RNA sequencing data, gene expression data, artificial nearest neighbors is related to: Seurat
has parent organization: University of California at San Francisco; California; USA
Damon Runyon Cancer Research Foundation ;
Department of Defense Breast Cancer Research Program ;
NICHD DP2 HD080351;
NSF Science and Technology Center ;
NSF MCB 1330864;
UCSF Center for Cellular Construction
PMID:30954475 Free, Available for download, Freely available SCR_018771 2026-09-05 06:28:42 1250
ROSIE
 
Resource Report
Resource Website
10+ mentions
ROSIE (RRID:SCR_018764) ROSIE application programming interface, data access protocol, software resource, web application Unified web framework for Rosetta applications. Web interface for selected Rosetta protocols. Web front end for Rosetta software suite. Provides common user interface for Rosetta protocols, stable application programming interface for developers to add additional protocols, flexible back-end to allow leveraging of computer cluster resources shared by Rosetta Commons member institutions, and centralized administration by Rosetta Commons to ensure continuous maintenance. Offers general and speedy paradigm for serverification of Rosetta applications. Lowers barriers to Rosetta use for broader biological community. Web interface for Rosetta, Rosetta online server, Rosetta application serverification, Rosetta user interface works with: Rosetta Howard Hughes Medical and Institute International Student Research Fellowship ;
NCI U54 CA143907;
NCRR R00 RR024107;
NEI PN2 EY016586;
NIGMS R01 GM073151;
NIGMS R01 GM07822;
NIGMS R21 GM102716;
NIGMS T32 GM 88118;
NSF ;
Taiwan Governmental Scholarship for Study Abroad
PMID:23717507 Restricted https://rosie.rosettacommons.org/ SCR_018764 Rosetta Online Server that Includes Everyone 2026-09-05 06:28:42 10
datasets.datalad.org
 
Resource Report
Resource Website
1+ mentions
datasets.datalad.org (RRID:SCR_019089) data or information resource, data repository, data set, service resource, storage service resource DataLad data distribution. Super dataset collating DataLad datasets from various sources including OpenNeuro, CRCNS, etc., to provide unified access to over 200TB of neural data. Version control system, data distribution, super dataset, DataLad dataset, neural data is related to: DataLad NIBIB P41 EB019936;
NSF 1429999;
NSF 1912266
Free, Freely available https://www.datalad.org/datasets.html SCR_019089 2026-09-05 06:28:46 8
runBioSimulations
 
Resource Report
Resource Website
1+ mentions
runBioSimulations (RRID:SCR_019110) software resource, web application Web tool for executing broad range of modeling studies and visualizing their results. Provides web interface for reusing any model. Models, simulations, and visualizations are available under licenses specified for each resource. Executing modeling studies, visualization, model reusing, simulation, bio.tools uses: BioSimulators
is listed by: bio.tools
is listed by: Debian
Center for Reproducible Biomodeling Modeling ;
National Institute of Bioimaging and Bioengineering ;
National Institute of General Medical Sciences ;
NIH ;
NSF
Free, Freely available biotools:runbiosimulations https://bio.tools/runbiosimulations SCR_019110 2026-09-05 06:28:46 3
HDBIG
 
Resource Report
Resource Website
HDBIG (RRID:SCR_014120) data processing software, image analysis software, software application, software resource, software toolkit A collection of software tools for high dimensional brain imaging genomics. These tools are designed to perform comprehensive joint analysis of heterogeneous imaging genomics data. HDBIG-SR is an HDBIG toolkit for sparse regression while HDBIG-SCCA is an HDBIG toolkit for sparse association. image analysis software, genomics, imaging, joint analysis, toolkit, sparse association, sparse regression is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC)
has parent organization: Indiana University; Indiana; USA
NLM R01 LM011360;
NSF IIS-1117335
http://www.iu.edu/~hdbig/ SCR_014120 High Dimensional Brain Imaging Genomics Toolkit 2026-09-05 06:27:43 0
Wisconsin Cortical Thickness Analysis (CTA) Toolbox
 
Resource Report
Resource Website
Wisconsin Cortical Thickness Analysis (CTA) Toolbox (RRID:SCR_014180) data analysis software, data processing software, software application, software resource, software toolkit A Matlab tool to perform statistical analysis on cortical thickness signals on brain surfaces obtained from Freesurfer. It is used for multi-resolutional analysis of such cortical thickness signals and detecting group differences. It is based on the Spectral Graph Wavelet Transform (SGWT) toolbox and provides plug and play methods for deriving Wavelet Multiscale Descriptor (WMD), cortical thickness smoothing using SGWT, Multivariate General Linear Model (MGLM), and False Discovery Rate (FDR). matlab, software toolkit, cortical thickness signal, data analysis software uses: FreeSurfer
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC)
Wisconsin Partnership Program ;
NIA R01AG040396;
NIA R01AG021155;
NSF RI 1116584;
NSF CAREER 1252725;
UW ADRC NIA P50 AG033514;
UW ICTR NCRR 1UL1RR025011;
NIA P30 AG010129;
NIA K01 AG030514
http://pages.cs.wisc.edu/~wonhwa/code/CTA_toolbox.html, http://pages.cs.wisc.edu/~wonhwa/project/ctdiscrim.html SCR_014180 2026-09-05 06:27:44 0
NeuroRD
 
Resource Report
Resource Website
10+ mentions
NeuroRD (RRID:SCR_014769) simulation software, software application, software resource Stochastic reaction-diffusion simulator in Java which is used for simulating neuronal signaling pathways. simulation software, simulator, java, neuronal signaling pathway, neuron HFSP ;
NIMH K21-MH01141;
NSF IBN 0077509;
CRCNS program R01 AA16022;
CRCNS program AA18066
Available for download https://github.com/neurord/stochdiff/releases SCR_014769 2026-09-05 06:27:50 13

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