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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
ScanImage
 
Resource Report
Resource Website
500+ mentions
ScanImage (RRID:SCR_014307) software application, data processing software, data acquisition software, software resource, signal processing software Open source software application for laser scanning microscopy, electrophysiology, laser scanning photostimulation, and other physiological methods focused on neurobiology. Used to control laser scanning microscopes without need for custom data acquisition hardware. Standard data acquisition boards are used to acquire data and control laser scanning. The tasks of signal integration and image processing are placed on the computer CPU. Multiple versions of ScanImage are available, each with their own features. Laser, scanning, microscopy, electrophysiology, photostimulation, neurobiology, control, data, acquisition, BRAIN Initiative is recommended by: BRAIN Initiative
has parent organization: Cold Spring Harbor Laboratory
has parent organization: Northwestern University; Illinois; USA
PMID:12801419 Restricted http://scanimage.vidriotechnologies.com/display/SIH/ScanImage+Home SCR_014307 Scan Image, ScanImage 2026-02-17 10:02:37 810
Cerebrovascular Disease Knowledge Portal
 
Resource Report
Resource Website
10+ mentions
Cerebrovascular Disease Knowledge Portal (RRID:SCR_015628) CDKP data or information resource, topical portal, disease-related portal, database, portal Portal enables browsing, searching, and analysis of human genetic information linked to cerebrovascular disease and related traits, while protecting the integrity and confidentiality of the underlying data. human, genetic, information, cerebrovascular, disease, data, knowledge is listed by: NIDDK Information Network (dkNET)
has parent organization: Massachusetts General Hospital Labs and Facilities
cerebrovascular disease NINDS ;
NIH ;
Accelerating Medicines Partnership in Type 2 Diabetes
Free, Available for download SCR_016535 SCR_015628 Cerebrovascular Disease Knowledge Portal (CDKP) 2026-02-17 10:03:17 14
BoxPlotR
 
Resource Report
Resource Website
100+ mentions
BoxPlotR (RRID:SCR_015629) software application, web application, data processing software, software resource, data visualization software Web tool written in R for generation of box plots with R packages shiny, beanplot4, vioplot, beeswarm and RColorBrewer, and hosted on shiny server to allow for interactive data analysis. Data are held temporarily and discarded as soon as session terminates.Represents both summary statistics and distribution of primary data. Enables visualization of minimum, lower quartile, median, upper quartile and maximum of any data set.Data matrix can be uploaded as file or pasted into application. May be downloaded to run locally or as virtual machine for VMware and VirtualBox. Box plot generation, customized box plot, data, plot, analysis is listed by: SoftCite
is related to: PlotsOfData
is related to: vioplot
Wellcome Trust ;
WTCCB ;
ERC ;
Genome Québec International Recruitment Award
PMID:24481215 Free, Available for download, Freely available SCR_018327 https://github.com/VizWizard/BoxPlotR.shiny SCR_015629 2026-02-17 10:02:35 360
Fred Hutchinson Cancer Research Center Co-operative Center for Excellence in Hematology Bioinformatics Resource
 
Resource Report
Resource Website
Fred Hutchinson Cancer Research Center Co-operative Center for Excellence in Hematology Bioinformatics Resource (RRID:SCR_015324) data or information resource, production service resource, analysis service resource, access service resource, service resource, core facility THIS RESOURCE IS NO LONGER IN SERVICE.Documented on July 27,2022. Core provides bioinformatics specialists available to assist researchers with processing, exploring, and understanding genomics data. hematology, bioinformatics, explore, understand, genomic, data, cancer is listed by: NIDDK Information Network (dkNET)
has parent organization: Fred Hutchinson Cancer Center
Cancer NIDDK P30 DK056465 THIS RESOURCE IS NO LONGER IN SERVICE SCR_015907 SCR_015324 Hutch, Bioinformatic Resource, Fred, Co-operative Center for Excellence in Hematology, Cancer Center 2026-02-17 10:03:12 0
BOINC - Berkeley Open Infrastructure for Network Computing
 
Resource Report
Resource Website
1+ mentions
BOINC - Berkeley Open Infrastructure for Network Computing (RRID:SCR_015896) BOINC software application, data or information resource, data processing software, data distribution software, project portal, data acquisition software, software resource, portal Software to orchestrate the distribution of computational work units (data and applications) to volunteers and have results collected back. It supports diverse applications, including those with large storage or communication requirements, and addresses unsolved issues in biology, medicine, physics, astronomy and computer science. infrastructure, computing, network, volunteer, data, application, distribution, storage, communication, biology, medicine, physics, astronomy, computer science has parent organization: University of California at Berkeley; Berkeley; USA PMID:27547555 Open source, Free, Available for download, The public can contribute to this resource, The research community can contribute to this resource, Available on Google Play Store, Available on Kindle Store, Available on Amazon App Store SCR_015896 Berkeley Open Infrastructure for Network Computing, Berkeley Open Infrastructure for Network Computing (BOINC) 2026-02-17 10:02:55 3
ChemSpider
 
Resource Report
Resource Website
1000+ mentions
ChemSpider (RRID:SCR_006360) ChemSpider data access protocol, mobile app, software application, data or information resource, database, software resource, web service, service resource Collection of chemical structures. Provides access to structures, properties and associated information from hundreds of data sources to find compounds of interest and provides services to improve this data by curation and annotation and to integrate it with users applications. collection, chemical, structure, property, data, compound, bio.tools, FASEB list is used by: Open PHACTS
is used by: GEROprotectors
is listed by: re3data.org
is listed by: bio.tools
is listed by: Debian
has parent organization: Royal Society of Chemistry
Waters ;
GGA Software Services
Free, Freely available, Registration required for some sites nlx_152101, biotools:chemspider, r3d100010205 https://bio.tools/chemspider
https://doi.org/10.17616/R38P4P
SCR_006360 2026-02-17 10:01:03 1759
Proteome Commons
 
Resource Report
Resource Website
10+ mentions
Proteome Commons (RRID:SCR_006234) Proteome Commons community building portal, storage service resource, data or information resource, database, service resource, software resource, portal, data repository THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 17, 2013. A public resource for sharing general proteomics information including data (Tranche repository), tools, and news. Joining or creating a group/project provides tools and standards for collaboration, project management, data annotation, permissions, permanent storage, and publication. proteomics, protein, peptide, data sharing, data, tool, news, annotation, proteome, genome is listed by: re3data.org
has parent organization: University of Michigan; Ann Arbor; USA
is parent organization of: Proteome Commons Tranche repository
NCI ;
Clinical Proteomics Technologies for Cancer ;
NCRR P41-RR018627
PMID:20356086 THIS RESOURCE IS NO LONGER IN SERVICE nlx_151800 SCR_006234 ProteomeCommons.org, ProteomeCommons 2026-02-17 10:01:05 12
EDAM Ontology
 
Resource Report
Resource Website
1+ mentions
EDAM Ontology (RRID:SCR_006620) EDAM data or information resource, ontology, controlled vocabulary An ontology of bioinformatics operations (tool, application, or workflow functions), types of data including identifiers, topics (application domains), and data formats. The applications of EDAM are within organizing tools and data, finding suitable tools in catalogues, and integrating them into complex applications or workflows. Semantic annotations with EDAM are applicable to diverse entities such as for example Web services, databases, programmatic libraries, standalone tools and toolkits, interactive applications, data schemas, data sets, or publications within bioinformatics. Annotation with EDAM may also contribute to data provenance, and EDAM terms and synonyms can be used in text mining. EDAM - and in particular the EDAM Data sub-ontology - serves also as a markup vocabulary for bioinformatics data on the Semantic Web. bioinformatics, operation, data, topic, type, identifier, format, semantic annotation, obo format, owl is listed by: BioPortal
is related to: DRCAT Resource Catalogue
is related to: bioDBcore
has parent organization: European Bioinformatics Institute
Acknowledgement required, Permission required nlx_151281 http://purl.bioontology.org/ontology/EDAM SCR_006620 EMBRACE Data and Methods Ontology, EDAM Ontology - Bioinformatics operations types of data topics and data formats, EMBRACE Data And Methods 2026-02-17 10:00:55 9
NIDDK Central Repository
 
Resource Report
Resource Website
50+ mentions
NIDDK Central Repository (RRID:SCR_006542) CDR, NIDDKCDR biospecimen repository, material storage repository, storage service resource, data or information resource, database, service resource, data repository NIDDK Central Repositories are two separate contract funded components that work together to store data and samples from significant, NIDDK funded studies. First component is Biorepository that gathers, stores, and distributes biological samples from studies. Biorepository works with investigators in new and ongoing studies as realtime storage facility for archival samples.Second component is Data Repository that gathers, stores and distributes incremental or finished datasets from NIDDK funded studies Data Repository helps active data coordinating centers prepare databases and incremental datasets for archiving and for carrying out restricted queries of stored databases. Data Repository serves as Data Coordinating Center and website manager for NIDDK Central Repositories website. clinical supply resource, data, clinical, sample sharing, genotyping, genotype, phenotype, genetic analysis, data sharing, genetics, serum, plasma, stool, urine, dna, red blood cell, buffy coat, tissue, immortalized cell line, cell line, data set, digestive organ, kidney, diabetes, kidney disease, digestive disease, genome-wide association study, sequencing, FASEB list uses: DataCite
is used by: NIDDK Information Network (dkNET)
is used by: NIF Data Federation
is used by: NIH Heal Project
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
lists: HEALTHY study
lists: Nonalcoholic Steatohepatitis Clinical Research Network
lists: HALT-C Trial
lists: Type 1 Diabetes Genetics Consortium
lists: TEDDY
lists: Type 1 Diabetes TrialNet
lists: Rare and Atypical Diabetes Network
lists: Diabetes Prevention Program
lists: Diabetes Prevention Program Outcomes Study
lists: Restoring Insulin Secretion Consortium (RISE)
lists: Epidemiology of Diabetes Interventions and Complications
lists: Diabetes Control and Complications Trial
lists: Treatment Options for type 2 Diabetes in Adolescents and Youth
is listed by: One Mind Biospecimen Bank Listing
is listed by: re3data.org
is listed by: Biospecimens/Biorepositories: Rare Disease-HUB (RD-HUB)
is listed by: NIDDK Information Network (dkNET)
is related to: NCBI database of Genotypes and Phenotypes (dbGap)
is related to: Peginterferon and Ribavirin for Pediatric Patients with Chronic Hepatitis C
is related to: Chronic Renal Insufficiency Cohort Study
has parent organization: RTI International
NIDDK PMID:23396299
PMID:21959867
PMID:16595012
Restricted nlx_152673, r3d100010377 https://doi.org/10.17616/R3WP48 https://www.niddkrepository.org, SCR_006542 NIDDK Central Repository, National Institute of Diabetes and Digestive and Kidney Diseases Central Repository, NIDDKCentral Repositories 2026-02-17 10:00:54 85
Germplasm Resources Information Network
 
Resource Report
Resource Website
100+ mentions
Germplasm Resources Information Network (RRID:SCR_006675) GRIN department portal, organization portal, data or information resource, database, portal Web server to provide germplasm information about plants, animals, microbes, invertebrates and access to databases that maintain passport, characterization, evaluation, inventory, and distribution data for the management and utilization of national germplasm collections. Under control of the U.S. Department of Agriculture's Agricultural Research Service to support the National Genetic Resources Program (NGRP). Operated by the Database Management Unit of the National Germplasm Resource Laboratory in Beltsville, Maryland. agriculture, food, germplasm, information, plant, animal, microbe, invertebrate, access, database, distribution, data, management, , FASEB list has parent organization: U.S. Department of Agriculture the U.S. Department of Agriculture SCR_016462, nlx_21883 SCR_006675 GRIN, Germplasm Resources Information Network 2026-02-17 10:00:57 326
Federal Interagency Traumatic Brain Injury Research Informatics System
 
Resource Report
Resource Website
50+ mentions
Federal Interagency Traumatic Brain Injury Research Informatics System (RRID:SCR_006856) FITBIR narrative resource, storage service resource, data or information resource, topical portal, database, service resource, standard specification, portal, data repository Platform for Traumatic Brain Injury relevant data. System was developed to share data across entire TBI research field and to facilitate collaboration between laboratories and interconnectivity between informatics platforms. FITBIR implements interagency Common Data Elements for TBI research and provides tools and resources to extend data dictionary. Established submission strategy to ensure high quality and to provide maximum benefit to investigators. Qualified researchers can request access to data stored in FITBIR and/or data stored at federated repositories. Traumatic, brain, injury, platform, common, data, element, medical, imaging, clinical, assessment, environment, behavior, brain, magnetic, resonance is recommended by: National Library of Medicine
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC)
is listed by: NIH Data Sharing Repositories
is related to: NIH Data Sharing Repositories
has parent organization: Center for Information Technology
Traumatic Brain Injury NINDS ;
U.S. Army Medical Research and Material Command ;
Center for Information Technology
Restricted nlx_151755, r3d100012837 https://doi.org/10.17616/R31NJMED SCR_006856 Federal Interagency Traumatic Brain Injury Research (FITBIR) Informatics System, FITBIR Informatics System 2026-02-17 10:01:00 57
RSEM
 
Resource Report
Resource Website
50+ mentions
RSEM (RRID:SCR_000262) data analysis software, software application, data processing software, software resource Software package for quantifying gene and isoform abundances from single end or paired end RNA Seq data. Accurate transcript quantification from RNA Seq data with or without reference genome. Used for accurate quantification of gene and isoform expression from RNA-Seq data. quantifying, gene, isoform, abundance, single, end, paired, RNA seq, data, transcript, reference, genome, bio.tools is listed by: OMICtools
is listed by: GitHub
is listed by: bio.tools
is listed by: Debian
has parent organization: University of Wisconsin-Madison; Wisconsin; USA
PMID:21816040 Free, Available for download, Freely available OMICS_01966, OMICS_01287, biotools:rsem, SCR_013027 https://github.com/deweylab/RSEM
https://github.com/deweylab/RSEM/releases
https://bio.tools/rsem
https://sources.debian.org/src/rsem/
SCR_000262 RSEM, RNA-Seq by Expectation-Maximization, RSEM-v1.3.0 2026-02-17 09:59:25 94
UNAVCO Geodetic Web Services
 
Resource Report
Resource Website
UNAVCO Geodetic Web Services (RRID:SCR_000181) data access protocol, web service, software resource THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Web services to access UNAVCO data collection. Adding /gps, /met, /pore, /tilt, and /strain gives the sensor JSON description. geodesy, geophysics, gps, pore, tilt, strain, json, met, data is listed by: CINERGI
has parent organization: UNAVCO
THIS RESOURCE IS NO LONGER IN SERVICE SciRes_000177 SCR_000181 2026-02-17 09:59:25 0
Harvard Partners HealthCare Center for Personalized Genetic Medicine Bioinformatics Core Facility
 
Resource Report
Resource Website
Harvard Partners HealthCare Center for Personalized Genetic Medicine Bioinformatics Core Facility (RRID:SCR_000882) production service resource, analysis service resource, access service resource, core facility, service resource Core to provide gene expression data analysis service. Activities range from the provision of services to fully collaborative grant funded investigations. affymetrix, array, PCPGM, gene, expression, data, analysis, service is listed by: Eagle I
has parent organization: Harvard University; Cambridge; United States
THIS RESOURCE IS NO LONGER IN SERVICE nlx_156324 http://www.partners.org/researchcores/trash/bioinformatics_HPCGG.html SCR_000882 PCPGM, bioinformatics, The Partners HealthCare Center for Personalized Genetic Medicine 2026-02-17 09:59:32 0
Jmosaics
 
Resource Report
Resource Website
Jmosaics (RRID:SCR_001094) software application, data processing software, data analysis software, software resource, sequence analysis software R software that detects enriched regions of ChIP-seq data sets jointly. chip seq, data, genomics, sequencing, r, sequence analysis software is listed by: OMICtools
is hosted by: Bioconductor
Free, Available for download, Freely available OMICS_00445 SCR_001094 2026-02-17 09:59:35 0
Vital Signs Ontology
 
Resource Report
Resource Website
1+ mentions
Vital Signs Ontology (RRID:SCR_001422) VSO data or information resource, ontology, controlled vocabulary Ontology for the four consensus human vital signs: blood pressure, body temperature, respiration rate, pulse rate. It provides a controlled structured vocabulary for describing vital signs measurement data, the various processes of measuring vital signs, and the various devices and anatomical entities participating in such measurements. ontology, controlled vocabulary, vital signs, data, measurement, blood pressure, body temperature, respiration rate, pulse rate is used by: TRANSFoRm Clinical Data Integration Model nif-0000-02605 https://bioportal.bioontology.org/ontologies/VSO http://code.google.com/p/vital-signs-ontology/ SCR_001422 vital-signs-ontology 2026-02-17 09:59:36 1
Farsight Toolkit
 
Resource Report
Resource Website
1+ mentions
Farsight Toolkit (RRID:SCR_001728) FARSIGHT software application, image processing software, data processing software, software resource, software toolkit, image analysis software THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23, 2022. A collection of software modules for image data handling, pre-processing, segmentation, inspection, editing, post-processing, and secondary analysis. These modules can be scripted to accomplish a variety of automated image analysis tasks. All of the modules are written in accordance with software practices of the Insight Toolkit Community. Importantly, all modules are accessible through the Python scripting language which allows users to create scripts to accomplish sophisticated associative image analysis tasks over multi-dimensional microscopy image data. This language works on most computing platforms, providing a high degree of platform independence. Another important design principle is the use of standardized XML file formats for data interchange between modules. editing, 2d, 3d, algorithm, analysis, bio-format, computational, data, graphical, inspection, metadata, microscopy, morphological, morphology, pixel, processing, segmentation, taxonomy, image has parent organization: University of Houston; Texas; USA NIBIB R01-EB005157;
NSF EEC-9986821;
NIBIB R01EB005157
PMID:24808857 THIS RESOURCE IS NO LONGER IN SERVICE nif-0000-10227 SCR_001728 FARSIGHTWiki 2026-02-17 09:59:40 2
Waxholm Space
 
Resource Report
Resource Website
10+ mentions
Waxholm Space (RRID:SCR_001592) WHS, WSA, WSS narrative resource, data or information resource, atlas, standard specification, waxholm atlas THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 1st, 2023. Coordinate based reference space for the mapping and registration of neuroanatomical data. Users can download image volumes representing the canonical Waxholm Space (WHS) adult C57BL/6J mouse brain, which include T1-, T2*-, and T2-Weighted MR volumes (generated at the Duke Center for In-Vivo Microscopy), Nissl-stained optical histology (acquired at Drexel University), and a volume of labels. All volumes are represented at 21.5μ isotropic resolution. Datasets are provided as gzipped NIFTI files. mouse WHS atlas, neuroanatomy, mapping, atlas, digital, brain, reference, registration, neuroanatomical, data, mri is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC)
is related to: Waxholm Space
is related to: Duke University; North Carolina; USA
is related to: PMOD Software
is related to: ITK-SNAP
has parent organization: International Neuroinformatics Coordinating Facility
has parent organization: University of Oslo; Oslo; Norway
works with: MeshView
works with: VisuAlign
PMID:20600960
PMID:21304938
THIS RESOURCE IS NO LONGER IN SERVICE SCR_009594, nlx_153838, nlx_155839 http://software.incf.org/software/waxholm-space/home, http://www.nitrc.org/projects/incf_waxholm-sp SCR_001592 Waxholm Space Atlas, Waxholm Space, Waxholm Standard Space, Mouse WHS atlas 2026-02-17 09:59:38 16
National Center for Integrative Biomedical Informatics
 
Resource Report
Resource Website
1+ mentions
National Center for Integrative Biomedical Informatics (RRID:SCR_001538) data or information resource, portal, organization portal The Center develops conceptual models, computational infrastructure, an integrated knowledge repository, and query and analysis tools that enable scientists to effectively access and integrate the wealth of biological data. The National Center for Integrative Biomedical Informatics (NCIBI) was founded in October 2005 and is one of seven National Centers for Biomedical Computing (NCBC) in the NIH Roadmap. NCIBI is based at the University of Michigan as a part of the Center for Computational Medicine and Biology (CCMB). NCIBI is composed of biomedical researchers, computational biologists, computer scientists, developers and human-computer interaction specialists organized into seven major core functions. They work in interdisciplinary teams to collectively develop tools that are not only computationally powerful but also biologically relevant and meaningful. The four initial Driving Biological Projects (prostate cancer progression, Type 1 and type 2 diabetes and bipolar disorder) provide the nucleation point from which tool development is informed, launched, and tested. In addition to testing tools for function, a separate team is dedicated to testing usability and user interaction that is a unique feature of this Center. Once tools are developed and validated the goal of the Center is to share and disseminate data and software throughout the research community both internally and externally. This is achieved through various mechanisms such as training videos, tutorials, and demonstrations and presentations at national and international scientific conferences. NCIBI is supported by NIH Grant # U54-DA021519. analysis tools, bipolar disorder, code, computational infrastructure, conceptual models, data, diabetes, knowledge repository, presentations, prostate cancer, query tools, seminar material, tool development, tutorials, videos, model is listed by: 3DVC
is related to: Biological Concept Diagram Editor
is related to: Gene Interaction Extraction from the Literature
is related to: National Centers for Biomedical Computing
has parent organization: University of Michigan; Ann Arbor; USA
is parent organization of: Substructure Index-based Approximate Graph Alignment
is parent organization of: miniTUBA
is parent organization of: Michigan Molecular Interactions
is parent organization of: Cell Line Knowledge Base
is parent organization of: HubMed
is parent organization of: MiMI Plugin for Cytoscape
Type 1 diabetes, Type 2 diabetes, Diabetes, Cancer, Bipolar disorder PMID:22101971 Free, Freely available nif-0000-09660 http://portal.ncibi.org/gateway/ SCR_001538 NCIBI 2026-02-17 09:59:41 1
FreeSurfer
 
Resource Report
Resource Website
10000+ mentions
FreeSurfer (RRID:SCR_001847) FreeSurfer software application, data processing software, software resource, image analysis software, data visualization software Open source software suite for processing and analyzing human brain MRI images. Used for reconstruction of brain cortical surface from structural MRI data, and overlay of functional MRI data onto reconstructed surface. Contains automatic structural imaging stream for processing cross sectional and longitudinal data. Provides anatomical analysis tools, including: representation of cortical surface between white and gray matter, representation of the pial surface, segmentation of white matter from rest of brain, skull stripping, B1 bias field correction, nonlinear registration of cortical surface of individual with stereotaxic atlas, labeling of regions of cortical surface, statistical analysis of group morphometry differences, and labeling of subcortical brain structures.Operating System: Linux, macOS. processing, analysis, human, brain, MRI, image, reconstruction, cortical, surface, fMRI, data is used by: Wisconsin Cortical Thickness Analysis (CTA) Toolbox
is used by: freesurfR
is used by: Automatic Analysis
is used by: NHP Freesurfer
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC)
is listed by: Biositemaps
is listed by: Debian
is listed by: SoftCite
is related to: PySurfer
is related to: RFT FDR
is related to: FMRLAB
is related to: TRACULA
is related to: BASH4RfMRI
has parent organization: Harvard University; Cambridge; United States
has plug in: JOSA
works with: NIAG Addiction Data
NCRR U24 RR021382;
NINDS R01 NS052585;
NCRR RR014075
PMID:22248573 Free, Available for download, Freely available nif-0000-00304 https://sources.debian.org/src/freesurfer/
http://www.nitrc.org/projects/freesurfer
http://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall
SCR_001847 2026-02-17 09:59:46 11817

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