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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
MyGene.info
 
Resource Report
Resource Website
10+ mentions
MyGene.info (RRID:SCR_018660) web service, data access protocol, service resource, software resource Web service for querying or retrieving gene annotation data. Querying gene, gene, annotation, gene annotation, annotation data, gene annotation data, retrieving gene annotation data, bio.tools is listed by: Debian
is listed by: bio.tools
NHGRI U01 HG008473;
NIGMS GM083924;
NIGMS U54 GM114833;
NHGRI U01 HG006476;
NCI K22 CA188163;
NCATS UL1 TR001114;
Scripps Translational Science Institute
DOI:10.1186/s13059-016-0953-9 Free, Freely available biotools:mygene.info, BioTools:mygene.info https://bio.tools/mygene.info
https://bio.tools/mygene.info
https://bio.tools/mygene.info
SCR_018660 2026-02-15 09:21:40 20
ROSIE
 
Resource Report
Resource Website
1+ mentions
ROSIE (RRID:SCR_018764) ROSIE data access protocol, web application, application programming interface, software resource 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 NIGMS R01 GM073151;
NIGMS R01 GM07822;
NIGMS R21 GM102716;
NCRR R00 RR024107;
NCI U54 CA143907;
NEI PN2 EY016586;
NIGMS T32 GM 88118;
Taiwan Governmental Scholarship for Study Abroad ;
Howard Hughes Medical and Institute International Student Research Fellowship ;
NSF
PMID:23717507 Restricted https://rosie.rosettacommons.org/ SCR_018764 Rosetta Online Server that Includes Everyone 2026-02-15 09:22:18 7
CAIRN
 
Resource Report
Resource Website
CAIRN (RRID:SCR_019101) software application, data visualization software, data processing software, software resource, data access protocol, web service Web tool to graph all copy number alterations present in segment file. Custom data is permitted. Allows to display copy number alterations which overlap user specified region, to quantify number of amplified CNAs and deleted CNAs. Visualization tool to explore copy number alterations discovered in published cancer datasets. Intended to help oncology community observe of relative rates of amplification, deletion, and mutation of interesting genes and regions. Deleted CNAs quantification, Copy Number Alterations, segment file, data visualization, published cancer datasets CNAs, amplified CNA quantification Nine Girls Ask Foundation ;
NCI CA207729;
NIGMS GM132055;
NCI CA107263;
NCI CA177519;
NCI CA102310;
NIA AG033082;
NCI P30 CA138313
PMID:31923184 Free, Available for download, Freely available https://github.com/jrdelaney/CAIRN SCR_019101 Copy Alterations Intuitive Rendering Navigator 2026-02-15 09:22:26 0
RobotReviewer
 
Resource Report
Resource Website
1+ mentions
RobotReviewer (RRID:SCR_021064) text-mining software, software application, web application, software resource Open source web based system that uses machine learning and NLP to semi automate biomedical evidence synthesis, to aid practice of Evidence Based Medicine. Processes full text journal articles describing randomized controlled trials. Designed to automatically extract key data items from reports of clinical trials. Data automatic extraction, clinical trial reports, automatically extract key data, Evidence Based Medicine, text journal articles processing, randomized controlled trials is related to: Northeastern University; Massachusetts; USA
is related to: University of Texas at Austin; Texas; USA
NLM R01 LM012086;
Medical Research Council UK ;
NCI UH2 CA203711
PMID:29093610
DOI:10.1093/jamia/ocv044
Free, Available for download, Freely available https://github.com/ijmarshall/robotreviewer
https://robotreviewer.vortext.systems/
SCR_021064 Automating Biomedical Evidence Synthesis 2026-02-15 09:22:28 1
SnapATAC
 
Resource Report
Resource Website
10+ mentions
SnapATAC (RRID:SCR_020981) software application, data processing software, software resource, software toolkit, data analysis software Software package for analyzing scATAC-seq datasets.Used to dissects cellular heterogeneity in unbiased manner and map trajectories of cellular states. Can process data from up to million cells. Incorporates existing tools into comprehensive package for analyzing single cell ATAC-seq dataset. scATAC-seq datasets analysis, dissects cellular heterogeneity, cellular states, map trajectories NCI K99 CA252020;
UCSD School of Medicine ;
NIMH U19 MH114831
PMID:33637727 Free, Available for download, Freely available https://github.com/r3fang/SnapATAC SCR_020981 Single Nucleus Analysis Pipeline for ATAC-seq 2026-02-15 09:22:30 22
Exemplar Microscopy Images of Tissues
 
Resource Report
Resource Website
1+ mentions
Exemplar Microscopy Images of Tissues (RRID:SCR_021052) EMIT immunofluorescence, data set, 2d spatial image, service resource, storage service resource, image, data repository, immuno detection protocol, data or information resource, image collection, experimental protocol, narrative resource, image repository Reference dataset of multiplexed immunofluorescence microscopy images collected at HMS Laboratory of Systems Pharmacology. Includes set of images of different types for development and benchmarking of computational methods for image processing. As of 4/2/2021, EMIT comprises tissue microarray containing cores from 34 cancer, non-neoplastic diseases, and normal tissue collected from clinical discards under IRB supervised protocol. TMA was imaged using cyclic immunofluorescence method. Additional extensions of EMIT are currently in the planning stages. Long term goal is to compose ImageNet like resource for highly multiplexed images of tissues and tumors by consolidating high quality curated datasets. Reference dataset, multiplexed immunofluorescence microscopy images, tissue microarray, cyclic immunofluorescence, tissues images, tumors images is related to: Synapse
is related to: Harvard Medical School; Massachusetts; USA
glioblastoma, lung adenocarcinoma, prostate adenocarcinoma, seminoma, meningioma, mesothelioma, GI stromal tumor, liver cirrhosis, leiomyosarcoma, high-grade serous ovarian cancer, diverticulitis, acute appendicitis, metastatic melanoma, dedifferentiated liposarcoma NIH U54 CA225088;
NCI U2C CA233262;
NCI U2C CA233280;
Ludwig Center at Harvard Medical School and the Ludwig Cancer Research Foundation
DOI:10.1101/2021.03.15.435473 Restricted SCR_021052 Exemplar Microscopy Images of Tissues ( and Tumors) 2026-02-15 09:21:56 3
GenePattern Notebook
 
Resource Report
Resource Website
1+ mentions
GenePattern Notebook (RRID:SCR_015699) systems interoperability software, software application, software resource, web application, electronic laboratory notebook Interactive analysis notebook environment that streamlines genomics research by interleaving text, multimedia, and executable code into unified, sharable, reproducible “research narratives.” It integrates the dynamic capabilities of notebook systems with an investigator-focused, simple interface that provides access to hundreds of genomic tools without the need to write code. gene, genomics research, research narrative, notebook system, analysis notebook, bio.tools is listed by: bio.tools
is listed by: Debian
is affiliated with: GenePattern
NIGMS R01-GM074024;
NCI U24-CA194107
PMID:28822753 Open Source, Free, Available for download, Account required biotools:GenePattern_notebook https://bio.tools/GenePattern_notebook SCR_015699 GenePattern Notebook environment 2026-02-15 09:21:36 3
TISSUES
 
Resource Report
Resource Website
10+ mentions
TISSUES (RRID:SCR_015665) web application, data or information resource, database, software resource Database that integrates evidence on tissue expression from manually curated literature, proteomics and transcriptomics screens, and automatic text mining. It maps all evidence to common protein identifiers and Brenda Tissue Ontology terms, and further unifies it by assigning confidence scores that facilitate comparison of the different types and sources of evidence. tissue expression, proteomic, transcriptomic, text-mining, brenda tissue ontology, protein identifier, bio.tools uses: BRENDA Tissue and Enzyme Source Ontology
is listed by: Debian
is listed by: bio.tools
Novo Nordisk Foundation NNF14CC0001;
NCI U54 CA189205-01;
CSIRO’s OCE Science Leader program
PMID:26157623 Freely available, Free, Available for download biotools:tissues https://bio.tools/tissues SCR_015665 TISSUES: Tissue Expression Database, Tissue Expression Database 2026-02-15 09:21:23 42
ImmuneDB
 
Resource Report
Resource Website
1+ mentions
ImmuneDB (RRID:SCR_017125) data analysis service, database, service resource, production service resource, data or information resource, analysis service resource Software system for storing and analyzing high throughput B and T cell immune receptor sequencing data. Comprised of web interface and of Python analysis tools to process raw reads for gene usage, infer clones, aggregate data, and run downstream analyses, or in conjunction with other AIRR tools using its import and export features. collect, store, analysis, B cell, T cell, immune, receptor, sequencing, data, process, raw, read is used by: AIRR Data Commons NIAID P01 AI106697;
NIAID P30 AI0450080;
NIDDK UC4 DK112217;
NCI P30 CA016520
PMID:30298069 Free, Available for download, Freely available https://github.com/arosenfeld/immunedb SCR_017125 2026-02-15 09:21:15 8
exRNA Atlas
 
Resource Report
Resource Website
10+ mentions
exRNA Atlas (RRID:SCR_017221) organization portal, portal, expression atlas, data analysis service, software resource, database, ontology, data access protocol, atlas, service resource, storage service resource, consortium, production service resource, data repository, data or information resource, controlled vocabulary, analysis service resource, application programming interface Software tool as data and metadata repository of Extracellular RNA Communication Consortium. Atlas includes small RNA sequencing and qPCR derived exRNA profiles from human and mouse biofluids. All RNAseq datasets are processed using version 4 of exceRpt small RNAseq pipeline. Atlas accepts submissions for RNAseq or qPCR data. Differential, expression, RNA, sequencing, qPCR, data, visualization, extracellular, exRNA, atlas, repository, dataset is recommended by: National Library of Medicine
has parent organization: Baylor College of Medicine; Houston; Texas
has parent organization: exRNA
gastric cancer, colon carcinoma, colorectal cancer, prostate carcinoma, pancreatic carcinoma, multiple sclerosis, glioblastoma multiforme, ulcerative colitis, Alzheimer's disease, ischemic stroke, intraparenchymal hemorrhage of brain, asthma, cardiovascular disorder, myocardial infarction, lupus, nephrotic syndrome, transplanted kidney present, liver disease, transplanted liver present, pre-eclampsia, Parkinson disease, intraventricular brain hemorrhage, subarachnoid hemorrhage NIDA U54 DA036134;
NCI R01 CA163849;
NIGMS R25 GM056929;
NCATS UH3 TR000906;
NCI U19 CA179512;
NIDDK P30 DK63720;
NHLBI K23 HL127099;
NHLBI R01 HL136685;
NIA R01 AG059729;
NCATS UH3 TR000943;
NCI R35 CA209904;
NCI CA217685;
NHLBI R01 HL122547;
American Cancer Society ResearchProfessor Award ;
Frank McGraw Memorial Chair in CancerResearch
PMID:30951672 Restricted SCR_017221 2026-02-15 09:21:59 24
Appyters
 
Resource Report
Resource Website
1+ mentions
Appyters (RRID:SCR_021245) web application, software resource Collection of web-based software applications that enable users to execute bioinformatics workflows without coding. Turns Jupyter notebooks into fully functional standalone web-based bioinformatics applications. Each Appyter application introduces data entry form for uploading or fetching data, as well as for selecting options for various settings. Once user presses Submit, Appyter is executed in cloud and user is presented with Jupyter Notebook report that contain results. Report includes markdown text, interactive and static figures, and source code. Appyter users can share the link to the output report, as well as download the fully executable notebook for execution on other platforms. Jupyter Notebooks, data-driven web apps collection, Jupyter Notebook results report is used by: Hypothesis Center
has parent organization: Icahn School of Medicine at Mount Sinai; New York; USA
NCI U24 CA224260;
NHLBI U54 HL127624;
NIH Office of the Director OT2 OD030160
DOI:10.1016/j.patter.2021.100213 Free, Available for download, Freely available https://github.com/MaayanLab/appyter
https://github.com/MaayanLab/appyter-catalog
SCR_021245 2026-02-15 09:22:31 9
CNVpytor
 
Resource Report
Resource Website
10+ mentions
CNVpytor (RRID:SCR_021627) software application, sequence analysis software, data processing software, software resource, data analysis software Software Python package and command line tool for CNV/CNA analysis from depth of coverage by mapped reads. Software tool for CNV/CNA detection and analysis from read depth and allele imbalance in whole genome sequencing. Copy number variations, copy number alternations, whole genome sequencing, Python has parent organization: Mayo Clinic NCI U24 CA220242 DOI:10.1101/2021.01.27.428472 Free, Available for download, Freely available SCR_021627 2026-02-15 09:22:08 19
Cumulus
 
Resource Report
Resource Website
1+ mentions
Cumulus (RRID:SCR_021644) software application, data processing software, data analysis software, software resource Software tool as cloud based single cell genomics and spatial transcriptomics data analysis framework that is scalable to massive amounts of data and able to process variety of data types. Consists of cloud analysis workflow, Python analysis package and visualization application. Supports analysis of single-cell RNA-seq, CITE-seq, Perturb-seq, single-cell ATAC-seq, single-cell immune repertoire and spatial transcriptomics data. Single cell genomics, spatial transcriptomics, single-cell RNA-seq, CITE-seq, Perturb-seq, single-cell ATAC-seq, single-cell immune repertoire, data uses: Pegasus
uses: Cirrocumulus
uses: Pegasus-fus
is listed by: Terra
is related to: BICCN
has parent organization: Broad Institute
Klarman Cell Observatory ;
Manton Foundation ;
HHMI ;
Ludwig Center at MIT ;
Leidos Biomedical Research ;
Frederick National Laboratory for Cancer Research ;
NCI
DOI:10.1038/s41592-020-0905-x Free, Available for download, Freely available https://app.terra.bio/#workspaces/kco-tech/Cumulus
https://github.com/klarman-cell-observatory/cumulus/blob/91336094646217564a4f8e7b31c03c3c6bf2e84b/docs/index.rst
SCR_021644 2026-02-15 09:22:08 2
Motif Mutation Analysis for Regulatory Genomic Elements
 
Resource Report
Resource Website
500+ mentions
Motif Mutation Analysis for Regulatory Genomic Elements (RRID:SCR_021902) MMARGE software application, data processing software, software resource, software toolkit, data analysis software Software package that integrates genome wide genetic variation with epigenetic data to identify collaborative transcription factor pairs. Optimized to work with chromatin accessibility assays such as ATAC-seq or DNase I hypersensitivity, as well as transcription factor binding data collected by ChIP-seq. Used to identify combinations of cell type specific transcription factors while simultaneously interpreting functional effects of non-coding genetic variation. genome wide genetic variation, epigenetic data, identify collaborative transcription factor pairs, interpreting functional effects, non-coding genetic variation NCI CA173903;
NIGMS GM085764;
NIDDK DK091183;
NHLBI R00 123485
PMID:29893919 Free, Available for download, Freely available SCR_021902 2026-02-15 09:22:44 608
VAMPIRE
 
Resource Report
Resource Website
1+ mentions
VAMPIRE (RRID:SCR_021721) software application, data processing software, software resource, image analysis software, data analysis software Software tool for analysis of cell and nuclear morphology from fluorescence or bright field images. Enables profiling and classification of cells into shape modes based on equidistant points along cell and nuclear contours. Robust method to quantify cell morphological heterogeneity. cell morphology analysis, nuclear morphology analysis, fluorescence images, bright field images NCI U54 CA143868;
NCI R01 CA174388;
NIA P30 AG021334;
NIA U01 AG060903
DOI:10.1038/s41596-020-00432-x Free, Available for download, Freely available SCR_021721 Visually Aided Morpho-Phenotyping Image Recognition 2026-02-15 09:22:40 2
SEER Datasets and Software
 
Resource Report
Resource Website
10+ mentions
SEER Datasets and Software (RRID:SCR_003293) portal, software resource, data or information resource, topical portal, disease-related portal Portal provides SEER research data and software SEER*Stat and SEER*Prep. SEER incidence and population data associated by age, sex, race, year of diagnosis, and geographic areas can be used to examine stage at diagnosis by race/ethnicity, calculate survival by stage at diagnosis, age at diagnosis, and tumor grade or size, determine trends and incidence rates for various cancer sites over time. SEER releases new research data every Spring based on the previous November’s submission of data. NCI, cancer, statistics, epidemiology, analysis lists: SEER*Stat
lists: NCI SEER Cancer Stage Variable Documentation
is related to: Surveillance Epidemiology and End Results
has parent organization: National Cancer Institute
cancer NCI Free, Freely available nif-0000-31490 SCR_003293 The Surveillance Epidemiology and End Results (SEER) Program, SEER Datasets Software, SEER Datasets & Software, The Surveillance Epidemiology and End Results (SEER) Program of the National Cancer Institute 2026-02-15 09:18:29 28
SOURCE
 
Resource Report
Resource Website
50+ mentions
SOURCE (RRID:SCR_005799) SOURCE data analysis service, database, service resource, production service resource, data or information resource, analysis service resource SOURCE compiles information from several publicly accessible databases, including UniGene, dbEST, UniProt Knowledgebase, GeneMap99, RHdb, GeneCards and LocusLink. GO terms associated with LocusLink entries appear in SOURCE. The mission of SOURCE is to provide a unique scientific resource that pools publicly available data commonly sought after for any clone, GenBank accession number, or gene. SOURCE is specifically designed to facilitate the analysis of large sets of data that biologists can now produce using genome-scale experimental approaches Platform: Online tool genomic, functional annotation, ontology, gene expression, gene, genome, statistical analysis, bio.tools, FASEB list is listed by: Gene Ontology Tools
is listed by: Debian
is listed by: bio.tools
is related to: Gene Ontology
has parent organization: SMD
NIGMS ;
NCI CA85129-04;
NIGMS GM07365
PMID:12519986 Restricted biotools:source, nlx_149287 https://login.stanford.edu/idp/profile/SAML2/Redirect/SSO?execution=e1s1
https://bio.tools/source
SCR_005799 2026-02-15 09:19:04 69
Pathbase
 
Resource Report
Resource Website
10+ mentions
Pathbase (RRID:SCR_006141) Pathbase ontology, database, software resource, data access protocol, web service, service resource, storage service resource, data repository, data or information resource, image collection, controlled vocabulary, image repository Database of histopathology photomicrographs and macroscopic images derived from mutant or genetically manipulated mice. The database currently holds more than 1000 images of lesions from mutant mice and their inbred backgrounds and further images are being added continuously. Images can be retrieved by searching for specific lesions or class of lesion, by genetic locus, or by a wide set of parameters shown on the Advanced Search Interface. Its two key aims are: * To provide a searchable database of histopathology images derived from experimental manipulation of the mouse genome or experiments conducted on genetically manipulated mice. * A reference / didactic resource covering all aspects of mouse pathology Lesions are described according to the Pathbase pathology ontology developed by the Pathbase European Consortium, and are available at the site or on the Gene Ontology Consortium site - OBO. As this is a community resource, they encourage everyone to upload their own images, contribute comments to images and send them their feedback. Please feel free to use any of the SOAP/WSDL web services. (under development) histopathology, photomicrograph, macroscopic, mutant, genetically manipulated, pathology, transgenic, rodent, mpath ontology, mouse pathology ontology, skinbase, genotype, skin, gene, tissue, hair, mutant mouse strain, bio.tools is listed by: bio.tools
is listed by: Debian
is related to: Gene Ontology
has parent organization: University of Cambridge; Cambridge; United Kingdom
is parent organization of: Mouse Pathology Ontology
Lesion, Mutant mouse strain, Inbred mouse strain North American Hair Research Society ;
Ellison Medical Foundation ;
European Union QLRI-1999-00320;
European Union LSHG-CT-2006-037188;
NCI CA089713;
NCRR RR17436;
NIH AR49288
PMID:20587689
PMID:15623888
PMID:14681470
Except where otherwise noted, Creative Commons Attribution-NonCommercial-ShareAlike License, v3 Unported, Images on the database remain the property of the persons generously allowing their images to be used and are acknowledged within each record. Images should not be modified, Reproduced or disseminated without the express permission of the submitter. biotools:pathbase, nlx_151637 https://bio.tools/pathbase SCR_006141 Pathbase - European mutant mouse pathology database 2026-02-15 09:19:09 11
nondetects
 
Resource Report
Resource Website
1+ mentions
nondetects (RRID:SCR_001702) software application, standalone software, software resource Software R package to model and impute non-detects in results of qPCR experiments.Used to directly model non-detects as missing data. mac os x, unix/linux, windows, r, assay domain, gene expression, preprocessing, technology, workflow step, qpcr, bio.tools is listed by: OMICtools
is listed by: Debian
is listed by: bio.tools
has parent organization: Bioconductor
NCI CA009363;
NCI CA138249;
NHGRI HG006853;
Edelman-Gardner Foundation
PMID:24764462 Free, Available for download, Freely available OMICS_03938, biotools:nondetects https://bio.tools/nondetects SCR_001702 nondetects - Non-detects in qPCR data 2026-02-15 09:18:09 1
Adenoma Polyp Tissue Bank
 
Resource Report
Resource Website
Adenoma Polyp Tissue Bank (RRID:SCR_005366) APTB material resource, biomaterial supply resource THIS RESOURCE IS NO LONGER IN SERVICE, documented August 29, 2016. The Adenoma Polyp Tissue Bank (APTB) receives whole blood from patients enrolled in the Prevention of Sporadic Colorectal Adenomas with Celecoxib clinical trial. We have reached our accrual on blood submissions, so we will no longer be receiving blood specimens The objectives of this trial are as follows: A. To determine the efficacy and safety of celecoxib versus placebo in preventing the occurrence of newly detected colorectal adenomas in subjects at increased risk for colorectal carcinoma. In addition to incidence, other established risk factors will be evaluated for their association with occurrence of new colorectal adenomas, including cancer family history and adenoma size, histopathologic grade, multiplicity and location. Primary assessment of treatment efficacy will be the reduction in the number of subjects with adenomas at colonoscopy after Year 1 and Year 3 of study drug use. Secondary assessments of treatment efficacy will be 1) the number of adenomas 2) the histopathologic grade of adenomas and 3) the size of adenomas, also measured after one year and three years of study drug use. These factors will be incorporated into a risk model for predicting adenoma occurrence and response to celecoxib. B. To determine the efficacy of celecoxib versus placebo in modulating one or more of a panel of biomarkers for colorectal cancer at the cellular and molecular level sampled in a subset of subjects at selective sites at baseline and after Year 1 and Year 3 of study drug use. These biomarkers will include measurements of aberrant crypt foci (ACF), proliferation (index and crypt distribution), apoptosis (index and crypt distribution), COX expression and activity. If modulation of one or more mucosal biomarkers occur, we will explore whether it correlates with the development of incident colorectal neoplasia (adenomas/carcinomas), thereby attempting to validate the surrogacy of that biomarker. C. To develop a specimen bank. Serum and white blood cells are isolated from whole blood and adenoma tissue blocks and slides are banked. Banked specimens will become available for use in correlative science studies at a later point. This project began in 1999 and will be extended through 2006. The lead principal investigator is Monica M. Bertagnolli, MD, Brigham and Women''s Hospital, Boston, MA, and the APTB Director is Scott Jewell, Ph.D., Department of Pathology, The Ohio State University. The APTB is supported by the NIH, NCI Division of Cancer Prevention, in connection with the Strang Cancer Prevention Center, Cornell University, New York., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. blood, serum, white blood cell, adenoma tissue, tissue, whole blood, block, slide, colorectal adenoma, celecoxib, adenoma, cancer, colorectal cancer, clinical trial, polyp, risk factor is listed by: One Mind Biospecimen Bank Listing
has parent organization: Human Tissue Resource Network
has parent organization: Human Tissue Resource Network
Increased risk for colorectal carcinoma NCI THIS RESOURCE IS NO LONGER IN SERVICE nlx_144435 SCR_005366 APTB Specimen Bank 2026-02-15 09:18:57 0

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