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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 Specification URL Alternate IDs Alternate URLs Old URLs Parent Organization Resource ID Authority Synonyms Record Last Update Mentions Count
Osprey: Network Visualization System
 
Resource Report
Resource Website
10+ mentions
Osprey: Network Visualization System (RRID:SCR_007138) data processing software, data visualization software, simulation software, software application, software resource Osprey is a software platform for visualization of complex interaction networks. Osprey builds data-rich graphical representations from Geno Ontology (GO) annotated interaction data maintained by The Grid. The following list describes some of the important characteristics of the Osprey Network Visualization System: * Portability ( cross platform availability ) o Osprey is available on almost all Platforms that support the latest Java Plugin * Tools for Biological Analysis o Osprey provides many features such as network filters, connectivity filters, advanced layouts, and dataset superimposing which are extremely useful to biologists who are interested in analyzing their data * Powerful Support Database o Integrated with Osprey is a powerful database of interactions and annotation, see section 8. The GRID ( The General Repository of Interaction Datasets ). * Ease of use o Osprey provides an extremely user friendly interface for working with interaction data * Online Database Add-on Ability o Osprey can be incorporated as a standard visualization tool with online databases such as The GRID * Support for figures o Osprey networks can be saved in SVG, PNG and JPG format so they can be used with image programs Sponsors: Development of Osprey was funded by a grant from the Canadian Institutes of Health Research. filter, biological analysis, biologist, interaction, software, visualization nif-0000-10394 SCR_007138 SciCrunch Registry Osprey 2026-09-26 02:14:14 27
Chromosome 7 Annotation Project
 
Resource Report
Resource Website
10+ mentions
Chromosome 7 Annotation Project (RRID:SCR_007134) Chromosome 7 Annotation Project data or information resource, data repository, database, service resource, storage service resource Database containing the DNA sequence and annotation of the entire human chromosome 7, encompassing nearly 158 million nucleotides of DNA and 1917 gene structures, are presented; the most up to date collation of sequence, gene, and other annotations from all databases (eg. Celera published, NCBI, Ensembl, RIKEN, UCSC) as well as unpublished data. To generate a higher order description, additional structural features such as imprinted genes, fragile sites, and segmental duplications were integrated at the level of the DNA sequence with medical genetic data, including 440 chromosome rearrangement breakpoints associated with disease. The objective of this project is to generate a comprehensive description of human chromosome 7 to facilitate biological discovery, disease gene research and medical genetic applications. There are over 360 disease-associated genes or loci on chromosome 7. A major challenge ahead will be to represent chromosome alterations, variants, and polymorphisms and their related phenotypes (or lack thereof), in an accessible way. In addition to being a primary data source, this site serves as a weighing station for testing community ideas and information to produce highly curated data to be submitted to other databases such as NCBI, Ensembl, and UCSC. Therefore, any useful data submitted will be curated and shown in this database. All Chromosome 7 genomic clones (cosmids, BACs, YACs) listed in GBrowser and in other data tables are freely distributed. duplication, gene expression, family, fish, gene, gene annotation, genome, breakpoint, chromosome, chromosome 7, clinical, deletion, disease, dna sequence, human, insertion, inversion, polymorphism, rearrangement, segmental duplication, snp, translocation, annotation, data analysis service, blat, cosmid, bac, yac, biomaterial supply resource, malignant, non malignant, bio.tools is listed by: One Mind Biospecimen Bank Listing
is listed by: Debian
is listed by: bio.tools
PMID:12690205 Free, (Genomic clones) nif-0000-03550, biotools:chr7, r3d100012136 https://bio.tools/chr7, https://doi.org/10.17616/R3VP9V SCR_007134 SciCrunch Registry The Chromosome 7 Annotation Project, Chromosome 7 Annotation Project 2026-09-26 02:14:14 13
Jinx
 
Resource Report
Resource Website
1+ mentions
Jinx (RRID:SCR_007012) Jinx data processing software, image analysis software, segmentation software, software application, software resource THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 2, 2019. Ontology-based segmentation and analysis tools for electron tomographic data. electron tomography is related to: Subcellular Anatomy Ontology
has parent organization: Cell Centered Database
THIS RESOURCE IS NO LONGER IN SERVICE nlx_156722 SCR_007012 SciCrunch Registry 2026-09-26 02:14:13 5
Matlab Neuroshare Library
 
Resource Report
Resource Website
Matlab Neuroshare Library (RRID:SCR_006957) NeuroshareLibrary software library, software resource, software toolkit This is MATLAB library to create Neuroshare data format. You can convert your own data into Neuroshare format file. console (text based), eeg, meg, electrocorticography, format conversion, japanese, linux, macos, matlab, microsoft, posix/unix-like, windows, neuroshare, data format, data sharing is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC)
has parent organization: ATR; Kyoto; Japan
Japanese Ministry of Education Culture Sports Science and Technology MEXT GNU General Public License nlx_155880 http://www.nitrc.org/projects/nslib_v1_3_1 SCR_006957 SciCrunch Registry Neuroshare Library 2026-09-26 02:14:12 0
The WWW Virtual Library: Model Organisms
 
Resource Report
Resource Website
The WWW Virtual Library: Model Organisms (RRID:SCR_007007) data or information resource, portal, topical portal Catalog of internet resources relating to biological model organisms, and is part of the Biosciences area of the Virtual Library project. The main Model Organisms Library discussed in this website are: * E. coli (bacterium) * Yeasts (Saccharomyces cerevisiae, and other species) * Dictyostelium discoideum (slime mold) * Drosophila melanogaster (fruit fly) * Xenopus laevis (African clawed frog) Many aspects of biology are similar in most or all organisms, but it is frequently much easier to study particular aspects in particular organisms - for instance, genetics is easier in small organisms that breed quickly, and very difficult in humans! The most popular model organisms have strong advantages for experimental research, and become even more useful when other scientists have already worked on them, discovering techniques, genes and other useful information. bacterium, cerevisiae, model organism, saccharomyces, s. cerevisiae, slime mold, xenopus, catalog, link aggregator is listed by: 3DVC nif-0000-20953 SCR_007007 SciCrunch Registry VL 2026-09-26 02:14:13 0
MetMap
 
Resource Report
Resource Website
1+ mentions
MetMap (RRID:SCR_006954) MetMap software resource A computational pipeline for the analysis of MethylSeq experiments., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. is listed by: OMICtools
has parent organization: University of California at Berkeley; Berkeley; USA
THIS RESOURCE IS NO LONGER IN SERVICE OMICS_00618 SCR_006954 SciCrunch Registry 2026-09-26 02:14:12 9
Comparative Sequencing of Plant Small RNAs
 
Resource Report
Resource Website
1+ mentions
Comparative Sequencing of Plant Small RNAs (RRID:SCR_007003) analysis service resource, data analysis service, data or information resource, data set, production service resource, service resource This project has developed a sequence dataset of plant small RNAs based on the hypothesis that most if not all plants utilize important small RNA signaling networks. Different plant families are likely to have both common and lineage-specific miRNAs or other small RNAs with important biological roles. Comparative genomics approaches can be applied to distinguish potential miRNAs from siRNAs and to match the miRNAs to the target sequences. This project develops an unparalleled resource of millions of plant small RNAs for comparative analyses. The project includes sequencing of small RNAs from a diverse and agronomically-relevant set of plant species, focused analyses of important members of the Solanaceae and Poaceae, and development of a small RNA database and web interface for public access and analysis of data. These data will allow the experimental characterization of the majority of biologically important small RNAs for a range of plant species, and will be tremendously useful to a broad set of plant biologists interested in development, stress responses, epigenetics, evolution, RNA biology and other traits impacted by small RNAs. We offer a variety of tools to query the small RNA data set, with options to identify sequences based on homology, expression levels, conservation, or potential function: 1. Small RNA mapping tool: searches for small RNAs perfectly matching a genomic sequence provided by the user. 2. Small RNA mismatch tool: searches the database for small RNAs or other short sequences provided by the user, allowing mismatches. 3. Library-comparison tool to identify conserved small RNAs. 4. Library-comparison tool to identify differentially regulated small RNAs. 5. Reverse Target Prediction. has parent organization: University of Delaware; Delaware; USA NSF 0638525 nlx_37749 SCR_007003 SciCrunch Registry 2026-09-26 02:14:13 1
Myrna
 
Resource Report
Resource Website
1+ mentions
Myrna (RRID:SCR_006951) Myrna software resource A cloud computing tool for calculating differential gene expression in large RNA-seq datasets. It uses Bowtie for short read alignment and R/Bioconductor for interval calculations, normalization, and statistical testing. These tools are combined in an automatic, parallel pipeline that runs in the cloud (Elastic MapReduce in this case) on a local Hadoop cluster, or on a single computer, exploiting multiple computers and CPUs wherever possible. mapreduce, hadoop, cloud computing, differential expression, gene expression, rna-seq, bio.tools is listed by: OMICtools
is listed by: Debian
is listed by: bio.tools
is related to: ReCount - A multi-experiment resource of analysis-ready RNA-seq gene count datasets
has parent organization: Johns Hopkins University; Maryland; USA
PMID:20701754 Artistic License OMICS_01310, biotools:myrna https://github.com/BenLangmead/myrna, https://bio.tools/myrna SCR_006951 SciCrunch Registry Myrna: Cloud-scale differential gene expression for RNA-seq 2026-09-26 02:14:12 2
CCDB Image Converter
 
Resource Report
Resource Website
CCDB Image Converter (RRID:SCR_007005) Image Converter software resource THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 4th,2023. A command line program in Unix to convert images to a variety of formats (PNG, TIFF, JPEG, PPM..etc). It is uniquely different from other programs such as Adobe Photoshop or ImageMagick because it is designed for dealing with the high-resolution images with file sizes of several gigabytes. Image Converter does not require any additional RAM or virtual memory to run. Also, run-time is relatively fast for high resolution data. image has parent organization: Cell Centered Database THIS RESOURCE IS NO LONGER IN SERVICE nlx_156720 SCR_007005 SciCrunch Registry 2026-09-26 02:14:13 0
Genes to Cognition: Neuroscience Research Programme
 
Resource Report
Resource Website
10+ mentions
Genes to Cognition: Neuroscience Research Programme (RRID:SCR_007121) data or information resource, portal, topical portal A neuroscience research program that studies genes, the brain and behavior in an integrated manner, established to elucidate the molecular mechanisms of learning and memory, and shed light on the pathogenesis of disorders of cognition. Central to G2C investigations is the NMDA receptor complex (NRC/MASC), that is found at the synapses in the central nervous system which constitute the functional connections between neurons. Changes in the receptor and associated components are thought to be in a large part responsible for the phenomenon of synaptic plasticity, that may underlie learning and memory. G2C is addressing the function of synapse proteins using large scale approaches combining genomics, proteomics and genetic methods with electrophysiological and behavioral studies. This is incorporated with computational models of the organization of molecular networks at the synapse. These combined approaches provide a powerful and unique opportunity to understand the mechanisms of disease genes in behavior and brain pathology as well as provide fundamental insights into the complexity of the human brain. Additionally, Genes to Cognition makes available its biological resources, including gene-targeting vectors, ES cell lines, antibodies, and transgenic mice, generated for its phenotyping pipeline. The resources are freely-available to interested researchers. cognition, gene, neuroscience is listed by: 3DVC
has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom
Wellcome Trust ;
MRC ;
BBSRC ;
Gatsby Charitable Foundation ;
Human Frontiers Science Programme ;
European Union ;
Framework Programme ;
EPSRC ;
NSF
nif-0000-10235 SCR_007121 SciCrunch Registry G2C Neuroscience Research Program, G2C Research Programme, Genes to Cognition: Neuroscience Research Program, Genes to Cognition, G2C, Genes to Cognition - Neuroscience Research Programme, Genes to Cognition-Neuroscience Research Programme, G2C Research Program 2026-09-26 02:14:14 20
Minnesota Center for Twin and Family Research
 
Resource Report
Resource Website
1+ mentions
Minnesota Center for Twin and Family Research (RRID:SCR_006948) MCTFR data or information resource, disease-related portal, portal, research forum portal, topical portal Composed of many projects, including the Minnesota Twin Family Study (MTFS) and The Sibling Interaction and Behavior Study (SIBS), this research center seeks to identify genetic and environmental influences on development and psychological traits. Both projects are longitudinal research studies including twins, siblings, and parents. Over 9800 individuals have contributed to these exciting projects! By studying twins and siblings and their families, we can estimate how genes and environment interact to influence character, strengths, vulnerabilities and values. Participants in the MTFS include families with same-sex identical or fraternal twins who were born in Minnesota. The SIBS study is comprised of adoptive and biological siblings and their parents. Most participants partake in day-long visits to the MCTFR, and due to the longitudinal nature of our projects, they return every 3-4 years for follow-up visits. longitudinal study, clinical study, twin, sibling, parent, longitudinal, gene, environment, adolescent, development, behavior, dna has parent organization: University of Minnesota Twin Cities; Minnesota; USA Identical twin, Fraternal twin, Sibling, Parent, Twin NIH nlx_151990 SCR_006948 SciCrunch Registry SIBS, Minnesota Twin Study, MTFS, Sibbling Interaction and Behavior Study, Minnesota Twin Family Study 2026-09-26 02:14:12 3
SimSeq
 
Resource Report
Resource Website
10+ mentions
SimSeq (RRID:SCR_006947) SimSeq simulation software, software application, software resource An illumina paired-end and mate-pair short read simulator. This project attempts to model as many of the quirks that exist in Illumina data as possible. Some of these quirks include the potential for chimeric reads, and non-biotinylated fragment pull down in mate-pair libraries . bio.tools is listed by: OMICtools
is listed by: bio.tools
is listed by: Debian
Free biotools:simseq, OMICS_00258 https://bio.tools/simseq SCR_006947 SciCrunch Registry 2026-09-26 02:14:12 30
fMRI Data Center
 
Resource Report
Resource Website
10+ mentions
fMRI Data Center (RRID:SCR_007278) fMRIDC data or information resource, data repository, database, service resource, storage service resource THIS RESOURCE IS NO LONGER IN SERVICE, documented August 25, 2013 Public curated repository of peer reviewed fMRI studies and their underlying data. This Web-accessible database has data mining capabilities and the means to deliver requested data to the user (via Web, CD, or digital tape). Datasets available: 107 NOTE: The fMRIDC is down temporarily while it moves to a new home at UCLA. Check back again in late Jan 2013! The goal of the Center is to help speed the progress and the understanding of cognitive processes and the neural substrates that underlie them by: * Providing a publicly accessible repository of peer-reviewed fMRI studies. * Providing all data necessary to interpret, analyze, and replicate these fMRI studies. * Provide training for both the academic and professional communities. The Center will accept data from those researchers who are publishing fMRI imaging articles in peer-reviewed journals. The goal is to serve the entire fMRI community. fmri, cognitive, cortex, mri, talairach, neuroimaging, cognitive neuroscience, brain, structure, function, magnetic resonance, intellect, image collection, data set is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC)
is listed by: Biositemaps
is listed by: re3data.org
has parent organization: University of California at Santa Barbara; California; USA
NSF ;
W. M. Keck Foundation ;
NIMH ;
Sun Microsystems Center of Excellence
PMID:11545705 THIS RESOURCE IS NO LONGER IN SERVICE nif-0000-00025 http://www.fmridc.org/ SCR_007278 SciCrunch Registry The fMRI Data Center 2026-09-26 02:14:15 16
GEB
 
Resource Report
Resource Website
1+ mentions
GEB (RRID:SCR_007395) GEB software resource A Java application developed to visualise distribution of genomic features in high resolution. is listed by: OMICtools OMICS_00911 SCR_007395 SciCrunch Registry Genome Environment Browser 2026-09-26 02:14:17 2
Ikaros Project
 
Resource Report
Resource Website
50+ mentions
Ikaros Project (RRID:SCR_007391) simulation software, software application, software resource Ikaros is an open infrastructure for system level modeling of the brain including databases of experimental data, computational models and functional brain data. The system makes heavy use of the emerging standards for Internet based information and makes all information accessible through an open web-based interface. In addition, Ikaros can be used as a control architecture for robots which in the extension will lead to the development of a brain inspired robot architecture. The main components of the Ikaros systems are: a platform independent simulation kernel; a set of computational brain models; a set of I/O modules for interfacing with data files and peripheral such as robots or video cameras; tools for building systems of interconnected models; a plug-in architecture that allows new models to be easily added to the system; and a database with data from learning experiments that can be used for validation of the computational models. model, computational neuroscience, brain, robot, simulation, FASEB list is listed by: 3DVC
has parent organization: Lund University; Lund; Sweden
nif-0000-00426 SCR_007391 SciCrunch Registry Ikaros 2026-09-26 02:14:17 89
Biological General Repository for Interaction Datasets (BioGRID)
 
Resource Report
Resource Website
1000+ mentions
Biological General Repository for Interaction Datasets (BioGRID) (RRID:SCR_007393) BioGRID data or information resource, database Curated protein-protein and genetic interaction repository of raw protein and genetic interactions from major model organism species, with data compiled through comprehensive curation efforts. budding yeast, fission yeast, protein, gene, protein interaction, genetic interaction, model organism, interaction, dataset, gene annotation, phenotype, orthologous interaction, yeast, cellular interaction network, physical interaction, protein-peptide, protein-rna, protein-protein interaction, genetics, publication, raw protein, genetic interaction, web service, pathway, network, biology, gene mapping, statistics, bio.tools, FASEB list is used by: NIF Data Federation
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: OMICtools
is listed by: DataCite
is listed by: NIH Data Sharing Repositories
is listed by: bio.tools
is listed by: Debian
is related to: TissueNet - The Database of Human Tissue Protein-Protein Interactions
is related to: Pathway Commons
is related to: Cytoscape
is related to: Interaction Reference Index
is related to: ConsensusPathDB
is related to: FlyMine
is related to: IMEx - The International Molecular Exchange Consortium
is related to: Integrated Molecular Interaction Database
is related to: PSICQUIC Registry
is related to: PSI-MI
is related to: NIH Data Sharing Repositories
is related to: Agile Protein Interactomes DataServer
is related to: Integrated Manually Extracted Annotation
has parent organization: Princeton University; New Jersey; USA
has parent organization: University of Edinburgh; Scotland; United Kingdom
has parent organization: University of Montreal; Quebec; Canada
works with: IMEx - The International Molecular Exchange Consortium
BBSRC ;
Canadian Institutes of Health Research ;
NCRR R01 RR024031;
NHGRI HG02223;
NIH Office of the Director R24 OD011194
PMID:23203989
PMID:21071413
PMID:16381927
PMID:12620108
Free, Freely available nif-0000-00432, r3d100010350, OMICS_01901, biotools:the_grid https://orip.nih.gov/comparative-medicine/programs/genetic-biological-and-information-resources, https://bio.tools/the_grid, https://doi.org/10.17616/R34C7G SCR_007393 SciCrunch Registry , BioGRID, Biological General Repository for Interaction Datasets 2026-09-26 02:14:17 2824
Cavalli lab: Chromatin and Cell Biology
 
Resource Report
Resource Website
1+ mentions
Cavalli lab: Chromatin and Cell Biology (RRID:SCR_007267) data or information resource, laboratory portal, organization portal, portal This is the homepage of Dr. Cavalli''s Chromatin and Cell Biology Laboratory. Keywords: Chromatin, Cell, Biology, Scientific, Science, Research, Laboratory, nif-0000-30305 SCR_007267 SciCrunch Registry Cavalli lab 2026-09-26 02:14:15 1
Genetics of Learning Disability Study
 
Resource Report
Resource Website
1+ mentions
Genetics of Learning Disability Study (RRID:SCR_007266) data or information resource, portal, topical portal The Genetics of Learning Disability (GOLD) Study is aimed to identify the genes on the X chromosome that contribute to significant intellectual disability and to lead the way towards greater understanding of the mechanisms by which intellectual disability occurs. Ultimately the aim is to improve the services available to affected families. Sponsors: The work was supported by the European Community''s Seventh Framework Programme-the GEN2PHEN Project, the New South Wales Department of Health, the Australian NHMRC, the SMILE foundation, the WCH Foundation, D. Harwood, EU grant QLG3-CT- 2002-01810 (EURO-MRX), US National Institutes of Health (HD26202) to C.E.S., the South Carolina Department of Disabilities and Special Needs (SCDDSN), Action Medical Research and the Wellcome Trust. study, genetics, learning, disability, gene has parent organization: University of Cambridge; Cambridge; United Kingdom nif-0000-30285 SCR_007266 SciCrunch Registry GOLD Study 2026-09-26 02:14:15 6
Electronic Cell Project
 
Resource Report
Resource Website
10+ mentions
Electronic Cell Project (RRID:SCR_007381) modeling software, simulation software, software application, software resource Software platform, general technologies and theoretical supports for computational biology with the grand aim to make precise whole cell simulation at the molecular level possible.Technologies include formalisms and techniques, including technologies to predict, obtain or estimate parameters such as reaction rates and concentrations of molecules in the cell. The E-Cell System is a software platform for modeling, simulation and analysis of complex, heterogeneous and multi-scale system like the cell. The E-Cell Project is open to anyone who shares the view with u that development of cell simulation technology, and, even if such ultimate goal might not be within ten years of reach yet, solving various conceptual, computational and experimental problems that will continue to arise in the course of pursuing it, may have a multitude of eminent scientific, medical and engineering impacts on our society. gene, protein, ontology, binary executable; software development tool, cell is listed by: Debian nif-0000-00378 https://sources.debian.org/src/ecell/ SCR_007381 SciCrunch Registry E-Cell 2026-09-26 02:14:17 15
Primate Info Net
 
Resource Report
Resource Website
1+ mentions
Primate Info Net (RRID:SCR_007380) PIN data or information resource, database, portal, topical portal Portal covering the broad field of primatology, providing original content and links to resources about nonhuman primates in research, education and conservation. Through email lists and other resources, PIN also supports an informal primate information network comprised of thousands of individuals around the world working with nonhuman primates in a variety of roles. Services Provided: - Primate Info Net (PIN): A comprehensive Web site with links to research, conservation, and education resources related to nonhuman primates. - PrimateLit Database (1940 to date): PrimateLite is a free, bibliographic database of more than 200,000 citations to the nonhuman primate literature. Indexing for PrimateLit is provided by the Primate Information Center, Washington NPRC, Seattle. - International Directory of Primatology: The International Directory of Primatology is a searchable directory of the field of primatology with detailed information about organizations, field studies, population management groups, and contact information for more than 3,000 primatologists. - Primate-Science: Primate-Science is a professionally oriented, e-mail-based electronic discussion forum for people engaged in research with nonhuman primates. - Primate-News: Primate-News is an e-mailed-based news clipping service open to anyone interested in nonhuman primates. - Primate Enrichment Forum: Primate Enrichment Forum is a professionally oriented, e-mail-based electronic discussion forum for individuals interested in environmental enrichment for nonhuman primates. - AskPrimate: AskPrimate is a cooperative e-mail reference service available to the research community and the general public. - Primate-Jobs: Primate-Jobs is a job listing service that includes paid and volunteer positions, wanted and available. - Careers in Primatology: Careers in Primatology is a resource for people considering careers in primate research, education, conservation, or veterinary medicine. - Audiovisual Resources: Audiovisual Resources is a collection of primate-related videotapes, slides, and audiotapes available for research and educational uses. - The Callicam: The Callicam is a Webcam feature of the Wisconsin NPRC''s common marmoset site that allows students in the classroom to observe marmoset behavior and learn about their natural history, care, and management. primatology, conservation, network, database, literature, information, organization, field study, population has parent organization: Wisconsin National Primate Research Center NCRR RR000167;
NCRR RR015311
nif-0000-00371 SCR_007380 SciCrunch Registry 2026-09-26 02:14:17 3

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