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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 Synonyms Record Last Update Mentions Count
ARK-Genomics: Centre for Functional Genomics
 
Resource Report
Resource Website
10+ mentions
ARK-Genomics: Centre for Functional Genomics (RRID:SCR_002214) ARK Genomics data or information resource, access service resource, organization portal, core facility, portal, database, service resource Portal for studies of genome structure and genetic variation, gene expression and gene function. Provides services including DNA sequencing of model and non-model genomes using both Next Generation and Sanger sequencing , Gene expression analysis using both microarrays and Next Generation Sequencing, High throughput genotyping of SNP and copy number variants, Data collection and analysis supported in-house high performance computing facilities and expertise, Extensive EST clone collections for a number of animal species, all of commercially available microarray tools from Affymetrix, Illumina, Agilent and Nimblegen, Parentage testing using microsatellites and smaller SNP panels. ARK-Genomics has developed network of researchers whom they support through each stage of their genomics research, from grant application, experimental design and technology selection, performing wet laboratory protocols, through to analysis of data often in conjunction with commercial partners. gene expression, farm, function, gene, genetic, animal, dna, genome, genomic, genotype, knowledge base, model, structure, variation, job, comparative genome hybridization, parentage testing, microsatellite is listed by: ScienceExchange
is related to: Roslin Institute Labs and Facilities
has parent organization: Roslin Institute
works with: University of Edinburgh GenePool Next Generation Sequencing and Bioinformatics
BBSRC Free, Freely available nif-0000-20966, SciEx_157 https://genomics.ed.ac.uk/ SCR_002214 ARK Genomics, Roslin Institute ARK-Genomics 2026-08-10 09:31:39 13
Stanford Genomics Service Center Core Facility
 
Resource Report
Resource Website
10+ mentions
Stanford Genomics Service Center Core Facility (RRID:SCR_002050) SFGF, core facility, access service resource, service resource Stanford Genomics formerly Stanford Functional Genomics Facility provides services for high throughput sequencing, single cell assays, gene expression and genotyping studies utilizing microarray and real time PCR, and related services. High throughput sequencing (Illumina HiSeq 4000, NextSeq 500, MiSeq and MiniSeq), microarray gene expression and genotyping services (Affymetrix, Agilent and Illumina). Provides 24/7 access to instruments, equipment and software utilized within genomics field. ABRF, Stanford Genomics, genomics, high throughput sequencing, single cell assays, gene expression, genotyping, microarray, real time PCR, is listed by: ABRF CoreMarketplace
has parent organization: Stanford University; Stanford; California
NIAID ;
Comprehensive Cancer Center
Open SCR_008627, ABRF_200, nif-0000-31997, nif-0000-12246 https://coremarketplace.org/?FacilityID=200&citation=1 http://www.microarray.org/sfgf/ SCR_002050 Stanford Medicine Stanford Functional Genomics Facility, Stanford University Functional Genomics Core Facility, Stanford Functional Genomics Facility, Stanford Genomics, Stanford Genomics Service Center, Stanford School of Medicine Stanford Functional Genomics Facility 2026-08-10 09:31:36 11
Dataverse Network Project
 
Resource Report
Resource Website
10+ mentions
Dataverse Network Project (RRID:SCR_001997) Dataverse data or information resource, data repository, project portal, database, portal, service resource, catalog, storage service resource Project portal for publishing, citing, sharing and discovering research data. Software, protocols, and community connections for creating research data repositories that automate professional archival practices, guarantee long term preservation, and enable researchers to share, retain control of, and receive web visibility and formal academic citations for their data contributions. Researchers, data authors, publishers, data distributors, and affiliated institutions all receive appropriate credit. Hosts multiple dataverses. Each dataverse contains studies or collections of studies, and each study contains cataloging information that describes the data plus the actual data files and complementary files. Data related to social sciences, health, medicine, humanities or other sciences with an emphasis in human behavior are uploaded to the IQSS Dataverse Network (Harvard). You can create your own dataverse for free and start adding studies for your data files and complementary material (documents, software, etc). You may install your own Dataverse Network for your University or organization. data, repository, collection, publishing, citing, sharing, discovering, research, community, connection is used by: UCSF DataShare
is used by: Agri-environmental Research Data Repository
is used by: NIH Heal Project
is recommended by: NIDDK Information Network (dkNET)
is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases
is listed by: 3DVC
is listed by: re3data.org
is related to: PROMIS 2 MY Health
has parent organization: Harvard University; Cambridge; United States
is parent organization of: Universal Numerical Fingerprint
is parent organization of: Agri-environmental Research Data Repository
Alfred P. Sloan Foundation ;
NSF ;
Microsoft Research
Free, Available for download, Freely available r3d100010051, nif-0000-00316 https://doi.org/10.17616/R3C880 http://thedata.org/ SCR_001997 Harvard Dataverse, The Dataverse Project, Dataverse, Dataverse Network, Dataverse Network Project, Dataverse Project 2026-08-10 09:31:35 18
EarthChem
 
Resource Report
Resource Website
10+ mentions
EarthChem (RRID:SCR_002207) EarthChem data or information resource, data repository, database, service resource, storage service resource Accepts and makes available geochemical, geochronlogical, and petrological data (analytical and synthesis) through this community-driven effort to facilitate the preservation, discovery, access and visualization of data generated. * PetDB holds geochemical data from sub-oceanic igneous and metamorphic rocks generated at mid-ocean ridges including back-arc basins, young seamounts, and old oceanic crust. Data are compiled primarily from the published literature. * SedDB integrates marine and terrestrial sediment geochemical data compiled primarily from the published literature. * Deep Lithosphere Data Set contains geochemical and petrological data from lower crust and upper mantle xenoliths. (more info) * VentDB contains hydrothermal spring geochemistry that hosts and serves the full range of compositional data acquired on seafloor hydrothermal vents from all tectonic settings. * NAVDAT - The Western North American Volcanic and Intrusive Rock Database * Geochron is an application that helps with the onerous task of data management for geochronological and thermochronological studies. * EarthChemPortal is the one-stop-shop for geochemical data that gives users the ability to search federated databases PetDB, NAVDAT, and GEOROC simultaneously, integrated into a common output format. (more info) * The EarthChem Library is a repository for geochemical datasets (analytical data, experimental data, synthesis databases) and other digital resources relevant to the field of geochemistry, contributed by the geochemistry community. * SESAR - System for Earth SAmple Registration geochemical, geochronological, petrological is listed by: CINERGI
has parent organization: Columbia University; New York; USA
is parent organization of: VentDB
is parent organization of: PetDB
is parent organization of: SedDB
is parent organization of: System for Earth Sample Registration
NSF Free, Available for download, Freely available nlx_154721, r3d100011538 https://doi.org/10.17616/R3V644 SCR_002207 IEDA: EarthChem 2026-08-10 09:31:39 30
NormaCurve
 
Resource Report
Resource Website
1+ mentions
NormaCurve (RRID:SCR_001995) software application, software resource, data analysis software, data processing software Analysis methodology that allows simultaneous quantification and normalization of reverse phase protein array (RPPA) data. analysis, software, code, protein array, RPPA, reverse phase protein array, supplementary material is listed by: OMICtools
has parent organization: Curie Institute; Paris; France
PMID:22761696 Free, Available for download, Freely available OMICS_00814 SCR_001995 2026-08-10 09:31:35 9
MetPetDB
 
Resource Report
Resource Website
1+ mentions
MetPetDB (RRID:SCR_002208) MetPetDB data or information resource, data repository, database, service resource, storage service resource Database / data repository for metamorphic petrology that is being designed and built by a global community of metamorphic petrologists in collaboration with computer scientists at Rensselaer Polytechnic Institute as part of the National Cyberinfrastructure Initiative. metamorphic, petrology, geology, geochemistry is listed by: CINERGI
has parent organization: Rensselaer Polytechnic Institute; New York; USA
NSF EAR 0949318 THIS RESOURCE IS NO LONGER IN SERVICE nlx_154722, r3d100012514 SCR_002208 2026-08-10 09:31:39 1
Glomerular Activity Response Archive
 
Resource Report
Resource Website
10+ mentions
Glomerular Activity Response Archive (RRID:SCR_002089) GARA data or information resource, analysis service resource, production service resource, database, service resource, image collection, data analysis service THIS RESOURCE IS NO LONGER IN SERVICE, documented on April 24, 2017. Database of images depicting the spatial distribution of 2-deoxyglucose uptake evoked in the glomerular layer of the rat olfactory bulb in response to a wide range of defined odorant stimuli. A number of different display and comparison tools are provided allowing patterns to be viewed from different perspectives, and descriptions of the methods and interpretations of these data are provided. Some of the more advanced tools require you to download software. rat, olfactory bulb, odorant stimuli, odorant, odor, glomerular is used by: NIF Data Federation
is related to: Integrated Manually Extracted Annotation
has parent organization: University of California at Irvine; California; USA
Human Brain Project ;
NIMH ;
NIDCD
THIS RESOURCE IS NO LONGER IN SERVICE nif-0000-00339 SCR_002089 Glomerular Response Archive 2026-08-10 09:31:37 10
National Center for Marine Algae and Microbiota
 
Resource Report
Resource Website
50+ mentions
National Center for Marine Algae and Microbiota (RRID:SCR_002120) NCMA material resource, organism supplier, biomaterial supply resource National marine phytoplankton collection, maintaining over 2700 strains from around the world, most are marine phytoplankton but they also have benthic, macrophytic, freshwater and heterotrophic organisms - now incorporating bacteria and viruses. Strain records have (when available): * collection and isolation information * culturing medium recipes and growth conditions * photographs * GenBank accession link * collection site map * link to the taxonomic database Micro*scope The deposition of new strains are welcome if the strains are a valuable addition to the collection. Examples include strains that are referred to in publications, contain interesting molecular, biochemical or physiological properties, are the basis for taxonomic descriptions, are important for aquaculture, or are from an unusual geographical location or ecological habitat. The NCMA offers a course in phytoplankton culturing techniques and facilities for visiting scientists are available at the new laboratories in East Boothbay, Maine. Services include: Mass Culturing DNA and RNA, Purification, Private Holdings, Culture Techniques Course, Visiting Scientists, Single Cell Genomics, Flow Cytometry, Corporate Alliances and Technology Transfer. marine phytoplankton, marine, phytoplankton, virus, benthic, macrophytic, freshwater, heterotrophic, microbiota, seawater, FASEB list is listed by: One Mind Biospecimen Bank Listing
is listed by: CINERGI
NSF Restricted nlx_154729 SCR_002120 Provasoli-Guillard National Center for Culture of Marine Phytoplankton, Provasoli-Guillard National Center for Marine Algae and Microbiota, CCMP 2026-08-10 09:31:37 59
Protein Lounge
 
Resource Report
Resource Website
10+ mentions
Protein Lounge (RRID:SCR_002117) ProteinLounge data or information resource, training material, analysis service resource, production service resource, database, narrative resource, service resource, data analysis service Complete siRNA target database, complete Peptide-Antigen target database and a Kinase-Phosphatase database. They have also developed the largest database of illustrated signal transduction pathways, which are interconnected to their extensive protein database and online gene / protein analysis tools. The interactive web-based databases and software help life-scientists understand the complexity of systems biology. Systems biology efforts focus on understanding cellular networks, protein interactions involved in cell signaling, mechanisms of cell survival and apoptosis leading to development or identification of drug candidates against a variety of diseases. In the post-genomic era, one of the major concerns for life-science researchers is the organization of gene / protein data. Protein Lounge has met this concern by organizing all necessary data about genes / proteins into one portal. gene, antigen, bioinformatics, kinase, life science, peptide, phosphatase, signal transduction pathway, sirna, systems biology, protein, biology, cellular network, protein interaction, cell signaling, cell survival, apoptosis, peptide-antigen, kinase-phosphatase, image, pathway Restricted nif-0000-20903 SCR_002117 Protein Lounge - Redefining Biology 2026-08-10 09:31:37 31
Neotoma Paleoecology Database
 
Resource Report
Resource Website
10+ mentions
Neotoma Paleoecology Database (RRID:SCR_002190) Neotoma data or information resource, analysis service resource, data repository, production service resource, database, service resource, data analysis service, storage service resource Paleoecology database for plio-pleistocene to holocene fossil data with a centralized structure for interdisciplinary, multiproxy analyses and common tool development; discipline-specific data can also be easily accessed. Data currently include North American Pollen (NAPD) and fossil mammals (FAUNMAP). Other proxies (plant macrofossils, beetles, ostracodes, diatoms, etc.) and geographic areas (Europe, Latin America, etc.) will be added in the near future. Data are derived from sites from the last 5 million years. data sharing, paleoecology, plio-pleistocene, holocene, fossil is listed by: CINERGI
has parent organization: Pennsylvania State University
NSF Free, Available for download, Freely available nlx_154700, r3d100011761 SCR_002190 NeotomaDB, Neotoma DB 2026-08-10 09:31:39 38
SAMTOOLS
 
Resource Report
Resource Website
10000+ mentions
SAMTOOLS (RRID:SCR_002105) SAMtools data analysis software, software application, software toolkit, software resource, sequence analysis software, data processing software Original SAMTOOLS package has been split into three separate repositories including Samtools, BCFtools and HTSlib. Samtools for manipulating next generation sequencing data used for reading, writing, editing, indexing,viewing nucleotide alignments in SAM,BAM,CRAM format. BCFtools used for reading, writing BCF2,VCF, gVCF files and calling, filtering, summarising SNP and short indel sequence variants. HTSlib used for reading, writing high throughput sequencing data. Samtools, BCFtools, HTSlib, next generation sequencing, nucleotide alignments, sequence variant, genomic, c, perl, read, alignment, nucleotide, sequence, data, process, sam, bam, cram, vcf, bcf, bio.tools is used by: deFuse
is used by: Short Read Sequence Typing for Bacterial Pathogens
is used by: ROSE
is used by: Fcirc
is listed by: OMICtools
is listed by: Genetic Analysis Software
is listed by: SNVer
is listed by: Debian
is listed by: bio.tools
is listed by: SoftCite
is related to: Platypus
is related to: shovill
is related to: pysam
has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom
is parent organization of: SAMtools/BCFtools
is required by: RelocaTE
is required by: Wessim
is required by: SL-quant
is required by: smMIPfil
Wellcome Trust ;
NHGRI U54 HG002750
PMID:19505943
PMID:21903627
DOI:10.1093/bioinformatics/btp352
Free, Available for download, Freely available SCR_018682, biotools:samtools, OMICS_01074, nlx_154607, OMICS_00090 https://github.com/samtools/samtools, https://github.com/samtools/htslib, https://bio.tools/samtools, https://sources.debian.org/src/samtools/ http://samtools.sourceforge.net/ SCR_002105 samtools, Samtools, Sequence Alignment Map TOOLS, SAMtools, SAM tools 2026-08-10 09:31:37 33299
Concierge
 
Resource Report
Resource Website
10+ mentions
Concierge (RRID:SCR_002386) Concierge software application, data management software, software resource A data management tool which stores, classifies and manages digital resources such as publications, experimental data, presentation files, etc, together with its metadata. A key feature of the software is a high level of extensibility. By installing optional plug-ins, users can customize and extend the usability of the software based on their needs. It has a function of sharing data with open digital archives based on the XooNIps system, such as neuroinformatics platforms in operation and publicly available at J-Node (http://www.neuroinf.jp). The Concierge Project is a part of neuroinformatics research by Laboratory for Neuroinformatics in RIKEN Brain Science Institute. Concierge's primary goal is to encourage research resource sharing in neuroscience communities. A key feature of the software is its pluggable configuration. Based on the basic functions, various applications can be developed as plug-ins. It has already developed several application plug-ins specific to neuroscience research, e.g. literature manager, electronic laboratory notebook, etc. literature manager, labnote, electronic laboratory notebook, plug-in, resource management, resource sharing is related to: XooNIps - Neuroinformatics Base Platform System
has parent organization: RIKEN Brain Science Institute
PMID:18974800 Open unspecified license; Mac OS X and Windows XP versions nif-0000-00379 SCR_002386 Concierge: Personal Database Software for Managing Digital Research Resources, Concierge Project, Concierge: Personal Database Software for Digital Research Resources, The Concierge Project: Personal Database Software for Digital Research Resources 2026-08-10 09:31:43 12
NCI Mouse Repository
 
Resource Report
Resource Website
10+ mentions
NCI Mouse Repository (RRID:SCR_002264) NCIMR material resource, organism supplier, biomaterial supply resource The NCI Mouse Repository cryoarchives and distributes strains of genetically engineered mice that are of immediate interest to the cancer research community. These are either gene-targeted or transgenic mice that display a cancer-related phenotype, or tool strains (e.g., cre transgenics) that can be used to develop new cancer models. You do not have to be a member of the NCI Mouse Repository or a recipient of NCI funding to have your mouse model distributed through the NCI Mouse Repository. NCI Mouse Repository strains are maintained as live colonies or cryoarchived as frozen embryos, depending on demand. Up to three breeder pairs may be ordered from live colonies. Cryoarchived strains are supplied as frozen embryos or recovery of live mice by the NCI Mouse Repository may be requested. embryo, engineered, frozen, gene, genetically, breed, breeder, cancer, colony, cryoarchive, human, live, model, mouse model, phenotype, strain, transgenic, mutant, female, male is listed by: One Mind Biospecimen Bank Listing
has parent organization: NCI-Frederick
NCI Free, Freely available nif-0000-20985 http://mouse.ncifcrf.gov/ SCR_002264 MMHCC, MMHCC Repository, Mouse Models of Human Cancers Consortium (MMHCC) Repository, Mouse Models of Human Cancers Consortium Repository 2026-08-10 09:31:40 19
Cancer Genomics Consortium
 
Resource Report
Resource Website
1+ mentions
Cancer Genomics Consortium (RRID:SCR_002384) CGC data or information resource, organization portal, community building portal, portal Consortium promoting communication and collaboration among cancer cytogenomics laboratories, who are interested in applying microarray technologies to cancer diagnosis and cancer research. Their oals are to (1) establish platform-neutral and cancer specific microarray designs for diagnostic purposes, (2) share cancer microarray data between participating institutions for education purposes, (3) create a public cancer array database, and (4) carry out multicenter cancer genome translational research. Collaboration amongst the different laboratories and researchers will not only provide validation for the microarray design(s) but ultimately provide more comprehensive molecular information and more accurate interpretation to better serve cancer patients and further cancer research. The CGC was officially incorporated in June 2010 as a not-for-profit organization. cytogenetics, molecular genetics, molecular pathology, microarray technology, cancer diagnosis, cancer research, microarry, cytogenomics, cancer cytogenomics, cancer genetics, genetics is listed by: OMICtools Cancer Membership fee, Account required OMICS_01776 SCR_002384 CCMC, Cancer Cytogenomics Microarray Consortium 2026-08-10 09:31:42 6
dbMHC
 
Resource Report
Resource Website
10+ mentions
dbMHC (RRID:SCR_002302) dbMHC data or information resource, data repository, database, service resource, storage service resource THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 23, 2019 Database was open, publicly accessible platform for DNA and clinical data related to human Major Histocompatibility Complex (MHC). Data from IHWG workshops were provided as well., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. human leukocyte antigen, microsatellite, dna, clinical, major histocompatibility complex, primer, probe, sequence, allele, haplotype, sequence, histocompatibility, leucocyte, alignment is listed by: re3data.org
is related to: NIDDK Information Network (dkNET)
is related to: IMGT/HLA
has parent organization: NCBI
PMID:14705985 Free, Available for download, Freely available nif-0000-02729, r3d100010881 https://doi.org/10.17616/R37W4F http://www.ncbi.nlm.nih.gov/gv/mhc/main.cgi?cmd=init SCR_002302 Major Histocompatibility Complex Database 2026-08-10 09:31:41 22
GeneNetwork
 
Resource Report
Resource Website
100+ mentions
GeneNetwork (RRID:SCR_002388) GeneNetwork, WebQTL data or information resource, data repository, database, service resource, storage service resource Web platform that provides access to data and tools to study complex networks of genes, molecules, and higher order gene function and phenotypes. Sequence data (SNPs) and transcriptome data sets (expression genetic or eQTL data sets). Quantitative trait locus (QTL) mapping module that is built into GN is optimized for fast on-line analysis of traits that are controlled by combinations of gene variants and environmental factors. Used to study humans, mice (BXD, AXB, LXS, etc.), rats (HXB), Drosophila, and plant species (barley and Arabidopsis). Users are welcome to enter their own private data. Variation, trait, vertebrate trait ontology, phenotype, systems genetics, quantitative trait, gene mapping, experimental precision medicinenetwork analysis, causal modeling, genomic location, genotype, inbred strain, sex, heterogeneous stock, phenome, phenotype, QTL, expression QTL, genetic reference population, single nucleotide polymorphism, RNA expression, protein expression, metabolite expression, metagenomics, epigenomics, gene-by-environmental interaction, epistasis, FAIR data standards, open source software, FASEB list is used by: NIF Data Federation
is used by: Hypothesis Center
is related to: NIH Data Sharing Repositories
has parent organization: University of Tennessee Health Science Center; Tennessee; USA
NIGMS R01 GM123489;
NIAAA U01 AA016662;
NIAAA U01 AA13499;
NIAAA U24 AA13513;
NIAAA U01 AA014425;
NIA R01 AG043930;
NIDA P20 DA21131;
NCI U01 CA105417;
NCRR U24 RR021760
PMID:8043953
PMID:11737945
PMID:15043217
PMID:15114364
PMID:15043220
PMID:15043219
PMID:15711545
PMID:18368372
PMID:27933521
Restricted nif-0000-00380 SCR_002388 GeneNetwork and WebQTL, GeneNetwork / WebQTL, www.genenetwork.org, GeneNetwork WebQTL, The GeneNetwork / WebQTL 2026-08-10 09:31:42 499
Clinical and Laboratory Standards Institute
 
Resource Report
Resource Website
100+ mentions
Clinical and Laboratory Standards Institute (RRID:SCR_002382) CLSI data or information resource, knowledge environment, narrative resource, standard specification A not-for-profit membership organization that brings together the global laboratory community to foster excellence in laboratory medicine by facilitating the development of clinical laboratory testing standards based on input from and consensus among industry, government, and health care professionals. CLSI is setting the standard for quality in clinical laboratory testing around the world. clinical, laboratory testing, quality, clinical laboratory testing standard, laboratory, testing is listed by: OMICtools Membership fee OMICS_01777 SCR_002382 2026-08-10 09:31:42 195
Neuroscience Course - Atlas Images
 
Resource Report
Resource Website
1+ mentions
Neuroscience Course - Atlas Images (RRID:SCR_002381) data or information resource, training resource, portal Online educational resource for human brain and spinal cord anatomy through images. Each image is annotated with major structures and coarse dissections. anatomy atlas, brain dissection, spinal cord dissection has parent organization: University of Arkansas; Arkansas; USA Public, Unauthorized use is prohibited nif-0000-00117 SCR_002381 Neuroscience Course Atlas Images 2026-08-10 09:31:42 7
Quick-R
 
Resource Report
Resource Website
1+ mentions
Quick-R (RRID:SCR_002417) Quick-R data or information resource, training material, book, narrative resource Training material created for both current R users, and experienced users of other statistical packages (e.g., SAS, SPSS, Stata) who would like to transition to R to help you quickly access this language in your work. The book inspired by this site takes the material here and significantly expands upon it. r, programming language, code is listed by: OMICtools Free, Available for download, Freely available OMICS_01760 SCR_002417 Quick-R - accessing the power of R 2026-08-10 09:31:43 5
realSFS
 
Resource Report
Resource Website
10+ mentions
realSFS (RRID:SCR_002493) software application, software resource, data analysis software, data processing software Software program used to estimate allele frequency and SNP calling., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. allele frequency estimation, snp calling is listed by: OMICtools THIS RESOURCE IS NO LONGER IN SERVICE OMICS_00071 SCR_002493 2026-08-10 09:31:44 27

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