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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
HeadIT
 
Resource Report
Resource Website
1+ mentions
HeadIT (RRID:SCR_005657) HeadIT data or information resource, data repository, data set, service resource, storage service resource Platform for sharing, download, and re-analysis or meta-analysis of sophisticated, fully annotated, human electrophysiological data sets. It uses EEG Study Schema (ESS) files to provide task, data collection, and subject metadata, including Hierarchical Event Descriptor (HED) tag descriptions of all identified experimental events. Visospatial task data also available from, http://sccn.ucsd.edu/eeglab/data/headit.html: A 238-channel, single-subject EEG data set recorded at the Swartz Center, UCSD, by Arnaud Delorme, Julie Onton, and Scott Makeig is al. electrophysiology, data sharing, eeg, visual-auditory cued attention shift paradigm, adult, early adult human, late adult human, memory task, modified sternberg working memory task, visual, auditory, auditory oddball, memory, task uses: HED Tags
is related to: EEGLAB
has parent organization: University of California at San Diego; California; USA
Normal, Healthy, Others possible NIMH R01-MH084819;
NINDS R01-NS047293
Public, Must agree to Data Use Agreement and Terms of Use., Account required for collaboration and to upload data. nlx_149081 http://headit-beta.ucsd.edu/, http://sccn.ucsd.edu/eeglab/data/headit.html http://HeadIT.org SCR_005657 SciCrunch Registry Human Electrophysiology Anatomic Data & Integrated Tools (HeadIT) Resource, Human Electrophysiology Anatomic Data & Integrated Tools Resource, Human Electrophysiology Anatomic Data & Integrated Tools, Human Electrophysiology Anatomic Data and Integrated Tools (HeadIT) Resource 2026-10-24 12:45:30 5
DiProGB
 
Resource Report
Resource Website
1+ mentions
DiProGB (RRID:SCR_005651) DiProGB software resource Genome browser that encodes the genome sequence by physico-chemical dinucleotide properties such as stacking energy, melting temperature or twist angle. Analyses can be performed for the + and ?, as well as for the double strand. genome, browser, bio.tools is listed by: OMICtools
is listed by: bio.tools
is listed by: Debian
is related to: Dinucleotide Property Database
PMID:19605418 Free, Freely available biotools:diprogb, OMICS_00880 https://bio.tools/diprogb SCR_005651 SciCrunch Registry DiProGB - The Dinucleotide Properties Genome Browser, Dinucleotide Properties Genome Browser 2026-10-24 12:45:30 4
MagicViewer
 
Resource Report
Resource Website
10+ mentions
MagicViewer (RRID:SCR_005648) MagicViewer software resource Software to easily visualize the short reads alignment, identify the genetic variation and associate with the annotation information of reference genome. MagicViewer provides a user-friendly interface in which large-scale short reads and sequencing depth can be easily visualized in zoomable images under user definable color scheme through an operating system-independent manner with the implement of Java language. Meanwhile, it holds a versatile genetic variation annotation and visualization interface, providing details of the query options, functional classifications, subset selection, sequence association and primer design. dna methylation, bisulfite sequencing is listed by: OMICtools
has parent organization: Wenzhou Medical University; Zhejiang; China
PMID:20444865 Free, Public OMICS_00887 SCR_005648 SciCrunch Registry MagicViewer: Integrated Solution for Next-generation Sequencing Data Visualization and Genetic Variation Detection and Annotation 2026-10-24 12:45:30 16
Bambino
 
Resource Report
Resource Website
1+ mentions
Bambino (RRID:SCR_005649) Bambino analysis service resource, data analysis service, production service resource, service resource, software resource A variant detector and graphical alignment viewer for next-generation sequencing data in the SAM/BAM format, which is capable of pooling data from multiple source files. Bambino may be launched online via Java Web Start or downloaded and run locally. java, next-generation sequencing, bio.tools is listed by: OMICtools
is listed by: Debian
is listed by: bio.tools
has parent organization: National Cancer Institute
PMID:21278191 Https://cgwb.nci.nih.gov/goldenPath/bamview/documentation/Bambino_Click-thru-agreement-for-executable_final.txt OMICS_00876, biotools:bambino https://bio.tools/bambino SCR_005649 SciCrunch Registry Bambino: a variant detector and alignment viewer for next-generation sequencing data in the SAM/BAM format 2026-10-24 12:45:30 5
MATRICS - Measurement And Treatment Research to Improve Cognition in Schizophrenia
 
Resource Report
Resource Website
1+ mentions
MATRICS - Measurement And Treatment Research to Improve Cognition in Schizophrenia (RRID:SCR_005644) MATRICS knowledge environment Cognitive deficits -- including impairments in areas such as memory, attention, and executive function -- are a major determinant and predictor of long-term disability in schizophrenia. Unfortunately, available antipsychotic medications are relatively ineffective in improving cognition. Scientific discoveries during the past decade suggest that there may be opportunities for developing medications that will be effective for improving cognition in schizophrenia. The NIMH has identified obstacles that are likely to interfere with the development of pharmacological agents for treating cognition in schizophrenia. These include: (1) a lack of a consensus as to how cognition in schizophrenia should be measured; (2) differing opinions as to the pharmacological approaches that are most promising; (3) challenges in clinical trial design; (4) concerns in the pharmaceutical industry regarding the US Food and Drug Administration''s (FDA) approaches to drug approval for this indication; and (5) issues in developing a research infrastructure that can carry out clinical trials of promising drugs. The MATRICS program will bring together representatives of academia, industry, and government in a consensus process for addressing all of these obstacles. Specific goals of the NIMH MATRICS are: * To catalyze regulatory acceptance of cognition in schizophrenia as a target for drug registration. * To promote development of novel compounds to enhance cognition in schizophrenia. * Leverage economic research power of industry to focus on important but neglected clinical targets. * Identify lead compounds and if deemed feasible, support human proof of concept trials for cognition in schizophrenia. schizophrenia, cognitive deficit, memory, attention, executive function, disability, cognition, clinical has parent organization: University of California at Los Angeles; California; USA Schizophrenia NIMH nlx_146271 SCR_005644 SciCrunch Registry Measurement And Treatment Research to Improve Cognition in Schizophrenia, Measurement Treatment Research to Improve Cognition in Schizophrenia 2026-10-24 12:45:30 6
WISECONDOR
 
Resource Report
Resource Website
10+ mentions
WISECONDOR (RRID:SCR_005646) WISECONDOR software resource A set of python scripts that detects fetal chromosomal and subchromosomal duplications and deletions in maternal blood samples., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. is listed by: OMICtools
has parent organization: Netherlands Bioinformatics Centre
THIS RESOURCE IS NO LONGER IN SERVICE OMICS_00354 SCR_005646 SciCrunch Registry WIthin-SamplE COpy Number aberration DetectOR 2026-10-24 12:45:30 12
TRANSPATH
 
Resource Report
Resource Website
1+ mentions
TRANSPATH (RRID:SCR_005640) TRANSPATH analysis service resource, data analysis service, data or information resource, database, production service resource, service resource Database on eukaryotic transcription factors, their experimentally-proven binding sites, consensus binding sequences (positional weight matrices) and regulated genes. Its broad compilation of binding sites allows the derivation of positional weight matrices. It can either be used as an encyclopedia, for both specific and general information on signal transduction, or can serve as a network analyzer. Cross-references to important sequence and signature databases such as EMBL/GenBank UniProt/Swiss-Prot InterPro or Ensembl EntrezGene RefSeq are provided. The database is equipped with the tools for data visualization and analysis. It has three modules: the first one is the data, which have been manually extracted, mostly from the primary literature; the second is PathwayBuilder, which provides several different types of network visualization and hence facilitates understanding; the third is ArrayAnalyzer, which is particularly suited to gene expression array interpretation, and is able to identify key molecules within signalling networks (potential drug targets). These key molecules could be responsible for the coordinated regulation of downstream events. Manual data extraction focuses on direct reactions between signalling molecules and the experimental evidence for them, including species of genes/proteins used in individual experiments, experimental systems, materials and methods. This combination of materials and methods is used in TRANSPATH to assign a quality value to each experimentally proven reaction, which reflects the probability that this reaction would happen under physiological conditions. Another important feature in TRANSPATH is the inclusion of transcription factor-gene relations, which are transferred from TRANSFAC, a database focused on transcription regulation and transcription factors. Since interactions between molecules are mainly direct, this allows a complete and stepwise pathway reconstruction from ligands to regulated genes. signal transduction, network analyzer, transcriptional regulator, transcription factor, metabolic pathway, signaling pathway, protein-protein interaction, gene-regulatory pathway, signal transduction pathway, complex, signaling molecule, reaction, molecule, gene, pathway, gene expression is related to: TRANSFAC
is related to: GeneTrail
has parent organization: BIOBASE Corporation
BMBF 031U210B;
BMBF 0313092;
European Union FP6 contract LSHG-CT-2004-503568;
European Union MRTN-CT-2004-512285
PMID:18629064
PMID:16381929
PMID:12519957
PMID:11724734
Free for academic use, Free for non-profit use, Account required nif-0000-03580 http://transpath.gbf.de, http://www.gene-regulation.com/pub/databases.html, http://www.biobase.de/pages/products/databases.html SCR_005640 SciCrunch Registry 2026-10-24 12:45:30 3
BS Seeker
 
Resource Report
Resource Website
1+ mentions
BS Seeker (RRID:SCR_005641) data analysis software, data processing software, sequence analysis software, software application, software resource Software which performs accurate and fast mapping of bisulfite-treated short reads. Supplementary information and examples are provided on the site. bisulfite sequencing, sequence analysis software, short read, sequence mapping, bio.tools uses: Bowtie
is listed by: OMICtools
is listed by: bio.tools
is listed by: Debian
is related to: Bs-Seeker2
has parent organization: University of California at Los Angeles; California; USA
PMID:20416082 Free, Available for download, Freely available OMICS_00578, biotools:bs_seeker https://bio.tools/bs_seeker SCR_005641 SciCrunch Registry Bisulfite Sequence Seeker 2026-10-24 12:45:30 3
MRI Research Safety and Ethics
 
Resource Report
Resource Website
MRI Research Safety and Ethics (RRID:SCR_005642) MRI Research Safety and Ethics data or information resource, narrative resource, standard specification NIMH recognizes the need to consider safety and ethical issues related to both the administration of MR (magnetic resonance) facilities and the use of these facilities for research. This document summarizes the points to consider discussed by the National Advisory Mental Health Council (NAMHC) Workgroup. Examples of safe and ethical practices are discussed in relation to several issues. These examples are intended to be illustrative and should not be interpreted as an exhaustive or exclusive list. This document was presented to the full NIMH Council on September 15, 2006 and approved unanimously. By making the points to consider document available publicly, NIMH intends to provide a resource for researchers and institutions that use MRI in research. The agenda was organized into six topics, which provide the organization for the points to consider that follow: A. MRI screening B. Training, operating, and emergency procedures C. Physical facilities D. Scanning/participant health variables E. Context- Specific Considerations: University vs. medical settings F. Additional data needs and updating The NIMH believes that investigators, institutions and facilities can use this document as a resource for the development, administration, evaluation, and use of MRI research facilities. mri, research, neuroscience, imaging has parent organization: National Institute of Mental Health NIMH nlx_146267 SCR_005642 SciCrunch Registry MRI Research Safety and Ethics: Points to Consider, MRI Research Safety Ethics 2026-10-24 12:45:30 0
Internet Analysis Tools Registry
 
Resource Report
Resource Website
1+ mentions
Internet Analysis Tools Registry (RRID:SCR_005638) IATR data processing software, image analysis software, software application, software repository, software resource A centrally available listing of all image analysis tools that are available to the neuroscience community in order to facilitate the development, identification, and sharing of tools. It is hoped that this helps the tool developers to get their tools to a larger user community and to reduce redundancy (or at least utilize tool redundancy to facilitate optimal tool design) in tool development. This also helps tool users in identification of the existing tools for specific problems as they arise. The registry is designed to be self-moderated. This means that all tool entries are owned by some responsible party who enters the tool information, and keeps it up to date via the Web. database, tool, neuroimaging, image, analysis lists: Extensible MATLAB Medical image Analysis
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC)
has parent organization: Harvard Medical School; Massachusetts; USA
Human Brain Project Public Domain nlx_146252 SCR_005638 SciCrunch Registry IATR - Internet Analysis Tools Registry 2026-10-24 12:45:29 1
Hunan Normal University; Changsha; China
 
Resource Report
Resource Website
Hunan Normal University; Changsha; China (RRID:SCR_005639) university University founded in 1938, is a higher education institution in Changsha, Hunan Province. The university is a national 211 Project university, one of 100 key universities in the 21st century that enjoy priority in obtaining national funds. is parent organization of: Animal Toxin Database nlx_79811 http://www.hunnu.edu.cn/english/ SCR_005639 SciCrunch Registry Hunan Normal University 2026-10-24 12:45:30 0
COBrA
 
Resource Report
Resource Website
1000+ mentions
COBrA (RRID:SCR_005677) COBrA software resource COBrA is a Java-based ontology editor for bio-ontologies that distinguishes itself from other editors by supporting the linking of concepts between two ontologies, and providing sophisticated analysis and verification functions. In addition to the Gene Ontology and Open Biology Ontologies formats, COBrA can import and export ontologies in the Semantic Web formats RDF, RDFS and OWL. Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible, THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. ontology, anatomy, browser, ontology or annotation browser is listed by: Gene Ontology Tools
is related to: Gene Ontology
is related to: OBO
has parent organization: University of Edinburgh; Scotland; United Kingdom
BBSRC 15/BEP 17046 PMID:15513995 THIS RESOURCE IS NO LONGER IN SERVICE nlx_149117 SCR_005677 SciCrunch Registry COBrA - An Ontology Browser for Anatomy, COBrA: a bio-ontology editor 2026-10-24 12:45:30 1396
Roth Laboratory
 
Resource Report
Resource Website
1+ mentions
Roth Laboratory (RRID:SCR_005711) Roth Lab data or information resource, laboratory portal, organization portal, portal, software resource The Roth Laboratory is designing and interpreting large-scale experiments to understand pathway structure and its relationship to phenotype and human disease. Software for research focused on a specific research goal is available. Current experimental interests: * Exploiting parallel sequencing technology to phenotype all pairwise gene deletion combinations in S. cerevisiae, with initial application to genes involved in transcription. * Generation of S. cerevisiae strains carrying dozens of chosen targeted deletions, with initial application to delete all ABC transporters imparting multidrug resistance. * Targeted insertion of gene sets encoding entire human pathways into S. cerevisiae, with initial application to genes involved in drug metabolism. Current computational interests: * Systematic analysis of genetic interaction to reveal redundant systems and order of action in genetic pathways * Integrating large-scale studies - including phenotype, genetic epistasis, protein-protein and transcription-regulatory interactions and sequence patterns - to quantitatively assign function to genes and guide experimentation and disease association studies. * Alternative splicing and its relationship to protein interaction networks. gene, pathway, phenotype, disease, transcription, drug metabolism, drug, metabolism, protein-protein interaction, transcription-regulatory interaction, protein interaction, protein has parent organization: University of Toronto; Ontario; Canada
has parent organization: Harvard Medical School; Massachusetts; USA
is parent organization of: FuncAssociate: The Gene Set Functionator
nlx_149163 http://llama.med.harvard.edu SCR_005711 SciCrunch Registry 2026-10-24 12:45:31 5
netClass
 
Resource Report
Resource Website
netClass (RRID:SCR_005672) netClass software resource An R package for network-based feature (gene) selection for biomarkers discovery via integrating biological information. The package adapts the following 5 algorithms for classifying and predicting gene expression data using prior knowledge: # average gene expression of pathway (aep); # pathway activities classification (PAC); # Hub network classification (hubc); # filter via top ranked genes (FrSVM); # network smoothed t-statistic (stSVM). protein-protein interaction network, biomarker discovery, classification, micoarray, gene expression profile, protein-protein interaction, gene expression, gene, biomarker is listed by: OMICtools
has parent organization: SourceForge
PMID:24443376 Free, Public OMICS_02241 SCR_005672 SciCrunch Registry 2026-10-24 12:45:30 0
University of Pacific; California; USA
 
Resource Report
Resource Website
University of Pacific; California; USA (RRID:SCR_005706) university Private Methodist affiliated university with its main campus in Stockton, California, and graduate campuses in San Francisco and Sacramento. is parent organization of: University of the Pacific School of Pharmacy and Health Sciences nlx_70007 SCR_005706 SciCrunch Registry 2026-10-24 12:45:31 0
GUMC Department of Biostatistics Bioinformatics and Biomathematics - Liu Lab
 
Resource Report
Resource Website
GUMC Department of Biostatistics Bioinformatics and Biomathematics - Liu Lab (RRID:SCR_005708) GUMC Liu Lab data or information resource, laboratory portal, organization portal, portal THIS RESOURCE IS NO LONGER IN SERVCE, documented September 2, 2016. microarray, data mining, natural language processing, biomedical, ontology, biomedicine, data analysis, dna microarray, gene THIS RESOURCE IS NO LONGER IN SERVICE nlx_149157 SCR_005708 SciCrunch Registry Georgetown University Medical Center Department of Biostatistics Bioinformatics and Biomathematics - Liu Lab, Georgetown University Medical Center Liu Lab, GUMC Department of Biostatistics Bioinformatics Biomathematics - Liu Lab 2026-10-24 12:45:31 0
GeneMANIA
 
Resource Report
Resource Website
1000+ mentions
GeneMANIA (RRID:SCR_005709) GeneMANIA analysis service resource, data analysis service, data or information resource, database, production service resource, service resource, software resource Data analysis service to predict the function of your favorite genes and gene sets. Indexing 1,421 association networks containing 266,984,699 interactions mapped to 155,238 genes from 7 organisms. GeneMANIA interaction networks are available for download in plain text format. GeneMANIA finds other genes that are related to a set of input genes, using a very large set of functional association data. Association data include protein and genetic interactions, pathways, co-expression, co-localization and protein domain similarity. You can use GeneMANIA to find new members of a pathway or complex, find additional genes you may have missed in your screen or find new genes with a specific function, such as protein kinases. Your question is defined by the set of genes you input. If members of your gene list make up a protein complex, GeneMANIA will return more potential members of the protein complex. If you enter a gene list, GeneMANIA will return connections between your genes, within the selected datasets. GeneMANIA suggests annotations for genes based on Gene Ontology term enrichment of highly interacting genes with the gene of interest. GeneMANIA is also a gene recommendation system. GeneMANIA is also accessible via a Cytoscape plugin, designed for power users. Platform: Online tool, Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible gene, association data, protein interaction, genetic interaction, pathway, co-expression, co-localization, protein, software library, statistical analysis, term enrichment, analysis, browser, gene ontology, gene predicting, gene prioritization, database or data warehouse, other analysis, interaction browser, protein-protein interaction, interaction, FASEB list is listed by: Gene Ontology Tools
is related to: Cytoscape
is related to: Gene Ontology
is related to: PSICQUIC Registry
has parent organization: University of Toronto; Ontario; Canada
Genome Canada ;
Ontario Ministry of Research and Innovation 2007-OGI-TD-05
PMID:20576703
PMID:18613948
PMID:20926419
Open unspecified license, Free for academic use nlx_149159, r3d100013978 https://doi.org/10.17616/R31NJNA2 SCR_005709 SciCrunch Registry 2026-10-24 12:45:31 4535
DMRforPairs
 
Resource Report
Resource Website
1+ mentions
DMRforPairs (RRID:SCR_005702) software resource Software for identifying differentially methylated regions between unique samples using array based methylation profiles. It allows researchers to compare n greater than or equal to 2 unique samples with regard to their methylation profile. The (pairwise) comparison of n unique single samples distinguishesit from other existing pipelines as these often compare groups of samples in either single CpG locus or region based analysis. DMRforPairs defines regions of interest as genomic ranges with sufficient probes located in close proximity to each other. Probes in one region are optionally annotated to the same functional class(es). Differential methylation is evaluated by comparing the methylation values within each region between individual samples and (if the difference is sufficiently large), testing this difference formally for statistical significance. standalone software, mac os x, unix/linux, windows, r, annotation, dna methylation, differential methylation, microarray, report writing, visualization, bio.tools is listed by: OMICtools
is listed by: Debian
is listed by: bio.tools
has parent organization: Bioconductor
PMID:24884391 GNU General Public License, v2 or greater biotools:dmrforpairs, OMICS_04059 https://bio.tools/dmrforpairs SCR_005702 SciCrunch Registry DMR2+, DMRforPairs: identifying Differentially Methylated Regions between unique samples using array based methylation profiles 2026-10-24 12:45:31 4
Research at Cincinnati Childrens
 
Resource Report
Resource Website
Research at Cincinnati Childrens (RRID:SCR_005703) Research at Cincinnati Children's data or information resource, organization portal, portal, service resource, training resource, training service resource Foundation scientists and physicians conduct breakthrough research to improve care for children as well as train the next generation of investigators. Cincinnati Children's Research Foundation is dedicated to advancing basic, translational, clinical and outcomes-based research. Why choose our cores for your research? We can provide you with cutting-edge, cost-effective technology and data analysis that would be unattainable on an individual research basis. Our fee-for-service program also offers unique studies that you can't find anywhere else. Our faculty also has access to the research cores hosted at the University of Cincinnati College of Medicine. * Animal Behavioral Core * Cardiovascular Imaging Core * Cell Manipulations Laboratory * Cell Processing Core * Cincinnati Biobank * Cincinnati Center for Nutritional Research and Analysis * Comprehensive Mouse and Cancer Core * Gene Expression Microarray Core * Genetic Variation and Gene Discovery Core * Imaging Research Center * Laser Capture Microdissection Microscopy * Lenti-shRNA Library Core * Pathology Research Core * Pluripotent Stem Cell Facility * Research Flow Cytometry Core * Stem Cell Processing Core Lab * Transgenic and Gene Targeting Core * Translational Core Labs * Translational Trials Development and Support Laboratory (TTDSL) * Vector Production Facility * Veterinary Services * Viral Vector Core Support Services: We provide expert consultation, including grant proposal design, data management and regulatory compliance, to investigators at Cincinnati Children's. Research Education and Training: The Cincinnati Children's Research Foundation offers research-based education and training options for scientists, often in conjunction with the University of Cincinnati. High School Programs, Undergraduate Programs, Graduate Degree Programs, Medical Student Program, Postgraduate Programs, Postdoctoral Programs pediatric, child, young human nlx_149152 SCR_005703 SciCrunch Registry Cincinnati Children's Research Foundation 2026-10-24 12:45:31 0
University of Barcelona Statistics and Bioinformatics Research Group
 
Resource Report
Resource Website
University of Barcelona Statistics and Bioinformatics Research Group (RRID:SCR_005704) UB Statistics and Bioinformatics Research Group analysis service resource, data analysis service, data or information resource, portal, production service resource, service resource, topical portal The Statistics and Bioinformatics research group has as its main objectives the development of methods and tools to deal with problems appearing in the interface between Statistics and Bioinformatics. We started focusing in DNA microarrays but we are also interested in statistical methods for ''omics'' data integration and next generation sequencing (NGS). Our group collaborates with different research groups in the fields of biology and biomedicine, to whom it offers statistical support for problems which are specifically statistic in nature, such as experimental design or microarray data analysis, and also in more general aspects, such as modeling, analysis or data mining. After a first period of collaboration agreements with the Fundaci�� Vall d''Hebr��n Institut de Recerca we contributed to the creation of the Statistics and Bioinformatics Unit (UEB) which provides statistical and bioinformatical support to VHIR researchers. statistics, bioinformatics, next generation sequencing, dna microarray, dna, microarray, biology, biomedicine, data mining, modeling, analysis has parent organization: University of Barcelona; Barcelona; Spain nlx_149154 SCR_005704 SciCrunch Registry University of Barcelona Statistics Bioinformatics Research Group 2026-10-24 12:45:31 0

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