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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
GeneScissors
 
Resource Report
Resource Website
1+ mentions
GeneScissors (RRID:SCR_003146) data analysis software, data processing software, sequence analysis software, software application, software resource Software for detecting and correcting spurious transcriptome inference due to RNAseq reads misalignment. transcriptome inference, read misalignment, rna seq is listed by: OMICtools
has parent organization: University of North Carolina at Chapel Hill; North Carolina; USA
works with: Cufflinks
works with: TopHat
PMID:23812996 Free, Available for download, Freely available OMICS_01232 SCR_003146 Gene Scissors 2026-08-29 11:21:26 2
nematodes.org
 
Resource Report
Resource Website
10+ mentions
nematodes.org (RRID:SCR_003267) nematodes.org data or information resource, organism-related portal, portal, topical portal Nematode & Neglected Genomics (at) The Blaxter Lab is a nematode related portal including databases and services. Resources include genomic and transcriptomic databases for nematodes and other metazoan phyla and freely downloadable software tools for expressed sequence tag analysis, DNA barcode analysis and phylogenomics. Major categories include: * GenePool * 959 Nematode Genomes * Teaching * Research Projects * Bioinformatics Software Tools * Lab Personnel * Lab Wiki * Genomics Databases * NEMBASE4 * Tardigrada: Hypsibius dujardini * Earthworm: Lumbricus rubellus * MolluscDB * ArthropodDB * other Neglected Genomes nematode, genomics, genome, gene, database, transcriptome, analysis tool, bioinformatics, genomics databases, software, expressed sequence tag, analysis, dna barcode, phylogenomics, FASEB list has parent organization: University of Edinburgh; Scotland; United Kingdom
is parent organization of: 959 Nematode Genomes
is parent organization of: MolluscDB PartiGene database
is parent organization of: NEMBASE
is parent organization of: PartiGene ARTHROPODA Database
is parent organization of: Bombus terrestris PartiGene Database
THIS RESOURCE IS NO LONGER IN SERVICE nif-0000-03187 SCR_003267 Nematode & Neglected Genomics (at) The Blaxter Lab, Blaxter Lab, Nematode and Neglected Genomics, nematodes.org Nematode & Neglected Genomics (at) The Blaxter Lab, Nematode & Neglected Genomics 2026-08-29 11:21:27 31
Biological Collections Ontology
 
Resource Report
Resource Website
Biological Collections Ontology (RRID:SCR_003262) BCO controlled vocabulary, data or information resource, ontology Ontology developed as an application ontology as part of the Biocode Commons project whose goal is to support the interoperability of biodiversity data, including data on museum collections, environmental and metagenomic samples, and ecological surveys. It includes consideration of the distinctions between individuals, organisms, voucher specimens, lots, and samples the relations between these entities, and processes governing the creation and use of samples. Within scope as well are properties including collector, location, time, storage environment, containers, institution, and collection identifiers. owl, interoperability, biodiversity, museum collection, environmental sample, metagenomic sample, ecological survey is listed by: BioPortal
is listed by: OBO
is listed by: Google Code
is related to: Information Artifact Ontology
PMID:24595056 Free, Available for download, Freely available nlx_157333 http://purl.obolibrary.org/obo/bco.owl, http://purl.bioontology.org/ontology/BCO SCR_003262 2026-08-29 11:21:27 0
Primer3
 
Resource Report
Resource Website
10000+ mentions
Primer3 (RRID:SCR_003139) Primer3 analysis service resource, data analysis service, production service resource, service resource, software resource Tool used to design PCR primers from DNA sequence - often in high-throughput genomics applications. It does everything from mispriming libraries to sequence quality data to the generation of internal oligos. primer, primer design, polymerase chain reaction, pcr primer, dna sequence, c, perl, bio.tools is listed by: OMICtools
is listed by: Debian
is listed by: bio.tools
is listed by: SoftCite
is related to: Primer3Plus
is related to: Primer-BLAST
has parent organization: University of Tartu; Tartu; Estonia
NHGRI R01-HG00257;
NHGRI P50-HG00098
PMID:22730293
PMID:17379693
DOI:10.1385/1-59259-192-2:365
DOI:10.1385/1-59259-192-2:365
Free, Freely available nlx_156833, OMICS_02325, biotools:primer3 http://bioinfo.ut.ee/primer3-0.4.0/, http://sourceforge.net/projects/primer3/, http://frodo.wi.mit.edu/primer3, https://bio.tools/primer3, https://sources.debian.org/src/primer3/, https://sources.debian.org/src/primer3/ SCR_003139 Primer3web - Pick primers from a DNA sequence, Primer3 - PCR primer design tool, Primer3web 2026-08-29 11:21:26 11934
Talking Glossary of Genetic Terms
 
Resource Report
Resource Website
Talking Glossary of Genetic Terms (RRID:SCR_003215) Talking Glossary data or information resource, database, narrative resource, training material Glossary of Genetic Terms to help everyone understand the terms and concepts used in genetic research. In addition to definitions, specialists in the field of genetics share their descriptions of terms, and many terms include images, animation and links to related terms. glossary, image, genetic, gene, education is listed by: OMICtools
has parent organization: National Human Genome Research Institute
NHGRI The community can contribute to this resource nlx_156942, OMICS_01555 SCR_003215 NHGRI Talking Glossary, NHGRI Talking Glossary of Genetic Terms 2026-08-29 11:21:47 0
MorphoBank
 
Resource Report
Resource Website
100+ mentions
MorphoBank (RRID:SCR_003213) MorphoBank data or information resource, database Web application providing online database and workspace for evolutionary research, specifically systematics (the science of determining the evolutionary relationships among species). It enables researchers to upload images and affiliate data with those images (labels, species names, etc.) and allows researchers to upload morphological data and affiliate it with phylogenetic matrices. MorphoBank is project-based, meaning a team of researchers can create a project and share the images and associated data exclusively with each other. When a paper associated with the project is published, the research team can make their data permanently available for view on MorphoBank where it is now archived. phenotype, web service, phylogenetics, cladistics, histology, neurology, taxonomy, image, phylogeny, cladistic analysis, morphology, anatomy, evolution, homology, systems biology, FASEB list is listed by: re3data.org
is listed by: DataCite
is listed by: FAIRsharing
has parent organization: Stony Brook University; New York; USA
NOAA NA04OAR4700191;
NSF
PMID:34875801 Free, Freely available DOI:10.25504/FAIRsharing.1y63n8, DOI:10.17616/R3PC7F, DOI:10.7934, nlx_156938, r3d100010786 https://doi.org/10.17616/R3PC7F, https://doi.org/10.17616/r3pc7f, https://doi.org/10.7934/, https://dx.doi.org/10.7934/, https://fairsharing.org/10.25504/FAIRsharing.1y63n8, https://doi.org/10.17616/R3MK88 SCR_003213 2026-08-29 11:21:27 119
Mouse Phenome Database (MPD)
 
Resource Report
Resource Website
100+ mentions
Mouse Phenome Database (MPD) (RRID:SCR_003212) MPD data or information resource, data repository, database, experimental protocol, narrative resource, service resource, storage service resource Database enables integration of genomic and phenomic data by providing access to primary experimental data, data collection protocols and analysis tools. Data represent behavioral, morphological and physiological disease-related characteristics in naive mice and those exposed to drugs, environmental agents or other treatments. Collaborative standardized collection of measured data on laboratory mouse strains to characterize them in order to facilitate translational discoveries and to assist in selection of strains for experimental studies. Includes baseline phenotype data sets as well as studies of drug, diet, disease and aging effect., protocols, projects and publications, and SNP, variation and gene expression studies. Provides tools for online analysis. Data sets are voluntarily contributed by researchers from variety of institutions and settings, or retrieved by MPD staff from open public sources. MPD has three major types of strain-centric data sets: phenotype strain surveys, SNP and variation data, and gene expression strain surveys. MPD collects data on classical inbred strains as well as any fixed-genotype strains and derivatives that are openly acquirable by the research community. New panels include Collaborative Cross (CC) lines and Diversity Outbred (DO) populations. Phenotype data include measurements of behavior, hematology, bone mineral density, cholesterol levels, endocrine function, aging processes, addiction, neurosensory functions, and other biomedically relevant areas. Genotype data are primarily in the form of single-nucleotide polymorphisms (SNPs). MPD curates data into a common framework by standardizing mouse strain nomenclature, standardizing units (SI where feasible), evaluating data (completeness, statistical power, quality), categorizing phenotype data and linking to ontologies, conforming to internal style guides for titles, tags, and descriptions, and creating comprehensive protocol documentation including environmental parameters of the test animals. These elements are critical for experimental reproducibility. female, genomic location, genotype, inbred strain, male, mouse strain, phenome, phenotype, qtl, reference data, single-nucleotide polymorphism, strain allele, strain characteristic, strain, trait, gene expression, variation, hypothesis testing, data set, bio.tools, FASEB list is used by: NIF Data Federation
is used by: Integrated Datasets
is used by: NIH Heal Project
is listed by: re3data.org
is listed by: bio.tools
is listed by: Debian
is related to: Special Mouse Strains Resource
is related to: Vertebrate Trait Ontology
is related to: GenomeMUSter
has parent organization: Jackson Laboratory
NHGRI HG003057;
NHLBI HL66611;
NIA AG025707;
NIA AG038070;
NIDA ;
NIDA DA028420;
NIMH MH071984
PMID:24243846
PMID:22102583
PMID:18987003
PMID:17151079
Free, Freely available biotools:mpd, nif-0000-03160, r3d100010101 https://bio.tools/mpd, https://doi.org/10.17616/R3PC7F http://www.jax.org/phenome SCR_003212 Mouse Phenome Database 2026-08-29 11:21:47 230
Pipeliner
 
Resource Report
Resource Website
1+ mentions
Pipeliner (RRID:SCR_003171) software resource Software for evaluating the performance of bioinformatics pipelines for Next Generation re-Sequencing. standalone software, c++, bio.tools is listed by: OMICtools
is listed by: bio.tools
is listed by: Debian
PMID:24890372 Free, Available for download, Freely available OMICS_04844, biotools:pipeliner https://bio.tools/pipeliner SCR_003171 2026-08-29 11:21:45 7
EMDataResource.org
 
Resource Report
Resource Website
100+ mentions
EMDataResource.org (RRID:SCR_003207) EMDB, EMDataResource data or information resource, data repository, portal, project portal, service resource, storage service resource Portal for deposition and retrieval of cryo electron microscopy (3DEM) density maps, atomic models, and associated metadata. Global resource for 3 Dimensional Electron Microscopy structure data archiving and retrieval, news, events, software tools, data standards, validation methods. deposition, retrival, cryo, electron, microscopy, 3DEM, density, maps, atomic, model, metadata, structure 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 affiliated with: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB)
is related to: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB)
is related to: Electron Microscopy Data Bank at PDBe (MSD-EBI)
is related to: PDBe - Protein Data Bank in Europe
is related to: National Center for Macromolecular Imaging
has parent organization: Rutgers University; New Jersey; USA
has parent organization: European Bioinformatics Institute
has parent organization: Baylor University; Texas; USA
BBSRC BBG022577;
NIGMS R01 GM079429
PMID:20935055
PMID:20888470
Free, Freely available r3d100010552, nif-0000-30776 https://doi.org/10.17616/R3T61P EMDataBank.org SCR_003207 EMDataResource, EMDResource, EMDB, EMDataBank.org, EMDataBank - Unified Data Resource for 3DEM, EMDataBank 2026-08-29 11:21:25 183
Database of Interacting Proteins (DIP)
 
Resource Report
Resource Website
100+ mentions
Database of Interacting Proteins (DIP) (RRID:SCR_003167) DIP analysis service resource, data analysis service, data or information resource, data repository, database, production service resource, service resource, storage service resource Database to catalog experimentally determined interactions between proteins combining information from a variety of sources to create a single, consistent set of protein-protein interactions that can be downloaded in a variety of formats. The data were curated, both, manually and also automatically using computational approaches that utilize the the knowledge about the protein-protein interaction networks extracted from the most reliable, core subset of the DIP data. Because the reliability of experimental evidence varies widely, methods of quality assessment have been developed and utilized to identify the most reliable subset of the interactions. This CORE set can be used as a reference when evaluating the reliability of high-throughput protein-protein interaction data sets, for development of prediction methods, as well as in the studies of the properties of protein interaction networks. Tools are available to analyze, visualize and integrate user's own experimental data with the information about protein-protein interactions available in the DIP database. The DIP database lists protein pairs that are known to interact with each other. By interact they mean that two amino acid chains were experimentally identified to bind to each other. The database lists such pairs to aid those studying a particular protein-protein interaction but also those investigating entire regulatory and signaling pathways as well as those studying the organization and complexity of the protein interaction network at the cellular level. Registration is required to gain access to most of the DIP features. Registration is free to the members of the academic community. Trial accounts for the commercial users are also available. blast, cellular network, ligand-receptor complex, ligand, network, protein, protein interaction, protein ligand, protein-protein interaction, protein receptor, receptor, sequence, interaction, regulatory pathway, signaling pathway, protein binding, bio.tools, FASEB list is recommended by: NIDDK Information Network (dkNET)
is recommended by: National Library of Medicine
is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases
is listed by: OMICtools
is listed by: re3data.org
is listed by: NIH Data Sharing Repositories
is listed by: bio.tools
is listed by: Debian
is related to: IMEx - The International Molecular Exchange Consortium
is related to: IMEx - The International Molecular Exchange Consortium
is related to: MPIDB
is related to: TissueNet - The Database of Human Tissue Protein-Protein Interactions
is related to: InteroPorc
is related to: Interaction Reference Index
is related to: ConsensusPathDB
is related to: NIH Data Sharing Repositories
is related to: PSICQUIC Registry
is related to: Agile Protein Interactomes DataServer
has parent organization: University of California at Los Angeles; California; USA
NIGMS PMID:14681454 Free, Available for download, Freely available OMICS_01905, nif-0000-00569, r3d100010882, biotools:dip https://dip.doe-mbi.ucla.edu/dip/Main.cgi, https://bio.tools/dip, https://doi.org/10.17616/R3431F SCR_003167 , Database of Interacting Proteins, DIP, Database of Interacting Proteins (DIP) 2026-08-29 11:21:45 167
Piano
 
Resource Report
Resource Website
100+ mentions
Piano (RRID:SCR_003200) data analysis software, data processing software, software application, software resource Software R-package for running gene set analysis using various statistical methods, from different gene level statistics and a wide range of gene-set collections. The Piano package contains functions for combining the results of multiple runs of gene set analyses. r, omics, bio.tools is listed by: OMICtools
is listed by: bio.tools
is listed by: Debian
has parent organization: Chalmers University of Technology; Gothenburg; Sweden
has parent organization: Bioconductor
PMID:23444143 Free, Available for download, Freely available OMICS_01558, biotools:piano https://bio.tools/piano SCR_003200 2026-08-29 11:21:25 188
Allele Biotechnology
 
Resource Report
Resource Website
1+ mentions
Allele Biotechnology (RRID:SCR_003164) Allele Biotech commercial organization A private company offering a wide variety of Molecular Biology reagents, fluorescent proteins, luciferase assay substrates, genotyping kits, and various custom services. The company isalso in the RNAi field with its recent patents in Pol III promoter-driven siRNA, shRNA, and miRNA. They introduced high titer lentivirus, camelid antibodies, and cell based assays and also offer Baculovirus protein expression and Gryphon retrovirus systems. molecular biology, reagent, fluorescent protein, luciferase assay substrate, genotyping kit, custom service is related to: Phoenix Free, Available for download, Freely available nlx_156865 SCR_003164 Allele Biotechnology and Pharmaceuticals Inc 2026-08-29 11:21:24 1
Solas
 
Resource Report
Resource Website
1+ mentions
Solas (RRID:SCR_003168) data analysis software, data processing software, sequence analysis software, software application, software resource, source code Software package for the statistical language R, devoted to the analysis of next generation short read data of RNA-seq transcripts. It provides predictions of alternative exons in a single condition/cell sample, predictions of differential alternative exons between two conditions/cell samples, and quantification of alternative splice forms in a single condition/cell sample. r statistical package, rna seq, exon prediction, exon splicing, bio.tools is listed by: OMICtools
is listed by: bio.tools
is listed by: Debian
is related to: R Project for Statistical Computing
has parent organization: Max Planck Institute for Molecular Genetics; Berlin; Germany
Free, Available for download, Freely available biotools:solas, OMICS_01339 https://bio.tools/solas SCR_003168 2026-08-29 11:21:26 8
GenePattern
 
Resource Report
Resource Website
1000+ mentions
GenePattern (RRID:SCR_003201) GenePattern data analysis software, data processing software, software application, software resource A powerful genomic analysis platform that provides access to hundreds of tools for gene expression analysis, proteomics, SNP analysis, flow cytometry, RNA-seq analysis, and common data processing tasks. A web-based interface provides easy access to these tools and allows the creation of multi-step analysis pipelines that enable reproducible in silico research. gene expression, analysis, genomic, pattern, proteomics, silico, snp, workflow, analysis pipeline, flow cytometry, rna-seq, data processing, bio.tools is listed by: bio.tools
is listed by: Debian
is listed by: SoftCite
is affiliated with: GenePattern Notebook
is related to: TIGRESS
has parent organization: Broad Institute
NCI ;
NIGMS
PMID:16642009 Free, Freely available biotools:genepattern, OMICS_01855, nif-0000-30654 https://bio.tools/genepattern SCR_003201 2026-08-29 11:21:46 1135
rDiff
 
Resource Report
Resource Website
1+ mentions
rDiff (RRID:SCR_003162) data analysis software, data processing software, sequence analysis software, software application, software resource Software tool for detecting differential RNA processing from RNA-Seq data. It implements two statistical tests, rDiff.parametric and rDiff.nonparametric, to detect changes of the RNA processing between two samples. differential rna processing, rna processing, rna seq is listed by: OMICtools PMID:23585274 THIS RESOURCE IS NO LONGER IN SERVICE OMICS_01338 SCR_003162 2026-08-29 11:21:26 7
American Association for the History of Medicine
 
Resource Report
Resource Website
American Association for the History of Medicine (RRID:SCR_003161) AAHM nonprofit organization A professional association of historians, physicians, nurses, archivists, curators, librarians, and others that promotes and encourages research, study, writing, and interest in the history of medicine and allied fields. history, medicine Free, Freely available nlx_156861, grid.486311.9 https://ror.org/04w1hax42 SCR_003161 2026-08-29 11:21:45 0
PIRSF
 
Resource Report
Resource Website
10+ mentions
PIRSF (RRID:SCR_003352) PIRSF data or information resource, database, narrative resource, standard specification A SuperFamily classification system, with rules for functional site and protein name, to facilitate the sensible propagation and standardization of protein annotation and the systematic detection of annotation errors. The PIRSF concept is being used as a guiding principle to provide comprehensive and non-overlapping clustering of UniProtKB sequences into a hierarchical order to reflect their evolutionary relationships. The PIRSF classification system is based on whole proteins rather than on the component domains; therefore, it allows annotation of generic biochemical and specific biological functions, as well as classification of proteins without well-defined domains. There are different PIRSF classification levels. The primary level is the homeomorphic family, whose members are both homologous (evolved from a common ancestor) and homeomorphic (sharing full-length sequence similarity and a common domain architecture). At a lower level are the subfamilies which are clusters representing functional specialization and/or domain architecture variation within the family. Above the homeomorphic level there may be parent superfamilies that connect distantly related families and orphan proteins based on common domains. Because proteins can belong to more than one domain superfamily, the PIRSF structure is formally a network. The FTP site provides free download for PIRSF. protein annotation, classification, protein, superfamily, functional site, protein name, bio.tools is listed by: OMICtools
is listed by: bio.tools
is listed by: Debian
is related to: UniProtKB
has parent organization: Protein Information Resource
NHGRI U01-HG02712;
NSF DBI-0138188;
NSF ITR-0205470
PMID:19455212
PMID:14681371
Free, Freely available biotools:pirsf, OMICS_01697, nif-0000-03294 https://bio.tools/pirsf http://pir.georgetown.edu/pirsf/ SCR_003352 PIR SuperFamily, Protein Information Resource SuperFamily 2026-08-29 11:21:31 32
Emory University, Molecular and Systems Pharmacology
 
Resource Report
Resource Website
Emory University, Molecular and Systems Pharmacology (RRID:SCR_003351) data or information resource, department portal, graduate program resource, organization portal, portal The Molecular and Systems Pharmacology graduate program at Emory University offers broad training in the biomedical sciences for students interested in learning how the drugs of today work and how the novel therapeutics of tomorrow can be developed. The Program offers a specialization in toxicology. Emory University was recently rated by The Scientist magazine as the number 1 university in the world in terms of impact in pharmacology and toxicology research. Particular strengths within the MSP graduate school program at Emory include neuropharmacology, cancer biology, AIDS research, cardiovascular pharmacology, toxicology, and chemical biology. Ph.D. training in the Emory MSP program provides students with an ideal preparation for successful careers in the biotechnology and pharmaceutical industries as well as in academic research, teaching, government research, patent law and other disciplines that depend upon knowledge of fundamental pharmacological principles. has parent organization: Emory University; Georgia; USA Free, Freely available nif-0000-01944 http://www.pharm.emory.edu/MSP/ SCR_003351 EU MSP, Emory University Molecular and Systems Pharmacology Graduate Program, Emory MSP Graduate Program, Emory Molecular and Systems Pharmacology Graduate Program, Emory MSP 2026-08-29 11:21:30 0
George Washington University, Department of Pharmacology and Physiology
 
Resource Report
Resource Website
George Washington University, Department of Pharmacology and Physiology (RRID:SCR_003358) data or information resource, department portal, organization portal, portal The Department of Pharmacology & Physiology at the George Washington University provides unique research opportunities at the predoctoral and postdoctoral levels. They also offer courses in Pharmacology and Physiology for Medical and Health Sciences students, as well as a number of graduate-level courses. Our mission is to provide the highest quality of educational opportunities to our community, and to advance scientific knowledge and improve human health through leading-edge research in the biomedical sciences. has parent organization: George Washington University; Washington D.C.; USA Free, Freely available nif-0000-01952 SCR_003358 GWU Department of Pharmacology & Physiology, GWU Department of Pharmacology and Physiology, GWU Dept. of Pharmacology and Physiology 2026-08-29 11:21:31 0
MouseNET
 
Resource Report
Resource Website
1+ mentions
MouseNET (RRID:SCR_003357) mouseNet analysis service resource, data analysis service, data or information resource, database, production service resource, service resource A functional network for laboratory mouse based on integration of diverse genetic and genomic data. It allows the users to accurately predict novel functional assignments and network components. MouseNET uses a probabilistic Bayesian algorithm to identify genes that are most likely to be in the same pathway/functional neighborhood as your genes of interest. It then displays biological network for the resulting genes as a graph. The nodes in the graph are genes (clicking on each node will bring up SGD page for that gene) and edges are interactions (clicking on each edge will show evidence used to predict this interaction). Most likely, the first results to load on the results page will be a list of significant Gene Ontology terms. This list is calculated for the genes in the biological network created by the mouseNET algorithm. If a gene ontology term appears on this list with a low p-value, it is statistically significantly overrepresented in this biological network. The graph may be explored further. As you move the mouse over genes in the network, interactions involving these genes are highlighted.If you click on any of the highlighted interactions graph, evidence pop-up window will appear. The Evidence pop-up lists all evidence for this interaction, with links to the papers that produced this evidence - clicking these links will bring up the relevant source citation(s) in PubMed. gene, network, mouse, protein function, visualization, open reading frame, graph is listed by: OMICtools
is related to: Gene Ontology
is related to: mouseMAP
has parent organization: Princeton University; New Jersey; USA
NSF DBI-0546275;
NIGMS R01 GM071966;
NSF IIS-0513552;
NIGMS P50 GM071508
PMID:18818725 Free, Freely available OMICS_01550, nif-0000-32003 SCR_003357 MouseNET 2026-08-29 11:21:53 3

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