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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
U.S. Department of Defense
 
Resource Report
Resource Website
50+ mentions
U.S. Department of Defense (RRID:SCR_012712) DOD institution Executive branch department of the federal government charged with coordinating and supervising all agencies and functions of the government directly related to national security and the United States Armed Forces. Government granting agency is parent organization of: Defense Advanced Research Projects Agency
is parent organization of: Office of Naval Research
is parent organization of: Defense and Veterans Brain Injury Center
is parent organization of: Defense Centers of Excellence for Psychological Health and Traumatic Brain Injury
is parent organization of: Congressionally Directed Medical Research Program
is parent organization of: BHSAI; Maryland; USA
ISNI: 0000 0004 0478 6223, grid.420391.d, Crossref funder ID: 100000005, nlx_143670, Wikidata: Q11209 https://ror.org/0447fe631 SCR_012712 Department of Defense, United States Department of Defense, US Department of Defense 2026-09-02 05:41:00 64
AngioCalc Cerebral Aneurysm Calculator
 
Resource Report
Resource Website
10+ mentions
AngioCalc Cerebral Aneurysm Calculator (RRID:SCR_012805) AngioCalc data management software, software application, software resource Providing quality resources for the management of cerebral aneurysms and features an online calculator that calculates cerebral aneurysm volume and percent packing volume after coil embolization. The site also host an imaging Library with neuroanatomy and neurovascular images. is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) nlx_155693 SCR_012805 AngioCalc Cerebral and Peripheral Aneurysm Calculator, AngioCalc Cerebral Aneurysm Calculator 2026-09-02 05:41:01 12
USC Multimodal Connectivity Database
 
Resource Report
Resource Website
10+ mentions
USC Multimodal Connectivity Database (RRID:SCR_012809) UMCD data or information resource, data repository, database, service resource, storage service resource Web-based repository and analysis site for connectivity matrices that have been derived from neuroimaging data including different imaging modalities, subject groups, and studies. Users can analyze connectivity matrices that have been shared publicly and upload their own matrices to share or analyze privately. fmri, dti, dsi, mri, eeg, meg, data set, image, computational hosting, connectivity, neuroimaging, data sharing, brain, rendering, diffusion-weighted mri, functional connectivity, graph theory, resting-state fmri, structural connectivity, image display, magnetic resonance, python, rendering, visualization, connectivity matrix, network, brain network, matrix, de-identified, male, female, apoe, child, adult is used by: NIF Data Federation
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC)
has parent organization: MGH-USC Human Connectome Project
Normal, Lesioned, Attention deficit-hyperactivity disorder, Autism Spectrum Disorder, Obsessive-Compulsive Disorder, BDD, APOE 4/4, APOE 3/4, APOE 3/3, Alzheimer's disease NRSA ;
NIH Blueprint for Neuroscience Research ;
NIA F31AG035438-01;
NIDA HHSN271200800035C
PMID:23226127
PMID:20850551
The community can contribute to this resource, Some features require an account nlx_83091 http://www.nitrc.org/projects/umcd http://jessebrown.webfactional.com/welcome/default/index SCR_012809 UCLA Connectivity Database, UCLA Multimodal Connectivity Database: Web-based brain network analysis and data sharing, UCLA Multimodal Connectivity Database 2026-09-02 05:41:03 26
GNU.org
 
Resource Report
Resource Website
100+ mentions
GNU.org (RRID:SCR_012764) software resource Unix-like operating system that is free software. GNU (more precisely, GNU/Linux systems) are entirely free software. The GNU Project was launched in 1984 to develop the GNU system. A Unix-like operating system is a software collection of applications, libraries, and developer tools, plus a program to allocate resources and talk to the hardware, known as a kernel. The Hurd, GNU''s own kernel, is some way from being ready for daily use. Thus, GNU is typically used today with a kernel called Linux. This combination is the GNU/Linux operating system. GNU/Linux is used by millions, though many call it Linux by mistake. nlx_156924 SCR_012764 2026-09-02 05:41:01 178
CexoR
 
Resource Report
Resource Website
CexoR (RRID:SCR_012769) CexoR software resource Software for strand specific peak-pair calling in ChIP-exo replicates. is listed by: OMICtools
has parent organization: Bioconductor
MIT License OMICS_00519 SCR_012769 CexoR: An R package to uncover high-resolution protein-DNA interactions in ChIP-exo replicates 2026-09-02 05:41:12 0
edgeR
 
Resource Report
Resource Website
10000+ mentions
edgeR (RRID:SCR_012802) edgeR data analysis software, data processing software, software application, software resource Bioconductor software package for Empirical analysis of Digital Gene Expression data in R. Used for differential expression analysis of RNA-seq and digital gene expression data with biological replication. empirical, analysis, digital, gene, expression, data, R, RNA-seq data, bio.tools is used by: Glimma
is listed by: OMICtools
is listed by: Debian
is listed by: bio.tools
is related to: SARTools
is related to: Bioconductor
works with: tximport
Harris and IBS Honours scholarships ;
Independent Research Institutes Infrastructure Support Scheme 361646;
Melbourne International Research Scholarship ;
NHMRC 406657;
Victorian State Government OIS grant
PMID:19910308
DOI:10.1093/bioinformatics/btp616
Free, Available for download, Freely available OMICS_01308, biotools:edger https://bio.tools/edger, https://sources.debian.org/src/r-bioc-edger/ SCR_012802 edgeR, empirical analysis of digital gene expression data in R, Empirical analysis of Digital Gene Expression data in R 2026-09-02 05:41:01 23868
MotifLab
 
Resource Report
Resource Website
1+ mentions
MotifLab (RRID:SCR_012649) MotifLab software resource Software for a general workbench for analyzing regulatory sequence regions and discovering transcription factor binding sites and cis-regulatory modules. is listed by: OMICtools
has parent organization: Norwegian University of Science and Technology; Trondheim; Norway
Research Council of Norway PMID:23323883 Acknowledgement requested, Free, Public OMICS_00486 SCR_012649 2026-09-02 05:40:59 2
TGD
 
Resource Report
Resource Website
10+ mentions
TGD (RRID:SCR_012803) TGD, TGD LOCUS, TGD REF analysis service resource, data analysis service, data or information resource, database, narrative resource, production service resource, service resource, wiki TGD Wiki is a user-updatable database of information about the Tetrahymena thermophila genome sequence determined at The Institute for Genomic Research (TIGR). TGD Wiki provides information on the genome, genes, and proteins of Tetrahymena collected from the scientific literature, research community and many other resources. In order to keep the information in our database as current as possible, we will soon be inviting the members of the Tetrahymena community to add and update these annotations to reflect published research. TGD Wiki currently offers the following features: * Free, unrestricted read access to all available data * Sequence and annotation data for 24,725 genes (TIGR v.2008) * GBrowse genome browser with links to and from each gene page (TIGR v.2006) * BLAST searching of the TIGR gene models and genome sequence (TIGR v.2006) Tetrahymena Genome Database (TGD) Wiki began in 2004 at Stanford University using the schema and programs of its parent project, Saccharomyces Genome Database. TGD Wiki is now a collaboration between Bradley University, Stanford University, and Cornell University. As we begin TGD Wiki at its new home at Bradley University, the TGD Wiki database contains the following data from TGD: * Gene Names and Aliases * Gene Descriptions * Gene Ontology (GO) Annotations * Homologs (similar genes in selected organisms) * Protein Domains * Associated Literature * Paragraphs (longer, free-text descriptions of gene function, structure, and significance) * Coding and Protein Sequences We have updated the following fields to match the newest gene model sequences (TIGR v.2008): Coding and Protein Sequences, Protein Domains and Gene Descriptions. We will also be recalculating the GO Annotations (IEA evidence code) and Homologs as part of our effort to keep the annotations in TGD Wiki as current as possible. We will be relying on members of the Tetrahymena community to maintain high-quality, updated annotations in the remainder of the fields using our annotation interface. Also setting up new database superdb - for unpublished data Look at Ciliate.org for news on this and other new databases ciliate has parent organization: Bradley University; Illinois; USA NIH nlx_75432 SCR_012803 TGD REF, Tetrahymena Genome Database, TGD Wiki, TGD LOCUS, Tetrahymena Genome Database Wiki 2026-09-02 05:41:02 14
KEGG
 
Resource Report
Resource Website
10000+ mentions
KEGG (RRID:SCR_012773) KEGG analysis service resource, data access protocol, data analysis service, data or information resource, database, portal, production service resource, service resource, software resource, topical portal, web service Integrated database resource consisting of 16 main databases, broadly categorized into systems information, genomic information, and chemical information. In particular, gene catalogs in completely sequenced genomes are linked to higher-level systemic functions of cell, organism, and ecosystem. Analysis tools are also available. KEGG may be used as reference knowledge base for biological interpretation of large-scale datasets generated by sequencing and other high-throughput experimental technologies. model, pathway, functional hierarchy, module, cancer, disease, drug, drug classification, orthology, ortholog, genome, gene, protein, compound, classification, biochemical reaction, pathway, ligand, biosynthesis, pathway prediction, sequence, chemical structure, human, enzyme, database, molecular interaction, metabolism, metabolomics, cellular process, structure, drug development, reaction, cell is used by: NIF Data Federation
is used by: Arabidopsis Reactome
is used by: LIPID MAPS Proteome Database
is used by: globaltest
is used by: MitoMiner
is used by: Database for Annotation Visualization and Integrated Discovery
is used by: Biochemical Pathways Reaction Kinetics Database
is used by: Ultimate Rough Aggregation of Metabolic Map
is used by: GEMINI
is used by: In vivo - In silico Metabolite Database
is listed by: 3DVC
is listed by: OMICtools
is affiliated with: Kyoto Encyclopedia of Genes and Genomes Expression Database
is related to: PathCase Pathways Database System
is related to: ExplorEnz
is related to: NCBI BioSystems Database
is related to: Allen Institute Neurowiki
is related to: eQuilibrator
is related to: GeneTrail
is related to: KegTools
is related to: PRODORIC
is related to: hiPathDB - human integrated Pathway DB with facile visualization
is related to: METLIN
is related to: Kidney and Urinary Pathway Knowledge Base
is related to: DAVID
is related to: ConsensusPathDB
is related to: ENZYME
is related to: FlyMine
is related to: Babelomics
is related to: SynSysNet
is related to: Cotton EST Database
is related to: Integrated Molecular Interaction Database
is related to: SEGS
is related to: INMEX
is related to: BioExtract
is related to: ClueGO
is related to: MalaCards
is related to: TrED
is related to: FunTree
is related to: MOPED - Model Organism Protein Expression Database
is related to: ProOpDB
is related to: KOBAS
is related to: GeneTerm Linker
is related to: WebGestalt: WEB-based GEne SeT AnaLysis Toolkit
is related to: GeneCodis
is related to: FunNet - Transcriptional Networks Analysis
is related to: LegumeIP
is related to: Algal Functional Annotation Tool
is related to: aGEM
is related to: DINIES
is related to: KEGG PATHWAY Database
is related to: ShinyGO
is related to: KEGGREST
has parent organization: Kyoto University; Kyoto; Japan
has parent organization: University of Tokyo; Tokyo; Japan
is parent organization of: KegTools
works with: DIANA-mirPath
works with: MiMeDB
Japan Science and Technology Agency ;
Japanese Ministry of Education Culture Sports Science and Technology MEXT
PMID:22700311
PMID:22130871
PMID:22080510
PMID:19880382
PMID:19172790
PMID:18428742
PMID:18287706
PMID:18077471
PMID:16381885
PMID:16014746
PMID:14681412
PMID:12539951
PMID:11752249
PMID:10928937
PMID:10592173
PMID:9847135
Restricted nlx_31015, OMICS_01583, OMICS_03010, OMICS_01582, OMICS_03974, OMICS_05434, OMICS_05360 http://www.genome.jp/kegg/ SCR_012773 KEGG - Kyoto Encyclopedia of Genes and Genomes, Kyoto Encyclopedia of Genes and Genomes 2026-09-02 05:41:02 81488
Institute of Molecular and Cell Biology; Singapore; Singapore
 
Resource Report
Resource Website
Institute of Molecular and Cell Biology; Singapore; Singapore (RRID:SCR_012775) IMCB institution The Institute of Molecular and Cell Biology (IMCB) was established in 1987 at the National University of Singapore (NUS) before becoming an autonomous research institute (RI) of A*STAR. Its mission is to develop and foster a vibrant research culture for cutting-edge basic biomedical sciences and for training high-quality Ph.D. students for the flourishing biotechnology and pharmaceutical industries in Singapore. Funded primarily by the Biomedical Research Council (BMRC) of A*STAR, IMCB now boasts about 30 core research labs and 8 core facility units consisting of over 300 research scientists in total. IMCB''s research activities focus on six major fields: Cell Biology, Developmental Biology, Structural Biology, Infectious Diseases, Cancer Biology and Translational Research with core strengths in cell cycling, cell signalling, cell death, cell motility and protein trafficking. IMCB continues to strive for excellence in biomedical R&D to see the vision of Singapore being a world class hub for the Biomedical Sciences in Asia and beyond. IMCB''s achievements include being part of the international consortium that successfully sequenced the entire pufferfish (Fugu rubripes) in 2002. IMCB was awarded the Nikkei Prize 2000 for Technological Innovation in recognition of its growth into a leading international research centre and its collaboration with industry and research institutes worldwide. IMCB continues to publish in renowned international journals, with more than 1300 publications to its credit since 1987. has parent organization: Agency for Science Technology and Research
is parent organization of: Fugu Genome Project
is parent organization of: Elephant shark genome sequencing
is parent organization of: Japanese Lamprey Genome Project
grid.418812.6, Crossref funder ID: 501100007674, ISNI: 0000 0004 0620 9243, Wikidata: Q16999819, nlx_91982 https://ror.org/04xpsrn94 SCR_012775 2026-09-02 05:41:00 0
tRanslatome
 
Resource Report
Resource Website
1+ mentions
tRanslatome (RRID:SCR_012810) tRanslatome software resource Detection of differentially expressed genes (DEGs) from the comparison of two biological conditions among different levels of gene expression, using several statistical methods: Rank Product, t-test, SAM, Limma, ANOTA, DESeq, edgeR. is listed by: OMICtools
has parent organization: Bioconductor
PMID:24222209 Free OMICS_01316 SCR_012810 tRanslatome - Comparison between multiple levels of gene expression 2026-09-02 05:41:01 2
IMGT - the international ImMunoGeneTics information system
 
Resource Report
Resource Website
500+ mentions
IMGT - the international ImMunoGeneTics information system (RRID:SCR_012780) IMGT analysis service resource, data analysis service, data or information resource, database, portal, production service resource, service resource, topical portal A high-quality integrated knowledge resource specialized in the immunoglobulins (IG) or antibodies, T cell receptors (TR), major histocompatibility complex (MHC) of human and other vertebrate species, and in the immunoglobulin superfamily (IgSF), MHC superfamily (MhcSF) and related proteins of the immune system (RPI) of vertebrates and invertebrates, serving as the global reference in immunogenetics and immunoinformatics. IMGT provides a common access to sequence, genome and structure Immunogenetics data, based on the concepts of IMGT-ONTOLOGY and on the IMGT Scientific chart rules. IMGT works in close collaboration with EBI (Europe), DDBJ (Japan) and NCBI (USA). IMGT consists of sequence databases, genome database, structure database, and monoclonal antibodies database, Web resources and interactive tools. immunogenetics, immunoinformatics, immunoglobulin, antibody, t cell receptor, major histocompatibility complex, immunoglobulin superfamily, major histocompatibility complex superfamily, protein, immune system, sequence, genome, structure, monoclonal antibody, gold standard, bio.tools is listed by: bio.tools
is listed by: Debian
is related to: IMGT Repertoire
has parent organization: Montpellier 2 University; Montpellier; France
is parent organization of: IMGT/LIGM-DB
is parent organization of: IMGT/GENE-DB
is parent organization of: IMGT-ONTOLOGY
is parent organization of: IMGT/V-QUEST
is parent organization of: IMGT/HLA
CNRS ;
MESR ;
Reseau National des Genopoles ;
Region Languedoc-Roussillon ;
European Union BIOMED1 BIOCT930038;
European Union Biotechnology BIOTECH2 BIO4CT960037;
European Union 5th PCRDT Quality of Life and Management of Living Resources QLG2-2000-01287;
Agence Nationale de la recherche ANR BIOSYS06_135457;
EU ImmunoGrid IST-028069
PMID:18978023 nif-0000-03011, biotools:imgt https://bio.tools/imgt http://imgt.cines.fr SCR_012780 ImMunoGeneTics Information System, IMGT/LIGM, ImMunoGeneTics 2026-09-02 05:41:02 779
Krona
 
Resource Report
Resource Website
50+ mentions
Krona (RRID:SCR_012785) Krona software resource Software that allows hierarchical data to be explored with zoomable pie charts. bio.tools is listed by: bio.tools
has parent organization: SourceForge
PMID:21961884 OMICS_01498, biotools:krona https://bio.tools/krona SCR_012785 Krona - Hierarchical data browser 2026-09-02 05:41:12 97
U.S. Social Security Administration
 
Resource Report
Resource Website
1+ mentions
U.S. Social Security Administration (RRID:SCR_012905) SSA institution Independent agency of the U.S. federal government that administers Social Security, a social insurance program consisting of retirement, disability, and survivor benefits. Government granting agency is parent organization of: New Beneficiary Data System Crossref funder ID: 100005225, ISNI: 0000 0001 0726 0196, nlx_151831, grid.453277.0, Wikidata: Q2824618 https://ror.org/04b7xxn32 SCR_012905 Social Security Administration, Social Security Administration (SSA) 2026-09-02 05:41:03 6
Meharry Medical College
 
Resource Report
Resource Website
Meharry Medical College (RRID:SCR_012863) MMC university Founded in 1876, Meharry is a non-profit university in Tennessee. Meharry includes a medical school, dental school, and a graduate school. undergraduate, graduate, master's, doctoral, phD, institution, university is related to: Clinical and Translational Science Awards Consortium
is parent organization of: Meharry Endocrine core
is parent organization of: Meharry Flow Cytometry and BSL3 Core
is parent organization of: Meharry Human Tissue Acquistion and Pathology Core
is parent organization of: Meharry Molecular Biology Core Facility
is parent organization of: Meharry Morphology Core
is parent organization of: Meharry Medical College School of Graduate Studies and Research; Tennessee; USA
is parent organization of: Meharry Proteomics Core
is parent organization of: Meharry Microarray and Bioinformatics Core
is parent organization of: Meharry Medical College Molecular Biology Core Facility
is parent organization of: Meharry Medical College Labs and Facilities
ISNI:0000 0001 0286 752X, nlx_66976, grid.259870.1, Wikidata:Q4026847 https://ror.org/00k63dq23 SCR_012863 Meharry Medical, Meharry, Meharry Medical College 2026-09-02 05:41:03 0
BEDOPS
 
Resource Report
Resource Website
100+ mentions
BEDOPS (RRID:SCR_012865) BEDOPS software resource A suite of tools to address common questions raised in genomic studies - mostly with regard to overlap and proximity relationships between data sets. is listed by: OMICtools
is listed by: Debian
PMID:22576172
DOI:10.1093/bioinformatics/bts277
GNU General Public License, v3 OMICS_00949 https://sources.debian.org/src/bedops/ SCR_012865 BEDOPS: high-performance genomic feature operations 2026-09-02 05:41:02 237
AASLD - American Association for the Study of Liver Diseases
 
Resource Report
Resource Website
AASLD - American Association for the Study of Liver Diseases (RRID:SCR_012900) AASLD data or information resource, portal, topical portal A non-profit organization of scientists and healthcare professionals committed to preventing and curing liver disease, which runs three journals and an annual meeting. Its mission is to Advance the Science and Practice of Hepatology, Liver Transplantation and Hepatobiliary Surgery, Thereby Promoting Liver Health and Optimal Care of Patients with Liver and Biliary Tract Diseases. AASLD was founded in 1950 by a small group of leading liver specialists (including Hans Popper, Leon Schiff, Fred Hoffbauer, Cecil Watson, Jesse Bollman, and Sheila Sherlock, to name a few) to bring together those who had contributed to the field of hepatology. AASLD has grown to an international society responsible for all aspects of hepatology, and our annual meeting, The Liver Meeting, has grown in attendance from 12 to over 7,000 physicians, surgeons, researchers, and allied health professionals from around the world. AASLD sponsors two to four Single Topic Conferences each year in clinical, basic, hepatitis, or pediatric hepatology. Our two monthly journals, HEPATOLOGY and Liver Transplantation, provide the latest research findings for hepatology and surgery of the liver. AASLD''s membership includes ALL professionals dedicated to hepatobiliary discoveries and patient care. Mentoring, the sharing of knowledge, and dedication to professional growth and development are among the core values of AASLD and its members. hepatology, liver transplantation, liver, transplantation is parent organization of: American Liver Foundation Liver disease nlx_149391 SCR_012900 American Association for the Study of Liver Diseases 2026-09-02 05:41:03 0
EYE-EEG (combined eye-tracking & EEG)
 
Resource Report
Resource Website
10+ mentions
EYE-EEG (combined eye-tracking & EEG) (RRID:SCR_012903) EYE-EEG software resource A plugin for the open-source MATLAB toolbox EEGLAB developed with the goal to facilitate integrated analyses of electrophysiological and oculomotor data. The plugin parses, imports, and synchronizes simultaneously recorded eye tracking data and adds it as extra channels to the EEG. Saccades and fixations can be imported from the eye tracking raw data or detected with an adaptive velocity-based algorithm. Eye movements are then added as new time-locking events to EEGLAB's event structure, allowing easy saccade- and fixation-related EEG analysis (e.g., fixation-related potentials, FRPs). Alternatively, EEG data can be aligned to stimulus onsets and analyzed according to oculomotor behavior (e.g. pupil size, microsaccades) in a given trial. Saccade-related ICA components can be objectively identified based on their covariance with the electrically independent eye tracker. All functions can be accessed via EEGLAB's GUI or called from the command line. eeg, meg, electrocorticography, matlab, os independent, eye, electrophysiology, oculomotor, eye tracking device is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC)
is related to: EEGLAB
has parent organization: Humboldt University of Berlin; Berlin; Germany
DFG PMID:21744985 GNU General Public License nlx_155755 http://www.nitrc.org/projects/eye-eeg SCR_012903 EYE-EEG: Eye tracking & EEG 2026-09-02 05:41:14 13
GENSCAN
 
Resource Report
Resource Website
100+ mentions
GENSCAN (RRID:SCR_012902) service resource Resource out of service. Documented on February 24,2021. has parent organization: German Cancer Research Center Resource out of service. Documented on February 24,2021. nif-0000-30609 SCR_012902 GENSCAN 2026-09-02 05:41:04 192
Flash Gviewer
 
Resource Report
Resource Website
1+ mentions
Flash Gviewer (RRID:SCR_012870) Flash GViewer software resource Flash GViewer is a customizable Flash movie that can be easily inserted into a web page to display each chromosome in a genome along with the locations of individual features on the chromosomes. It is intended to provide an overview of the genomic locations of a specific set of features - eg. genes and QTLs associated with a specific phenotype, etc. rather than as a way to view all features on the genome. The features can hyperlink out to a detail page to enable to GViewer to be used as a navigation tool. In addition the bands on the chromosomes can link to defineable URL and new region selection sliders can be used to select a specific chromosome region and then link out to a genome browser for higher resolution information. Genome maps for Rat, Mouse, Human and C. elegans are provided but other genome maps can be easily created. Annotation data can be provided as static text files or produced as XML via server scripts. This tool is not GO-specific, but was built for the purpose of viewing GO annotation data. Platform: Online tool visualization, chromosome, video, gene, qtl, genome, navitgation, phenotype, ontology or annotation visualization is listed by: Gene Ontology Tools
is related to: Gene Ontology
has parent organization: Medical College of Wisconsin; Wisconsin; USA
Free for academic use nlx_149333 http://gmod.org/flashgviewer SCR_012870 2026-09-02 05:41:02 2

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