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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 Website Status Alternate IDs Alternate URLs Old URLs Parent Organization Resource ID Synonyms Record Last Update Mentions Count
Parametric Time Warping
 
Resource Report
Resource Website
Parametric Time Warping (RRID:SCR_003053) ptw software resource Software that aligns patterns, i.e. it aims to put corresponding features at the same locations. The algorithm searches for an optimal polynomial describing the warping. It is possible to align one sample to a reference, several samples to the same reference, or several samples to several references. One can choose between calculating individual warpings, or one global warping for a set of samples and one reference. Two optimization criteria are implemented: RMS (Root Mean Square error) and WCC (Weighted Cross Correlation). standalone software, mac os x, unix/linux, windows, r is listed by: OMICtools
has parent organization: CRAN
PMID:14719890 Free, Freely available OMICS_02392 SCR_003053 ptw: Parametric Time Warping 2026-02-14 02:00:29 0
Gutentag
 
Resource Report
Resource Website
Gutentag (RRID:SCR_003051) software resource An interactive, user-editable genetic sequence database tool, targeted at molecular biology research groups that can be browsed using tags. The tool is Web 2.0-flavoured, allowing users to do more than just retrieve information. Its focus on user-editability is supported by the use of tags (metadata) associated with genetic sequences. Several methods of retrieving stored data are available including tag-clouds, BLAST and keyword searches. Also, sequence tags related to HGNC gene names, conserved domains (CDD) and GO terms can be automatically generated given sequence data. The tool is constructed using the high-level Python web framework, Django, with a SQLite3 backend. standalone software, python, django, genetics, sequence is listed by: OMICtools
has parent organization: Google Code
PMID:14640709 Free, Available for download, Freely available OMICS_02396 SCR_003051 gutentag - A genetic sequence database for labs that can be browsed using tags 2026-02-14 02:00:21 0
Brain Operation Database
 
Resource Report
Resource Website
Brain Operation Database (RRID:SCR_003050) BODB data or information resource, storage service resource, database, service resource THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 4, 2023. BODB offers a way to document computational models of brain function by linking each model to Brain Operating Principles (BOPs), related brain regions, Summaries of Simulation Results (SSRs)and Summaries of Experimental Data (SEDs) used either to design or to test the model. Tools are provided to search for related models and to compare their coverage of SEDs. This allows automatic benchmarking of a model against a cluster of models addressing similar BOPs or SEDs or brain regions. Tools allow display of brain imaging results against a human brain applet; a new tool will link data to a macaque brain applet. model, brain operating principle, summary of experimental data, summary of simulation results, neural networks, mirror neuron, action, vision, language, usc brain project has parent organization: University of Southern California; Los Angeles; USA
is parent organization of: Model: Hebbian Mirror Neuron System (H-MNS) (Keysers - Perrett)
NSF 0924674 THIS RESOURCE IS NO LONGER IN SERVICE nif-0000-03080 http://bodb.usc.edu SCR_003050 BODB (Brain Operation DataBase) 2026-02-14 02:00:38 0
Brian Simulator
 
Resource Report
Resource Website
10+ mentions
Brian Simulator (RRID:SCR_002998) Brian software resource, simulation software, software application Software Python package for simulating spiking neural networks. Useful for neuroscientific modelling at systems level, and for teaching computational neuroscience. Intuitive and efficient neural simulator. simulation, spiking, neuron, brain, communication, modelling, computational neuroscience, python, spiking neuron, neural network is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC)
has parent organization: Ecole Normale Superieure; Paris; France
European Union ;
French National Research Agency ;
CNRS ;
Ecole Normale Superieure; Paris; France
DOI:10.7554/eLife.47314
DOI:10.3389/neuro.01.026.2009
DOI:10.7554/eLife.47314
Free, Available for download, Freely available nif-0000-30223 http://www.nitrc.org/projects/brian SCR_002998 Brian 2, Brian spiking neural network simulator, Brian2 2026-02-14 02:00:28 26
Allen Developing Mouse Brain Atlas
 
Resource Report
Resource Website
100+ mentions
Allen Developing Mouse Brain Atlas (RRID:SCR_002990) reference atlas, expression atlas, data or information resource, atlas, database Map of gene expression in developing mouse brain revealing gene expression patterns from embryonic through postnatal stages. Provides information about spatial and temporal regulation of gene expression with database. Feature include seven sagittal reference atlases created with a developmental ontology. These anatomic atlases may be viewed alongside in situ hybridization (ISH) data as well as by itself. gene, expression, developing, mouse, brain, pattern, embryonic, postnatal, stage, data, database, reference, atlas, ontology, anatomy, ISH is related to: Allen Brain Atlas API
is related to: Allen Human Brain Atlas: BrainSpan (Atlas of the Developing Brain)
has parent organization: Allen Institute for Brain Science
has parent organization: Allen Brain Atlas
PMID:22832508 Free, Public nif-0000-00509 SCR_002990 Allen Brain Atlas Developing Mouse Brain 2026-02-14 02:00:28 195
PacBioToCA
 
Resource Report
Resource Website
10+ mentions
PacBioToCA (RRID:SCR_003044) software resource A module in the Celera Assembler software package that performs error correction on PacBio long reads by mapping shorter, high accuracy reads onto the long reads. standalone software is listed by: OMICtools PMID:22750884 Free, Available for download, Freely available OMICS_05093 https://rhallpb.github.io/Applications/pacBioToCA.html SCR_003044 pacBioToCA (error correction via Celera Assembler) 2026-02-14 02:00:29 13
R-pbutils
 
Resource Report
Resource Website
R-pbutils (RRID:SCR_002995) software resource An R software package providing plotting and convenience functions. software package, r is listed by: OMICtools THIS RESOURCE IS NO LONGER IN SERVICE OMICS_05140 SCR_002995 2026-02-14 02:00:21 0
DIALIGN
 
Resource Report
Resource Website
10+ mentions
DIALIGN (RRID:SCR_003041) DIALIGN web service, data analysis service, analysis service resource, production service resource, service resource, data access protocol, software resource Tool for multiple sequence alignment using various sources of external information that is particularly useful to detect local homologies in sequences with low overall similarity. While standard alignment methods rely on comparing single residues and imposing gap penalties, DIALIGN constructs pairwise and multiple alignments by comparing entire segments of the sequences. No gap penalty is used. This approach can be used for both global and local alignment, but it is particularly successful in situations where sequences share only local homologies. Several versions of DIALIGN are available online at GOBICS, http://dialign.gobics.de/ dna, protein, sequence alignment, sequence, alignment, fasta, genome, genomic sequence, homology, bio.tools is listed by: OMICtools
is listed by: Debian
is listed by: bio.tools
is listed by: SoftCite
has parent organization: Bielefeld University; North Rhine-Westphalia; Germany
PMID:15215344
PMID:23620293
DOI:10.1186/1748-7188-3-6
Free, Available for download, Freely available nif-0000-30417, OMICS_24606, OMICS_00973, biotools:dialign-tx http://dialign.gobics.de/
https://bio.tools/dialign-tx
https://sources.debian.org/src/dialign-tx/ SCR_003041 DIALIGN at GOBICS 2026-02-14 02:00:21 43
Dana-Farber Cancer Institute
 
Resource Report
Resource Website
1+ mentions
Dana-Farber Cancer Institute (RRID:SCR_003040) DFCI institution Cancer institute that provides expert, compassionate care to children and adults with cancer while advancing the understanding, diagnosis, treatment, cure, and prevention of cancer and related diseases. As an affiliate of Harvard Medical School and a Comprehensive Cancer Center designated by the National Cancer Institute, the Institute also provides training for new generations of physicians and scientists, designs programs that promote public health particularly among high-risk and underserved populations, and disseminates innovative patient therapies and scientific discoveries to their target community across the United States and throughout the world.
child, adult human, pediatric, young human has parent organization: Harvard Medical School; Massachusetts; USA
is parent organization of: Spotfinder
is parent organization of: TM4 Microarray Software Suite - TIGR MultiExperiment Viewer
is parent organization of: Gene Index Project
is parent organization of: CistromeMap
is parent organization of: BINOCh
is parent organization of: Dana Farber Tissue Bank
is parent organization of: CistromeFinder
is parent organization of: TM4
is parent organization of: WorfDB
is parent organization of: Predictive Networks
is parent organization of: RamiGO
is parent organization of: DFCI Animal Resources Facility
is parent organization of: DFCI Biohazard Containment Core Facility
is parent organization of: DFCI Biospecimen Repository Core Facility
is parent organization of: DFCI Blais Proteomics Center
is parent organization of: DFCI Clinical Research Laboratory
is parent organization of: DFCI Survey and Data Management Core
is parent organization of: DFCI Flow Cytometry Core Facility
is parent organization of: DFCI Medical Arts Core Facility
is parent organization of: DFCI Microarray Core Facility
is parent organization of: Dana-Farber Cancer Institute Molecular Biology Core Facility
is parent organization of: DFCI RNA Interference Screening Facility
is parent organization of: DFCI Shannon McCormack Advanced Molecular Diagnostics Laboratory
is parent organization of: MAnorm
is parent organization of: NPS
is parent organization of: DFCI Confocal and Light Microscopy Core Facility
is parent organization of: DFCI Monoclonal Antibody Core Facility
is parent organization of: Dana-Farber Cancer Institute Labs and Facilities
is parent organization of: DFCI Center for Cancer Computational Biology
is parent organization of: GeneSigDB
is parent organization of: MACS
is parent organization of: DGAP
Cancer NCI ;
Jimmy Fund
Free, Freely available Crossref funder ID: 100007886, grid.65499.37, Wikidata: Q1159198, ISNI: 0000 0001 2106 9910, nif-0000-30432 https://ror.org/02jzgtq86 SCR_003040 Dana Farber Cancer Institute, Dana-Farber 2026-02-14 02:00:37 6
JournalGuide
 
Resource Report
Resource Website
1+ mentions
JournalGuide (RRID:SCR_003236) JournalGuide web service, data or information resource, data access protocol, software resource, database Database of journal information that provides tools to search, sort, filter, compare, and evaluate scholarly journals. In addition to searching by journal name, category or publisher, authors can use title and abstract of paper to discover journals that have already published articles on similar topics. Data sources include major industry data sets, public resources, information submitted directly by journal editors, and real-life publishing experiences submitted by authors. scholarly, journal is listed by: FORCE11 Free, Freely available nlx_157276 SCR_003236 Journal Guide 2026-02-14 02:00:31 4
EnablingOpenScholarship
 
Resource Report
Resource Website
EnablingOpenScholarship (RRID:SCR_003235) EOS knowledge environment An organization for universities and research institutions that is an information service and a forum for raising and discussing issues around the mission of modern universities and research institutions, particularly with regard to the creation, dissemination and preservation of research findings. Its aim is to further the opening up of scholarship and research that we are now seeing through the growing open access, open education, open science and open innovation movements. These, and other, "open" approaches to scholarship are changing the way research and learning are done and there are profound implications for universities and research institutions. EOS has been established to help guide developments and to assist others in understanding the issues and their implications. The context in which EOS has been established is that of increasing interest from governments, funders and the research community itself in opening up the way research is carried out and communicated. This interest is complemented by new research practices and processes that can work effectively only in an open, collaborative environment. Developments of relevance to the mission of EnablingOpenScholarship are reported on and news and details of forthcoming meetings, briefings and discussion sessions is provided. scholarship, open research, open access is listed by: FORCE11
has parent organization: University of Liege; Wallonia; Belgium
THIS RESOURCE IS NO LONGER IN SERVICE nlx_157274 SCR_003235 2026-02-14 02:00:43 0
Citation Style Language
 
Resource Report
Resource Website
1+ mentions
Citation Style Language (RRID:SCR_003234) CSL data or information resource, interchange format, markup language, narrative resource, standard specification An open XML-based language used to describe the formatting of citations and bibliographies. CSL has become the standard way to add citation support to software. annotation, markup, language is used by: Mendeley
is used by: BibSonomy
is used by: ReadCube
is used by: Zotero
is used by: Colwiz
is listed by: FORCE11
is related to: CitationStyles
Zotero ;
Papers ;
Mendeley
Free, Freely available nlx_157273 https://www.force11.org/node/5067 SCR_003234 Citation Styles 2026-02-14 02:00:24 1
GOLEM An interactive, graphical gene-ontology visualization, navigation, and analysis tool
 
Resource Report
Resource Website
1+ mentions
GOLEM An interactive, graphical gene-ontology visualization, navigation, and analysis tool (RRID:SCR_003191) GOLEM data analysis service, analysis service resource, production service resource, source code, service resource, software resource THIS RESOURCE IS NO LONGER IN SERVICE, documented July 7, 2017. Welcome to the home of GOLEM: An interactive, graphical gene-ontology visualization, navigation,and analysis tool on the web. GOLEM is a useful tool which allows the viewer to navigate and explore a local portion of the Gene Ontology (GO) hierarchy. Users can also load annotations for various organisms into the ontology in order to search for particular genes, or to limit the display to show only GO terms relevant to a particular organism, or to quickly search for GO terms enriched in a set of query genes. GOLEM is implemented in Java, and is available both for use on the web as an applet, and for download as a JAR package. A brief tutorial on how to use GOLEM is available both online and in the instructions included in the program. We also have a list of links to libraries used to make GOLEM, as well as the various organizations that curate organism annotations to the ontology. GOLEM is available as a .jar package and a macintosh .app for use on- or off- line as a stand-alone package. You will need to have Java (v.1.5 or greater) installed on your system to run GOLEM. Source code (including Eclipse project files) are also available. GOLEM (Gene Ontology Local Exploration Map)is a visualization and analysis tool for focused exploration of the gene ontology graph. GOLEM allows the user to dynamically expand and focus the local graph structure of the gene ontology hierarchy in the neighborhood of any chosen term. It also supports rapid analysis of an input list of genes to find enriched gene ontology terms. The GOLEM application permits the user either to utilize local gene ontology and annotations files in the absence of an Internet connection, or to access the most recent ontology and annotation information from the gene ontology webpage. GOLEM supports global and organism-specific searches by gene ontology term name, gene ontology id and gene name. CONCLUSION: GOLEM is a useful software tool for biologists interested in visualizing the local directed acyclic graph structure of the gene ontology hierarchy and searching for gene ontology terms enriched in genes of interest. It is freely available both as an application and as an applet. gene ontology, ontology visualization, ontology analysis is related to: Gene Ontology
has parent organization: Princeton University; New Jersey; USA
NIGMS R01 GM071966;
NSF IIS-0513552;
NIGMS P50 GM071508
PMID:17032457 THIS RESOURCE IS NO LONGER IN SERVICE nif-0000-30620 https://lsi.princeton.edu/golem-interactive-graph-based-gene-ontology-navigation-and-analysis-tool SCR_003191 GOLEM An interactive graphical gene-ontology visualization navigation and analysis tool, GOLEM An interactive graphical gene-ontology visualization navigation analysis tool 2026-02-14 02:00:42 3
ARC Centre of Excellence in Vision Science
 
Resource Report
Resource Website
ARC Centre of Excellence in Vision Science (RRID:SCR_003196) ACEVS data or information resource, portal, topical portal Centre of Excellence in Vision Science that brings together major vision research programs at the The Australian National University with cognate programs at the Universities of Queensland, Sydney and Western Australia. The research is focused on unravelling the cellular basis of visual sensing and processing; on revealing the algorithms that underlie the visual control of behavior and perception; and on discovering the cellular mechanisms that make the eye and retina stable, and whose breakdown causes blindness. vision, eye, retina, blindness, perception, behavior, sense has parent organization: Australian National University; Acton; Australia Australian Research Council Free, Freely available nlx_157285 https://www.nature.com/nature-index/institution-outputs/australia/arc-centre-of-excellence-in-vision-science-acevs/55d3f273140ba0b6018b456f SCR_003196 ARC Center of Excellence in Vision Science, Australian Research Council Centre of Excellence in Vision Science 2026-02-14 02:00:23 0
Inter-university Consortium for Political and Social Research (ICPSR)
 
Resource Report
Resource Website
10+ mentions
Inter-university Consortium for Political and Social Research (ICPSR) (RRID:SCR_003194) ICPSR data or information resource, organization portal, portal, consortium Data archive of more than 500,000 files of research in the social sciences, hosting 16 specialized collections of data in education, aging, criminal justice, substance abuse, terrorism, and other fields. ICPSR comprises a consortium of about 700 academic institutions and research organizations providing training in data access, curation, and methods of analysis for the social science research community. ICPSR welcomes and encourages deposits of digital data. ICPSR's educational activities include the Summer Program in Quantitative Methods of Social Research external link, a comprehensive curriculum of intensive courses in research design, statistics, data analysis, and social methodology. ICPSR also leads several initiatives that encourage use of data in teaching, particularly for undergraduate instruction. ICPSR-sponsored research focuses on the emerging challenges of digital curation and data science. ICPSR researchers also examine substantive issues related to our collections, with an emphasis on historical demography and the environment. psychiatry, survey, digital, social science, data archive, education, criminal justice, terrorism, child care, early education, data sharing, health, medical care, minority, mental health, political science, demography, economics, history, gerontology, public health, terrorism, psychology, sociology, foreign policy, terrorism, psychology, law uses: DataCite
lists: Advanced Cognitive Training for Independent and Vital Elderly (ACTIVE)
lists: Mexican Health and Aging Study
lists: Human Mortality Database
lists: Religion Aging and Health Survey
lists: Resources for Enhancing Alzheimers Caregiver Health
lists: Seattle Longitudinal Study
lists: Social Environment and Biomarkers of Aging Study in Taiwan
lists: Indonesia Family Life Survey
lists: Piedmont Health Survey of the Elderly
lists: English Longitudinal Study of Ageing
lists: Luxembourg Income Study
lists: Alameda County Health and Ways of Living Study
lists: Second Malaysian Family Life Survey
lists: Charleston Heart Study
lists: Census Microdata Samples Project
lists: Chinese Longitudinal Healthy Longevity Survey (CLHLS)
lists: Established Populations for Epidemiologic Studies of the Elderly
lists: Los Angeles Family and Neighborhood Survey
lists: Health and Retirement Study
lists: Iowa 65+ Rural Health Study
lists: Longitudinal Study of Generations
lists: Longitudinal Study of Elderly Mexican American Health
lists: Matlab Health and Socio-Economic Survey
lists: National Long Term Care Survey
lists: National Longitudinal Mortality Study
lists: National Longitudinal Survey of Older Men
lists: National Nursing Home Survey Follow-Up
lists: National Social Life Health and Aging Project (NSHAP)
lists: National Survey of the Japanese Elderly
lists: National Survey of Midlife Development in the United States
lists: Nihon University Japanese Longitudinal Study of Aging
lists: Panel Study of Income Dynamics
lists: Public Use Microdata Sample for the Older Population
lists: International Data Base
lists: German Socio-Economic Panel
lists: New Beneficiary Data System
lists: Longitudinal Studies of Aging
lists: National Survey of Families and Households
lists: National Survey of Self-Care and Aging
lists: Epidemiology of Chronic Disease in the Oldest Old
lists: Aging Status and Sense of Control (ASOC)
is listed by: re3data.org
has parent organization: University of Michigan; Ann Arbor; USA
is parent organization of: National Addiction and HIV Data Archive Program (NAHDAP)
is parent organization of: National Archive of Computerized Data on Aging (NACDA)
is parent organization of: Substance Abuse and Mental Health Data Archive
Aging, Substance abuse, Addiction, HIV NIH ;
NIA ;
NICHD ;
NIDA
nif-0000-00615 http://www.icpsr.umich.edu/icpsrweb/landing.jsp SCR_003194 Interuniversity Consortium for Political Social Research, Inter-university Consortium for Political Social Research (ICPSR), Interuniversity Consortium for Political and Social Research 2026-02-14 02:00:30 39
Wikispaces
 
Resource Report
Resource Website
1+ mentions
Wikispaces (RRID:SCR_003228) Wikispaces narrative resource, data or information resource, wiki, commercial organization A social writing platform, free for education, to easily create a classroom workspace where teacher and students can communicate and work on writing projects alone or in teams. Rich assessment tools give the power to measure student contribution and engagement in real-time. Wikispaces Classroom works great on modern browsers, tablets, and phones. For a fee it is also available to non-educators including companies, organizations, universities, groups, etc. collaboration, authoring, social network is listed by: FORCE11
is parent organization of: Pathology Informatics Curriculum Wiki
is parent organization of: Wellness Wiki
THIS RESOURCE IS NO LONGER IN SERVICE nlx_157269 SCR_003228 Wikispaces Classroom 2026-02-14 02:00:43 2
Primer Designer
 
Resource Report
Resource Website
1+ mentions
Primer Designer (RRID:SCR_003189) Primer Designer software resource THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 19,2025. Software program to aid in designing of primers and creation of primer sheets. The program allows users to select a background and enter mutaions. An initial primer is then suggested. User can manipulate the selected primer to add or remove nucleotides from either 5? or 3? ends. A set of parameters reflecting the goodness of the primer is updated on the fly, as the user makes changes. Once happy with the primer, the information is saved in a primer sheet, which can then be uploaded to the BGME lab primer database on the Wiki. primer, primer design is listed by: OMICtools
is listed by: SoftCite
THIS RESOURCE IS NO LONGER IN SERVICE OMICS_02327 https://www.thermofisher.com/us/en/home/life-science/oligonucleotides-primers-probes-genes/custom-dna-oligos/oligo-design-tools.html?ef_id=Cj0KCQjw-NfDBhDyARIsAD-ILeBszOXU4wXumqZJ--N8Z5rguB5P2-7UmpEuidzHsK1sgSXJROQ3of8aAtkqEALw_wcB:G:s&s_kwcid=AL!3652!3!683518170873!e!!g!!primer%20designer!20841448243!155985486683&cid=bid_mol_pch_r01_co_cp1358_pjt0000_bid00000_0se_gaw_nt_pur_con&gad_source=1&gad_campaignid=20841448243&gbraid=0AAAAADxi_GTCU-6xCgQrctnmtmtMSDEQj&gclid=Cj0KCQjw-NfDBhDyARIsAD-ILeBszOXU4wXumqZJ--N8Z5rguB5P2-7UmpEuidzHsK1sgSXJROQ3of8aAtkqEALw_wcB SCR_003189 2026-02-14 02:00:41 2
SALT
 
Resource Report
Resource Website
1000+ mentions
SALT (RRID:SCR_003187) SALT software resource Software that can accurately and sensitivity classify short reads of next-generation sequencing (NGS) into protein domain families. It is based on profile HMM and a supervised graph contribution algorithm. Compared to existing tools, it has high sensitivity and specificity in classifying short reads into their native domain families. next-generation sequencing, protein, protein domain, short read, bio.tools is listed by: OMICtools
is listed by: bio.tools
is listed by: Debian
has parent organization: SourceForge
PMID:23782615 Free, Available for download, Freely available OMICS_01565, biotools:salt https://bio.tools/salt SCR_003187 SALT - Protein domain classifier 2026-02-14 02:00:30 1294
resExomeDB
 
Resource Report
Resource Website
resExomeDB (RRID:SCR_003224) resExomeDB data repository, storage service resource, data or information resource, service resource, database THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 28,2025. An online catalog for whole-exome sequencing (WES) results including mutations and gene-disease associations identified by WES. It is browsable and searchable by mutation, gene, study or publication. In addition, it centralizes all publications, software, platforms related to exome / whole genome sequencing. whole-exome sequencing, archiving, data management, mutation, gene, gene-disease association, exome, whole genome sequencing, genome, sequencing, exome sequencing is listed by: FORCE11 THIS RESOURCE IS NO LONGER IN SERVICE nlx_157263 SCR_003224 2026-02-14 02:00:43 0
XORRO
 
Resource Report
Resource Website
1+ mentions
XORRO (RRID:SCR_003181) XORRO software resource Efficient paired-read overlap software program for use with Illumina sequencing. illumina, next-generation sequencing is listed by: OMICtools
has parent organization: SourceForge
Free, Available for download, Freely available OMICS_01569 SCR_003181 XORRO: Rapid Paired-End Read Overlapper 2026-02-14 02:00:41 1

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