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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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DepthSizer Resource Report Resource Website 1+ mentions |
DepthSizer (RRID:SCR_021232) | data analysis software, data processing software, sequence analysis software, software application, software resource | Software tool for read-depth based genome size prediction. Wrapper for genome size estimate methods of Diploidocus.Uses long read depth of coverage and BUSCO single copy orthologue prediction to estimate genome size. | Genome size prediction, genome size estimate wrapper, estimate genome size | is used by: Diploidocus | Free, Available for download, Freely available | SCR_021232 | 2026-09-19 12:54:50 | 2 | ||||||||||
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Lung Disease Knowledge Portal Resource Report Resource Website 1+ mentions |
Lung Disease Knowledge Portal (RRID:SCR_021352) | LDKP | data or information resource, data repository, disease-related portal, portal, service resource, storage service resource, topical portal | Portal enables browsing, searching, and analysis of human genetic information linked to lung diseases and related traits, while protecting integrity and confidentiality of underlying data. | Human genetic information, lung diseases, data searching, data analysis | Free, Freely available | SCR_021352 | 2026-09-19 12:54:51 | 2 | ||||||||||
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Evidence Graph Ontology Resource Report Resource Website |
Evidence Graph Ontology (RRID:SCR_021225) | EVI | controlled vocabulary, data or information resource, ontology | Evidence Graph Ontology extends core concepts from W3C Provenance Ontology PROV-O to describe evidence for correctness of findings in biomedical publications. Semantic data model in EVI is expressed using OWL2 Web Ontology Language. | Biomedical ontology, W3C Provenance Ontology concepts, PROV-O, evidence for correctness of findings, biomedical publications, OWL2 Web Ontology Language, semantic data model, EVI semantic model | has parent organization: University of Virginia; Virginia; USA | Free, Freely available | SCR_021225 | 2026-09-19 12:54:50 | 0 | |||||||||
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GMSH Resource Report Resource Website 10+ mentions |
GMSH (RRID:SCR_021226) | software resource | Open source software tool as 3D finite element grid generator with build in CAD engine and post processor. Provides meshing tool with parametric input and advanced visualization capabilities. Built around geometry, mesh, solver and post processing modules.Specification of any input to these modules is done either interactively using graphical user interface, in ASCII text files using Gmsh own scripting language (.geo files), or using C plus plus, C, Python or Julia Application Programming Interface. | 3D finite element grid generator, CAD engine build in, post processor, meshing tool | Free, Available for download, Freely available | https://gitlab.onelab.info/gmsh/gmsh | SCR_021226 | 2026-09-19 12:54:50 | 27 | ||||||||||
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ploidyNGS Resource Report Resource Website 1+ mentions |
ploidyNGS (RRID:SCR_021320) | data analysis software, data processing software, data visualization software, software application, software resource | Open source software tool for visually exploring ploidy with Next Generation Sequencing data.Used to visualize and explore ploidy levels in newly sequenced genome, exploiting short read data. Allows identification of ploidy level of newly sequenced genome in visual way. Implemented in Python and R. | Visually exploring ploidy, Next Generation Sequencing, newly sequenced genome, exploiting short read data | Sao Paulo Research Foundation | PMID:28383704 | Free, Available for download, Freely available | SCR_021320 | 2026-09-19 12:54:51 | 8 | |||||||||
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Atria Resource Report Resource Website 1+ mentions |
Atria (RRID:SCR_021313) | 1d time-series analysis software, data analysis software, data processing software, software application, software resource, time-series analysis software | Open source software tool as adapter and quality trimmer for Next-Generation Sequence data. | Adapter, quality trimmer, Next-Generation Sequence data, NGS data | Free, Freely available | SCR_021690 | SCR_021313 | Atria Trimming Software v3.0.0 | 2026-09-19 12:54:51 | 3 | |||||||||
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BioSpherix: A-Chamber Resource Report Resource Website 1+ mentions |
BioSpherix: A-Chamber (RRID:SCR_021177) | instrument resource | Animal Cage Enclosures for use in in vivo models that require control of experimental gases such as O2, CO2, NO, or CO. May be used together with gas controllers from BioSpherix. Chamber is outfitted with adjustable ventilation holes which permit ventilation of animal vapors and gases while simultaneously ensuring stable control of experimental conditions within. Available in three standard sizes. | Animal Cage Enclosures, control of experimental gases, chamber adjustable ventilation holes, BioSpherix Ltd. | Commercially Available | https://raw.githubusercontent.com/SciCrunch/RRID-Instruments/refs/heads/main/PDF/SCR_021177.pdf | SCR_021177 | , A-Chamber, A-Chamber Animal Cage Enclosure | 2026-09-19 12:54:49 | 2 | |||||||||
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VanderBot Resource Report Resource Website |
VanderBot (RRID:SCR_021298) | data management software, software application, software resource | Software Python tool as Vanderbilt University curation tool.Used for exporting public profiles of university faculty from Vanderbilt University database into Wikidata.Used to create or update items in Wikidata using data from CSV spreadsheet data. | Curation tool, Vanderbilt University, Wikidata, biographical data, profile, profiling |
is related to: Wikidata is related to: Vanderbilt University; Tennessee; USA |
Free, Freely available | SCR_021306, Wikidata_Q107014192 | https://www.wikidata.org/wiki/Q107014192 | SCR_021298 | Vanderbot | 2026-09-19 12:54:51 | 0 | |||||||
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ALLMAPS Resource Report Resource Website 1+ mentions |
ALLMAPS (RRID:SCR_021171) | software resource | Software tool for computing scaffold ordering that maximizes colinearity to collection of maps, including genetic, physical or comparative maps into final chromosome build.Robust scaffold ordering based on multiple maps. | Scaffold ordering, maps collection, genetic maps, physical maps, comparative maps, chromosome build | Fujian 100 Talent Plan award ; Gordon and Betty Moore Foundation ; National Science Foundation DBI 0735191; National Science Foundation DBI 1265383 |
PMID:25583564 | Free, Available for download, Freely available | SCR_021171 | 2026-09-19 12:54:49 | 6 | |||||||||
|
Juicebox Resource Report Resource Website 100+ mentions |
Juicebox (RRID:SCR_021172) | data analysis software, data processing software, data visualization software, software application, software resource | Visualization and analysis software for Hi-C data. | Hi-C data, data visualization, data analysis | Free, Available for download, Freely available | SCR_021172 | 2026-09-19 12:54:49 | 222 | |||||||||||
|
BioSpherix: Biological Safety Hood Resource Report Resource Website |
BioSpherix: Biological Safety Hood (RRID:SCR_021206) | instrument resource | Hood holds any animal lab chambers while continuously sweeping all experiment related off gases away.Used to capture and exhaust gases or vapors which escape from animal chamber and directs them to safe location.Helps to control animal odor in the lab. Available in standard and customized dimensions. | Safety hood, animal chambers, capture gases, exhaust gases, BioSpherix, instrument, equipment, USEDit | is listed by: USEDit | Commercially Available | https://raw.githubusercontent.com/SciCrunch/RRID-Instruments/refs/heads/main/PDF/SCR_021206.pdf | SCR_021206 | Safety Hood, Safety Hood for Animal Chambers | 2026-09-19 12:54:50 | 0 | ||||||||
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Illumina Experiment Manager Resource Report Resource Website 1+ mentions |
Illumina Experiment Manager (RRID:SCR_021202) | IEM | data management software, software application, software resource | Software to create and edit sample sheet in order to perform next generation sequencing on Illumina paltforms. Used for MiniSeq, MiSeq, NextSeq 500/550, HiSeq, and NovaSeq 6000 Systems. | Create sample sheet, edit sample sheet, next generation sequencing, Illumina paltforms | Free, Available for download, Freely available | SCR_021202 | Illumina Experiment Manager software, Illumina Experiment Manager v1.18.1, Illumina Experiment Manager v1.19.1 | 2026-09-19 12:54:50 | 3 | |||||||||
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Noldus: CatWalk XT Resource Report Resource Website 10+ mentions |
Noldus: CatWalk XT (RRID:SCR_021262) | instrument resource | Gait analysis system for quantitative assessment of footfalls and locomotion in rats and mice. System includes corridor that directs free movement in straight line, hardened glass walkway that enables CatWalk XT Illuminated Footprints technology,high speed color camera for spatial and temporal resolution, CatWalk XT software for recording and automated analysis of locomotor ability of rodents. | CatWalk XT, gait analyses, gait analysis system, instrument, equipment, USEDit | is listed by: USEDit | Commercially available | SCR_021262 | CatWalk XT, Noldus | 2026-09-19 12:54:51 | 13 | |||||||||
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ChronoRoot Resource Report Resource Website 1+ mentions |
ChronoRoot (RRID:SCR_021259) | 2d time-series analysis software, data analysis software, data processing software, image processing software, software application, software resource, time-series analysis software | System which combines 3D printed open hardware with deep segmentation networks for high temporal resolution phenotyping of plant roots in agarized medium. Deep learning based root extraction method which leverages the latest advances in convolutional neural networks for image segmentation, and incorporates temporal consistency into the root system architecture reconstruction process. | 3D printed open hardware, deep segmentation networks, high temporal resolution phenotyping, plant roots, convolutional neural networks, image segmentation | Free, Available for download, Freely available | SCR_021259 | 2026-09-19 12:54:51 | 3 | |||||||||||
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Leica: Aperio AT2 scanner Resource Report Resource Website 10+ mentions |
Leica: Aperio AT2 scanner (RRID:SCR_021256) | instrument resource | Digital whole slide scanner.400 slide capacity brightfield scanner. High throughput with small footprint. 2x3 slide option available.Aperio AT2 runs on Microsoft Windows 10 operating system. | Digital whole slide scanner, scanner, instrument, equipment, USEDit | is listed by: USEDit | Model_Number_Aperio_AT2 | SCR_021256 | Aperio AT2 | 2026-09-19 12:54:51 | 28 | |||||||||
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TailTimer Resource Report Resource Website 1+ mentions |
TailTimer (RRID:SCR_021277) | instrument resource | Device for automating tail immersion assay. Used for measuring acute thermal pain in rodents. Software recognizes several specific RFID keys as user interface commands, which allows TailTimer to be operated via RFID fobs. | Automating tail immersion assay, measuring acute thermal pain, pain in rodents, thermal pain | SCR_021277 | 2026-09-19 12:54:51 | 1 | ||||||||||||
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KinTek Explorer Resource Report Resource Website 50+ mentions |
KinTek Explorer (RRID:SCR_021274) | data analysis software, data processing software, simulation software, software application, software resource | Software tool for fitting kinetic and equilibrium data based on numerical integration of rate equation from any model input user. Simulation and data-fitting software for research and education designed specifically for the field of chemical kinetics. | Kinetic data fitting, equilibrium data fitting, rate equation, data fitting, chemical kinetics | Restricted | SCR_021274 | 2026-09-19 12:54:51 | 54 | |||||||||||
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Software for generation of GB-speckles Resource Report Resource Website |
Software for generation of GB-speckles (RRID:SCR_021272) | GB-speckles | 1d time-series analysis software, 2d spatial image, data analysis software, data or information resource, data processing software, image, software application, software resource, time-series analysis software | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on March 23, 2022. | GB-speckles | RFBR 20-04-60349 | THIS RESOURCE IS NO LONGER IN SERVICE | SCR_021272 | 2026-09-19 12:54:51 | 0 | |||||||||
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COVTree Resource Report Resource Website |
COVTree (RRID:SCR_021307) | COVTree | analysis service resource, data access protocol, production service resource, service resource, software resource, web service | Web server providing online analysis of coevolving amino acid pairs in overlapping genes, where residues might be located inside or outside overlapping region. | Coevolution analysis, coevolving amino acid pairs, overlapping genes, overlapping region, residues location | French Government ; French National Agency for Research against HIV and Hepatitis |
PMID:32374885 | Free, Freely available | SCR_021307 | Coevolution in OVerlapped sequences by Tree | 2026-09-19 12:54:51 | 0 | |||||||
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Bash Resource Report Resource Website 10+ mentions |
Bash (RRID:SCR_021268) | software resource | GNU Project shell. Sh-compatible shell that incorporates useful features from Korn shell (ksh) and the C shell (csh). Improvements offered by Bash include command-line editing, unlimited size command history,job control,shell functions and aliases,indexed arrays of unlimited size,integer arithmetic in any base from two to sixty four. | GNU Project shell, command-line editing, unlimited size command history, job control, shell functions and aliases, indexed arrays of unlimited size, integer arithmetic | Free, Freely available | SCR_021268 | Bourne Again SHell | 2026-09-19 12:54:51 | 19 |
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The NIDDK Information Network (dkNET) serves the needs of basic and clinical investigators by providing seamless access to large pools of data and research resources relevant to the mission of The National Institute of Diabetes Digestive and Kidney Diseases (NIDDK). dkNET is hosted at University of California San Diego, and is supported by NIH NIDDK grant U24DK097771.
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