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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.
| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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RobotReviewer Resource Report Resource Website 1+ mentions |
RobotReviewer (RRID:SCR_021064) | software application, text-mining software, web application, software resource | Open source web based system that uses machine learning and NLP to semi automate biomedical evidence synthesis, to aid practice of Evidence Based Medicine. Processes full text journal articles describing randomized controlled trials. Designed to automatically extract key data items from reports of clinical trials. | Data automatic extraction, clinical trial reports, automatically extract key data, Evidence Based Medicine, text journal articles processing, randomized controlled trials |
is related to: Northeastern University; Massachusetts; USA is related to: University of Texas at Austin; Texas; USA |
NLM R01 LM012086; Medical Research Council UK ; NCI UH2 CA203711 |
PMID:29093610 DOI:10.1093/jamia/ocv044 |
Free, Available for download, Freely available | https://github.com/ijmarshall/robotreviewer, https://robotreviewer.vortext.systems/ | SCR_021064 | Automating Biomedical Evidence Synthesis | 2026-08-15 11:26:51 | 1 | ||||||
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Nikon: SMZ1500 Zoom Stereoscope Resource Report Resource Website |
Nikon: SMZ1500 Zoom Stereoscope (RRID:SCR_018605) | instrument resource | SMZ1500 stereoscopic zoom microscope is system with apochromatic objectives, zoom ratio of 15 to 1, range of magnifications from 0.75x to 11.25x for total magnifying capability of 3.75x up to 540x, and is best for in depth imaging.Zoom knob allows to zoom from 1x to 11x at 1x-intervals without interrupting observations. Other facets include high eyepoint eyepieces with built-in diopter adjustments, wide field of view, and built-in aperture diaphragm for achieving optimal depth of focus and improved photomicrography.Provides options of either low eye-level viewing tube or tilting eyepiece tube, with or without eye-level risers. Three different diascopic stands with built-in power supplies may also be utilized with instrument, or standard stand that features low profile for increased clearance. | Fluorescence Dissection Microscope, Instrument, Equipment, Nikon, USEDit, ABRF | Commercially available | https://raw.githubusercontent.com/SciCrunch/RRID-Instruments/refs/heads/main/PDF/SCR_018605.pdf | Model_Number_SMZ1500, SCR_020314, SCR_020327 | https://www.coherent.com.au/content/media/Nikon/SMZ1500.pdf | SCR_018605 | Nikon 1500 Fluorescence Dissection Microscope | 2026-08-15 11:25:55 | 0 | |||||||
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Packard: Cobra 5000 Gamma Counter Resource Report Resource Website 1+ mentions |
Packard: Cobra 5000 Gamma Counter (RRID:SCR_018609) | instrument resource | Gamma counter available in single, five, or ten detector configurations. Can count RIA tubes, 16x100mm and variety of smaller micro tubes using available adapter.This instrument has dot Matrix Printer, tube racks, and protocol ID tags.Single detector model is available in 2 inch or 3 inch crystal configurations for research grade capabilities. | Gamma Counter, Instrument, Equipment, USEDit, Packard Cobra, ABRF | is listed by: USEDit | Commercially available | Model_Number_Packard_Cobra_5000, SCR_020391 | SCR_018609 | 2026-08-15 11:25:56 | 2 | |||||||||
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Stanford Shimadzu 8030 LC/MS mass spectrometer Resource Report Resource Website |
Stanford Shimadzu 8030 LC/MS mass spectrometer (RRID:SCR_018699) | instrument resource | Shimadzu 8030 triple quadrupole mass spectrometer used for targeted quantitation applications. Listed by Stanford University Mass Spectrometry Vincent Coates Foundation Instruments. | Liquid chromatography mass spectrometry, Shimadzu 8030, triple quadrupole mass spectrometer, targeted quantitation, instrument, equipment, USEDit | is used by: Stanford University Vincent Coates Foundation Mass Spectrometry Laboratory Core Facility | https://raw.githubusercontent.com/SciCrunch/RRID-Instruments/refs/heads/main/PDF/SCR_018699.pdf | Model_Number_Shimadzu_LCMS-8030 | https://industry.pharmaceutical-tech.com/suppliers/shimadzu-asia-pacific-pte-ltd/products/1611295961-liquid-chromatograph-mass-spectrometer.pdf | SCR_018699 | Stanford University Vincent Coates Foundation Mass Spectrometry Laboratory Core FacilityLC/MS | 2026-08-15 11:25:57 | 0 | |||||||
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Promega: TBS-380 Fluorimeter Resource Report Resource Website |
Promega: TBS-380 Fluorimeter (RRID:SCR_018615) | instrument resource | Dual channel fluorimeter for fluorescence measurements when calibrated with known concentration to measure compounds at low concentration with low assay volume. | Fluorometer, Instrument, Equipment, USEDit, ABRF, Promega | is listed by: USEDit | Model_Number_TBS_380 | https://www.promega.com/-/media/files/products-and-services/instruments/detection/tbs-technical-support-docs/tbs380-manual.pdf?la=en | SCR_018615 | 2026-08-15 11:25:55 | 0 | |||||||||
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Promega: GloMax 96 Microplate Luminometer Resource Report Resource Website 1+ mentions |
Promega: GloMax 96 Microplate Luminometer (RRID:SCR_018614) | instrument resource | Microplate luminometer that features two optional injectors and reads both glow- and flash-luminescent reactions in 96-well plates. The sensitivity and range enable a wide range of luminescent assays, including Promega bioluminescent reporter, cell-based and biochemical assays., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | Microplate Luminometer, Instrument, Equipment, Luminometer, USEDit, Promega, ABRF | THIS RESOURCE IS NO LONGER IN SERVICE | https://raw.githubusercontent.com/SciCrunch/RRID-Instruments/main/PDF/SCR_019964.pdf | SCR_019964, Model_Number_GloMax_96 | https://www.promega.com/-/media/files/resources/protocols/technical-manuals/0/glomax-96-microplate-luminometer-protocol.pdf | SCR_018614 | GloMax 96 Microplate Luminometer | 2026-08-15 11:25:55 | 4 | |||||||
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Agilent: 7890/5975 GC/MS system Resource Report Resource Website 1+ mentions |
Agilent: 7890/5975 GC/MS system (RRID:SCR_018695) | instrument resource | Agilent GC/MS is single quadrupole instrument with electron ionization. GC/MS runs under ChemStation open access software, and trained open access users select from menu of standard methods to analyze their samples. | Agilent GC/MS, quadrupole instrument, electron ionization, ChemStation software, sample analyzer, instrument, equipment, USEDit | is used by: Stanford University Vincent Coates Foundation Mass Spectrometry Laboratory Core Facility | https://raw.githubusercontent.com/SciCrunch/RRID-Instruments/refs/heads/main/PDF/SCR_018695.pdf | https://www.agilent.com/cs/library/usermanuals/public/G3170-90036.pdf | SCR_018695 | Agilent 7890/5975 GC/MS | 2026-08-15 11:25:57 | 1 | ||||||||
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piNET Resource Report Resource Website 1+ mentions |
piNET (RRID:SCR_018693) | production service resource, web service, data access protocol, software resource, service resource, analysis service resource | Web platform for downstream analysis and visualization of proteomics data. Server that facilitates integrated annotation, analysis and visualization of quantitative proteomics data, with emphasis on PTM networks and integration with LINCS library of chemical and genetic perturbation signatures in order to provide further mechanistic and functional insights. Primary input for server consists of set of peptides or proteins, optionally with PTM sites, and their corresponding abundance values. | Analysis, visualization, proteomics data, integrated annotation, quantitative proteomics data, PTM network, LINCS library integration, genetic perturbation signature, peptide, protein, post translational modification site, PTM site, data | is related to: LINCS Project | NHLBI U54 HL127624; NIEHS P30 ES006096; NIMH R01 MH107487; NCI T32 CA236764; NCATS UL1 TR001425; NIGMS U01 GM120953 |
DOI:10.1093/nar/gkaa436 | Free, Freely available | SCR_018693 | 2026-08-15 11:25:58 | 4 | ||||||||
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Qiagen: PyroMark Q96 System Resource Report Resource Website 10+ mentions |
Qiagen: PyroMark Q96 System (RRID:SCR_018617) | instrument resource | Sequencing and quantification platform for epigenetics, mutation gene expression analysis, and microbial identification and resistance typing. With its 96-well format, automatic base-calling function, and dedicated software solutions for methylation analysis and assay design. | Pyrosequencer, Instrument, Equipment, Qiagen, USEDit, ABRF | is listed by: USEDit | SCR_020413, Model_Number_Q96 | SCR_018617 | 2026-08-15 11:25:56 | 11 | ||||||||||
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Rigaku: Alchemist II Liquid Handler Resource Report Resource Website |
Rigaku: Alchemist II Liquid Handler (RRID:SCR_018625) | instrument resource | Liquid handling system for production of complex liquid formulations produced from individual stock solutions of various chemical and liquid properties. With a CV of less than 2%. | Rigaku, Liquid Handler, Instrument Equipment, USEDit | is listed by: USEDit | SCR_019564, Model_Number_Alchemist_II | SCR_018625 | 2026-08-15 11:25:56 | 0 | ||||||||||
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rVista Resource Report Resource Website 10+ mentions |
rVista (RRID:SCR_018707) | production service resource, web service, data access protocol, software resource, service resource, analysis service resource | Web tool for analyzing regulatory potential of noncoding sequences. rVISTA web server is interconnected with TRANSFAC database, allowing users to either search for matrices present in TRANSFAC library collection or search for user defined consensus sequences. rVISTA 2.0 web server is used for high throughput discovery of cis-regulatory elements. Can process alignments generated by zPicture and blastz alignment programs or use pre-computed pairwise alignments of several vertebrate genomes available from ECR Browser and GALA database. Evolutionary analysis of transcription factor binding sites. | Noncoding sequence, regulatory potential analysis, matrices search, TRANSFAC library collection, cis regulatory element, process alignment, zPicture, blastz, pairwise alignment, genome, analysis, transcription factor binding site, bio.tools |
is listed by: Debian is listed by: bio.tools works with: TRANSFAC |
PMID:15215384 | Free, Freely available | biotools:rvista | https://bio.tools/rvista | SCR_018707 | rVista 2.0 | 2026-08-15 11:25:57 | 34 | ||||||
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FunCoup Resource Report Resource Website 1+ mentions |
FunCoup (RRID:SCR_018711) | database, web service, data or information resource, data access protocol, software resource, service resource | Database of genome wide functional coupling networks. Provides tools to explore predicted networks and to retrieve detailed information about data underlying each prediction. Web service for functional coupling search. | Genome, genome functional coupling network, coupling network, functional coupling, functional couplings search, gene identifier, genome data | has parent organization: Karolinska Institute; Stockholm; Sweden | Swedish Research Council ; Stockholm University |
PMID:24185702 | Free, Freely available | SCR_018711 | 2026-08-15 11:25:58 | 3 | ||||||||
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NGScloud2 Resource Report Resource Website 1+ mentions |
NGScloud2 (RRID:SCR_018716) | data processing software, software application, data analysis software, software resource | Software tool for RNA-seq analysis of non model species using cloud computing. Provides user friendly front end to operate Amazon hardware resources and to control workflows of bioinformatic analysis of de novo RNA-seq, reference-based RNA-seq and functional annotation specifically oriented to plant species. | RNAseq analysis, non model species, cloud computing, AWS, spot instances, RNAseq, RADseq, functional annotation, plant | Spanish National Parks Agency Ministry of Agriculture ; Spanish Ministry of Economy and Competitiveness ; Amazon Research Grant |
PMID:29726914 | Free, Available for download, Freely available | https://github.com/GGFHF/NGScloud/ | SCR_018716 | NGScloud | 2026-08-15 11:25:57 | 1 | |||||||
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Thermo Fisher: GeneAtlas System Resource Report Resource Website 1+ mentions |
Thermo Fisher: GeneAtlas System (RRID:SCR_018715) | instrument resource | System for processing Affymetrix microarrays. Microarray analysis system. Includes array strip and hybridization assembly, Fluidics station, Imaging station. | ABRF, Affymetrix, instrument, Thermo Fisher Scientific, Affymetrix Gene Atlas Fluidics Station, Affymetrix HuGene, Geneatlas system, imaging station, equipment |
is listed by: USEDit works with: Affymetrix Transcriptome Analysis Console Software works with: Affymetrix Transcriptome Analysis Console Software |
https://assets.thermofisher.com/TFS-Assets/LSG/brochures/geneatlas_system_brochure.pdf | SCR_018715 | GeneAtlas System, Affymetrix GeneAtlas System | 2026-08-15 11:25:58 | 1 | |||||||||
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Thermo Fisher: NanoDrop 8000 Spectrophotometer Resource Report Resource Website 1+ mentions |
Thermo Fisher: NanoDrop 8000 Spectrophotometer (RRID:SCR_018600) | instrument resource | Microvolume UV Vis spectrophotometer for nucleic acid and protein quantification that can measure multiple samples using 1 to 2 uL of samples. Can analyze spectrum of 220nm to 750nm and measure 96 samples in less than six minutes. Can measure multiple samples in one measurement cycle, up to eight samples at one time. Has single sample mode. Can analyze the full spectrum from 220 to 750nm and calculates sample purity ratios 260/280. | Spectrophotometer, Instrument, Equipment, Nanodrop, USEDit, ABRF |
is listed by: USEDit is related to: Thermo Fisher: NanoDrop Lite Spectrophotometer |
Commercially available | Model_Number_NanoDrop_8000, SCR_020315 | https://afns-labs.ualberta.ca/wp-content/uploads/sites/58/2018/05/Nanodrop-ND-8000-brochure.pdf.pdf | SCR_018600 | 2026-08-15 11:25:56 | 7 | ||||||||
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PRISMA Resource Report Resource Website 1000+ mentions |
PRISMA (RRID:SCR_018721) | PRISMA | narrative resource, data or information resource, portal, standard specification | Evidence based minimum set of items for reporting in systematic reviews and meta analyses. Focuses on reporting of reviews evaluating randomized trials, but can also be used as basis for reporting systematic reviews of other types of research, particularly evaluations of interventions. | MDAR, standard, report standard, reporting reviews, randomized trial, evaluating randomized trial, reporting systematic review, intervention evaluation, meta analysis | is listed by: SoftCite | Ottawa Hospital Research Institute ; University of Oxford |
Free, Freely available | SCR_018721 | Preferred Reporting Items for Systematic Reviews and Meta-Analyses | 2026-08-15 11:25:58 | 1593 | |||||||
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CONSORT Resource Report Resource Website 100+ mentions |
CONSORT (RRID:SCR_018720) | CONSORT | standard specification, portal, data or information resource, organization portal, narrative resource | Standards for transparent trials reporting. Encompasses various initiatives developed by CONSORT Group to alleviate problems arising from inadequate reporting of randomized controlled trials. Main product of CONSORT is CONSORT Statement, which is evidence based, minimum set of recommendations for reporting randomized trials. CONSORT Statement is endorsed by medical journals and leading editorial organizations. | MDAR, standard, transparent trial, trial reporting, CONSORT group, controlled trial, CONSORT Statement, randomized trials reporting, medical journal, editorial organization, reporting | is related to: CONSORT TM | Medical Research Council ; Family Health International ; University of Oxford ; Ottawa Hospital Research Institute |
Free, Freely available | SCR_018720 | Consolidated Standards of Reporting Trials | 2026-08-15 11:25:57 | 389 | |||||||
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Monocle3 Resource Report Resource Website 100+ mentions |
Monocle3 (RRID:SCR_018685) | software toolkit, data processing software, software application, data analysis software, software resource | Software analysis toolkit for single cell RNA-seq. Used for single cell RNA-Seq experiments. Unsupervised algorithm that increases temporal resolution of transcriptome dynamics using single-cell RNA-Seq data collected at multiple time points. | Data analysis, singel cell RNAseq data, single cell RNAseq experiment, transcriptome dynamics | has parent organization: University of Washington; Seattle; USA | NIH Office of the Director DP2 OD00667; NIGMS P01 GM099117; NIH Office of the Director DP2 0D008514; NHGRI P50 HG006193; Single Cell Genomics initiative |
PMID:24658644 | Free, Available for download, Freely available | https://github.com/cole-trapnell-lab/monocle3 | SCR_018685 | Monocle, Monocle 3 | 2026-08-15 11:25:56 | 342 | ||||||
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Nikon: AZ100 Confocal Microscope Resource Report Resource Website 1+ mentions |
Nikon: AZ100 Confocal Microscope (RRID:SCR_018603) | instrument resource | Nikon Instruments AZ100 C1si is macro confocal microscope system combining stereo and compound microscopes into single hybrid imaging system for dynamic imaging of single cells or whole specimens.System covers range of magnifications from 5x to 400x. Has triple nosepiece that can switch magnifications. AZ100 C1si boasts simultaneous 32 channel spectral image acquisition over spectral range of 320 nm in single scan. Simultaneous 32 channel acquisition at 10 nm, 5 nm or 2.5 nm bandwidths, all software controlled, is possible. | Confocal Microscope, Instrument, Equipment, Nikon, USEDit, ABRF | is listed by: USEDit | Commercially available | https://raw.githubusercontent.com/SciCrunch/RRID-Instruments/main/PDF/SCR_018603.pdf | Model_Number_AZ100, SCR_020325 | https://www.mvi-inc.com/wp-content/uploads/AZ100-Manual.pdf | SCR_018603 | 2026-08-15 11:25:55 | 2 | |||||||
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MicroFilePlus Resource Report Resource Website 1+ mentions |
MicroFilePlus (RRID:SCR_018724) | data processing software, software application, image processing software, software resource | Software tool as microscopy image file format converter by MBF Bioscience. Converts common microscopy image files to JPEG2000 and OME-TIFF. Used to view, analyze, and share big image data from many sources. | Image file format, image converter, converter, OME-TIFF Format, jpeg2000, jpx, JP2, MBF Bioscience | Restricted | SCR_018724 | MicroFilePlus, MicroFile+, microfileplus | 2026-08-15 11:25:57 | 2 |
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