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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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EpiModel Resource Report Resource Website 1+ mentions |
EpiModel (RRID:SCR_018539) | data analysis software, data processing software, software application, software resource, software toolkit | Software R package for mathematical modeling of infectious disease over networks. Provides tools for simulating and analyzing mathematical models of infectious disease dynamics. Mathematical Modeling of Infectious Disease Dynamics. | Infectious disease, mathematical modeling, simulation, analysis, infectious disease dynamic, bio.tools |
is listed by: Debian is listed by: bio.tools |
NIAID P30 AI027757; NIAID P30 AI050409; NICHD R01 HD068395; NICHD R21 HD075662; NICHD T32 HD007543; NIDA P30 DA027828; NIMH R21 MH112449 |
PMID:29731699 | Free, Available for download, Freely available | biotools:epimodel | https://bio.tools/epimodel | SCR_018539 | SciCrunch Registry | 2026-10-24 12:47:58 | 8 | ||||||
|
Phyutility Resource Report Resource Website 10+ mentions |
Phyutility (RRID:SCR_018545) | data analysis software, data processing software, software application, software resource | Command line program that performs analyses or modifications on both trees and data matrices. Software phyloinformatics tool for trees, alignments and molecular data. Used for summarizing and manipulating phylogenetic trees, manipulating molecular data and retrieving data from NCBI. | Data matrice analysis, data matrice modification, phyloinformatics, phylogenetic tree, alignment, molecular data manipulation, data analysis |
is listed by: Debian is listed by: OMICtools is listed by: SoftCite is related to: NCBI |
NSF Cyberinfrastructure for Phylogenetic Research EF 0331654 | PMID:18227120 | Free, Freely available | OMICS_21687 | https://sources.debian.org/src/phyutility/ | SCR_018545 | SciCrunch Registry | 2026-10-24 12:47:58 | 46 | ||||||
|
PhyDyn Resource Report Resource Website 10+ mentions |
PhyDyn (RRID:SCR_018544) | simulation software, software application, software resource | Sofware package for performing Bayesian phylogenetic inference under models that deal with structured populations with complex population dynamics. Enables simultaneous estimation of epidemiological parameters and pathogen phylogenies. Epidemiological modelling in BEAST. | Bayesian phylogenetic inference, epidemiological modelling, epidemiological parameter estimation, pathogen phylogeny estimation |
is related to: BEAST2 is related to: BEAST |
MRC Centre for Global Infectious Disease Analysis ; NIGMS U01 GM110749 |
PMID:30422979 | Free, Available for download, Freely available | SCR_018544 | SciCrunch Registry | 2026-10-24 12:47:58 | 10 | ||||||||
|
missForest Resource Report Resource Website 100+ mentions |
missForest (RRID:SCR_018543) | simulation software, software application, software resource | Software R package to impute missing values particularly in case of mixed type data. Non parametric, mixed type imputation method for any type of data for statistical software R. Predicts missing values. | Missing value prediction, mixed type data, non parametric, missing value, mixed data, predictor | is related to: CRAN | PMID:22039212 | Free, Available for download, Freely available | http://stat.ethz.ch/CRAN/ | SCR_018543 | SciCrunch Registry | 2026-10-24 12:47:58 | 173 | ||||||||
|
Machado Resource Report Resource Website 1+ mentions |
Machado (RRID:SCR_018428) | application programming interface, data access protocol, data or information resource, software resource, web service | Software tool as framework to store, search and visualize biological data. Django instance provides data management, visualization, and searching functionalities to Chado databases. Resulting object-relational framework enables users, not only to set up local instance containing data regarding their organisms of interest, but also to develop all sorts of tools by accessing open source code. | Python, genomics, data, framework, data visualization, data management, Chado datbase, bio.tools |
is listed by: bio.tools is listed by: Debian is related to: Plant Co-expression Annotation Resource |
Embrapa | Free, Available for download, Freely available | biotools:machado | https://bio.tools/machado | SCR_018428 | SciCrunch Registry | 2026-10-24 12:47:57 | 2 | |||||||
|
PyRx Resource Report Resource Website 500+ mentions |
PyRx (RRID:SCR_018548) | data processing software, simulation software, software application, software resource | Open source virtual screening software for computational drug discovery with intuitive user interface. Runs on operating systems Linux, Windows, and Mac OS. Used to screen libraries of compounds against potential drug targets. | Virtual screening, computational drug discovery, drug, medicinal chemistry, target compound, compound screening, compound library, library screening | Restricted | SCR_018548 | SciCrunch Registry | 2026-10-24 12:47:58 | 645 | |||||||||||
|
ProSA-web Resource Report Resource Website 100+ mentions |
ProSA-web (RRID:SCR_018540) | analysis service resource, data access protocol, production service resource, service resource, software resource, web service | Web service is extension of classic ProSA program used for refinement and validation of experimental protein structures and in structure prediction and modeling. | Protein structure, protein, protein structure refinement, protein structure validation, protein structure prediction, protein structure modeling, bio.tools |
is listed by: Debian is listed by: bio.tools |
FWF Austria ; University of Salzburg ; Austria. |
PMID:17517781 | Free, Freely available | biotools:prosa-web | https://bio.tools/prosa-web | SCR_018540 | SciCrunch Registry | Protein Structure Analysis web | 2026-10-24 12:47:58 | 109 | |||||
|
Barzooka Resource Report Resource Website 1+ mentions |
Barzooka (RRID:SCR_018508) | algorithm resource, analysis service resource, production service resource, service resource, software resource | Software automated screening tool that detects bar graphs of continuous data in preprints submitted to bioRxiv. Used for detection of bar graphs for continuous data in BioRxiv preprints. | Bar graph detection, continuous data, preprint, bioRxiv, bar graph, ASWG | PMID:35822444 | Free, Available for download, Freely available | SCR_018508 | SciCrunch Registry | 2026-10-24 12:47:58 | 5 | ||||||||||
|
CohortMethod Resource Report Resource Website 10+ mentions |
CohortMethod (RRID:SCR_018511) | data analysis software, data processing software, data visualization software, software application, software resource | Software R package for performing new user cohort studies in observational database in OMOP Common Data Model. | Cohort study, observational database, OMOP Common Data Model, data, drugs, diagnosis, procedure, age, comorbidity index, data visualization | NSF IIS 1251151 | Free, Available for download, Freely available | SCR_018511 | SciCrunch Registry | 2026-10-24 12:47:58 | 11 | ||||||||||
|
MP Biochemicals: FastPrep24 Sample Preparation Resource Report Resource Website 10+ mentions |
MP Biochemicals: FastPrep24 Sample Preparation (RRID:SCR_018599) | instrument resource | Sample disruption instrument that can homogenize, grind, or lyse biological samples. Samples are added to individual lysing matrix tubes and shaken in tridimensional motion. | Sample Preparation, Instrument, Equipment, USEDit, ABRF, MP Biochemicals | is listed by: USEDit | SCR_020301, Model_Number_FastPrep24 | https://www.mpbio.com/media/productattachment/LS042019-EN-Sample-Preparation-Brochure.pdf | SCR_018599 | SciCrunch Registry | 2026-10-24 12:47:59 | 34 | |||||||||
|
Waters: Xevo TQ-XS mass spectrometer Resource Report Resource Website 10+ mentions |
Waters: Xevo TQ-XS mass spectrometer (RRID:SCR_018510) | instrument resource | Advanced benchtop tandem quadrupole mass spectrometer which expands scope of ultimate sensitivity analysis. Fatures probe design which allows users much easier maintenance, optimization and improved reproducibility between operators. Method transfer onto Xevo TQ-XS is made simple by Xtended Dynamic Range detector which allows six orders of linear dynamic range. Wider compound coverage without changing ionization technique is delivered by the revolutionary UniSpray source option. | Benchtop mass spectrometer, instrument, equipment, USEDit | is used by: Stanford University Vincent Coates Foundation Mass Spectrometry Laboratory Core Facility | NIH S10 OD026962 | https://www.waters.com/waters/library.htm?cid=134889751&lid=134891088&locale=en_US, https://www.waters.com/webassets/cms/support/docs/715004990ra.pdf | SCR_018510 | SciCrunch Registry | TQ-XS Triple Quad Mass Spectrometer, Xevo TQ-XS, SUMS Xevo | 2026-10-24 12:47:58 | 12 | ||||||||
|
CovidNLP Resource Report Resource Website |
CovidNLP (RRID:SCR_018513) | data access protocol, service resource, software resource, web service | Web Application for distilling systemic implications of COVID-19 pandemic with Natural Language Processing. | COVID19, pandemic data, natural language processing | Free, Freely available | SCR_018513 | SciCrunch Registry | Covid Natural Language Processing | 2026-10-24 12:47:58 | 0 | ||||||||||
|
Mettler: PB303-S Milligram Balance Resource Report Resource Website |
Mettler: PB303-S Milligram Balance (RRID:SCR_018592) | instrument resource | Miligram balance that is used for weighing, tarring, percent weighing, and dynamic weighing for unstable samples. Has maximum capacity of 310 grams. Lab balance utilizes mono block weighing technology with permanent shock protection and built in overload protection as well as automatic calibration. | Milligram Balance, Instrument, Equipment, Mettler, USEDit, ABRF | is listed by: USEDit | Commercially available | SCR_020255, Model_Number_PB303_S | SCR_018592 | SciCrunch Registry | 2026-10-24 12:47:59 | 0 | |||||||||
|
Thermo Fisher: Life Technologies: Countess Automated Cell Counter Resource Report Resource Website 1+ mentions |
Thermo Fisher: Life Technologies: Countess Automated Cell Counter (RRID:SCR_018591) | instrument resource | Invitrogen benchtop automated cell counter. Can perform cell counts, viability calculations, hemocytometry, fluorescent protein expression, and measure fluorescence capabilities. There are also reusable slides, fluorescence capabilities, and brightfield fluorescence channels. | Automated cell counter, cell counter, instrument, equipment, USEDit, Life Technologies | is listed by: USEDit | Restricted | https://raw.githubusercontent.com/SciCrunch/RRID-Instruments/main/PDF/SCR_020236.pdf | SCR_020236 | SCR_020236, https://assets.thermofisher.com/TFS-Assets/BID/manuals/MAN0014293_Countess_II_Automated_Cell_Counter_UG.pdf | SCR_018591 | SciCrunch Registry | 2026-10-24 12:47:59 | 7 | |||||||
|
rSPRITE Resource Report Resource Website |
rSPRITE (RRID:SCR_018524) | data access protocol, service resource, software resource, web service | Web app to generate possible distributions of data matching given mean, SD, sample size, and range. Used for recovering data from summary statistics. Implementation of SPRITE in R programming environment. | data distribution generation, data matching, recovering data, summary statistics data, ASWG |
is related to: Shiny is related to: RStudio |
Free, Freely available | SCR_018524 | SciCrunch Registry | rSPRITE beta 0.15, SPRITE, Sample Parameter Reconstruction via Iterative TEchniques | 2026-10-24 12:47:58 | 0 | |||||||||
|
Conserved Domains Search Resource Report Resource Website 1000+ mentions |
Conserved Domains Search (RRID:SCR_018729) | data access protocol, data or information resource, service resource, software resource, web service | Web tool for conserved domains searching within protein or coding nucleotide sequence. | Conserved domain, protein, coding nucleotide sequence, domain search, domain, nucleotide sequence | works with: Conserved Domain Database | Free, Freely available | SCR_018729 | SciCrunch Registry | CD-search | 2026-10-24 12:48:02 | 2002 | |||||||||
|
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 | SciCrunch Registry | Nikon 1500 Fluorescence Dissection Microscope | 2026-10-24 12:47:59 | 0 | |||||||
|
Graph2GO Resource Report Resource Website 1+ mentions |
Graph2GO (RRID:SCR_018726) | data analysis software, data processing software, software application, software resource | Software tool as graph based representation learning method for protein function prediction. Multi modal graph based representation learning model that can integrate heterogeneous information including multiple types of interaction networks including sequence similarity network and protein-protein interaction network, and protein features including amino acid sequence, sub cellular location and protein domains, to predict protein functions on Gene Ontology. | Protein function prediction, graph neural network, attributed network embedding, representation learning, multi-modal model, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: Ohio State University College of Medicine; Ohio; USA |
Free, Available for download, Freely available | SCR_018727, biotools:graph2go | https://integrativeomics.shinyapps.io/graph2go/, https://bio.tools/graph2go | SCR_018726 | SciCrunch Registry | 2026-10-24 12:48:02 | 2 | ||||||||
|
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 | SciCrunch Registry | 2026-10-24 12:47:59 | 2 | |||||||||
|
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 | SciCrunch Registry | Stanford University Vincent Coates Foundation Mass Spectrometry Laboratory Core FacilityLC/MS | 2026-10-24 12:48:01 | 0 |
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