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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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Stoeling Co: Open Field Box Resource Report Resource Website |
Stoeling Co: Open Field Box (RRID:SCR_028738) | instrument resource | Specialized laboratory enclosure used in behavioral neuroscience to assess exploratory behavior, general locomotor activity, and anxiety-related responses in rodents like mice and rats. | behavioral neuroscience, assess exploratory behavior, general locomotor activity, anxiety-related responses, rodents, mice, rats, | is used by: Medical University of South Carolina MUSC Mouse Behavior Phenotyping Core Facility | Commercially available | https://raw.githubusercontent.com/SciCrunch/RRID-Instruments/refs/heads/main/PDF/SCR_028738.pdf | SCR_028738 | Open Field Box | 2026-08-08 12:08:33 | 0 | ||||||||
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Med Associates: Operant Chamber Resource Report Resource Website |
Med Associates: Operant Chamber (RRID:SCR_028739) | instrument resource | Laboratory testing system used by scientists to study animal behavior, learning, and addiction. Also known as a "Skinner box," it features levers, lights, sound generators, and food or water dispensers. | Laboratory testing system, study animal behavior, learning, addiction, Skinner box, | is used by: Medical University of South Carolina MUSC Mouse Behavior Phenotyping Core Facility | Commercially available | https://raw.githubusercontent.com/SciCrunch/RRID-Instruments/refs/heads/main/PDF/SCR_028739.pdf | SCR_028739 | Operant Chamber | 2026-08-08 12:08:34 | 0 | ||||||||
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San Diego Instruments: XY-axis Locomotor Activity Chamber Resource Report Resource Website |
San Diego Instruments: XY-axis Locomotor Activity Chamber (RRID:SCR_028736) | instrument resource | XY-axis Locomotor Activity Chamber (part of Photobeam Activity System or PAS Open Field) is used to track, measure, and analyze the physical movements and behavior of small laboratory animals like mice and rats. | track, measure, analyze, physical movements and behavior, small laboratory animals, mice, rats | is used by: Medical University of South Carolina MUSC Mouse Behavior Phenotyping Core Facility | https://raw.githubusercontent.com/SciCrunch/RRID-Instruments/refs/heads/main/PDF/SCR_028736.pdf | SCR_028736 | XY-axis Locomotor Activity Chamber | 2026-08-08 12:08:28 | 0 | |||||||||
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DeepNeo Resource Report Resource Website |
DeepNeo (RRID:SCR_028672) | web application, software resource | Webserver for predicting immunogenic neoantigens. Used to identify immunogenic neoepitopes by capturing the structural properties of peptide-MHC pairs with T cell reactivity. | identify immunogenic neoepitopes, capturing structural properties, peptide-MHC pairs, T cell reactivity, | PMID:37070174 | Restricted | SCR_028672 | 2026-08-08 12:08:32 | 0 | ||||||||||
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Menarini Silicon Biosystems Inc Resource Report Resource Website |
Menarini Silicon Biosystems Inc (RRID:SCR_028704) | commercial organization, service resource | Biotechnology and diagnostics company specializing in "liquid biopsy" technologies to detect and isolate rare cells like circulating tumor cells (CTCs) from blood or tissue samples. They provide precise single-cell analysis tools used in cancer research and personalized medicine. Offers commercial rare-cell laboratory service providing CD138-positive immunomagnetic enrichment of plasma cells from peripheral blood and immunofluorescence-based plasma-cell identification and enumeration, delivering an enriched circulating multiple myeloma cell fraction for downstream analysis. | Biotechnology, diagnostics, company, detect and isolate rare cells, blood, tissue, samples | SCR_028704 | 2026-08-08 12:08:33 | 0 | ||||||||||||
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Agilent: NovoCyte 3005 Flow Cytometer Resource Report Resource Website |
Agilent: NovoCyte 3005 Flow Cytometer (RRID:SCR_028708) | instrument resource | Benchtop flow cytometer used to analyze and count individual cells or particles. Flow cytometer with 3 lasers (488, 405, 640 nm) and up 14 colors. 6 colors from violet laser; 5 colors from blue laser; 3 colors from red laser. NovoExpress software used for acquisition. | Flow cytometer, laser, 488 nm, 405 nm, 640 nm | Commercially available | https://raw.githubusercontent.com/SciCrunch/RRID-Instruments/refs/heads/main/PDF/SCR_028708.pdf | Model_Number_NovoCyte_3005 | SCR_028708 | 2026-08-08 12:08:28 | 0 | |||||||||
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Thermo Scientific: Orbitrap Astral Mass Spectrometer Resource Report Resource Website |
Thermo Scientific: Orbitrap Astral Mass Spectrometer (RRID:SCR_028684) | instrument resource | Mass spectrometer for advanced, high-speed, and deep-coverage biological research, specifically targeting proteomics, clinical biomarker discovery, and single-cell analysis. It combines high-resolution accuracy with a rapid scan speed of up to 200 Hz. Powered by the synergy of the high resolution quadrupole mass filter, Thermo Scientific™ Orbitrap™ mass analyzer and the novel Thermo Scientific™ Astral™ mass analyzer. The combination of these three mass analyzers enables the acquisition of quality high resolution accurate mass (HRAM) data with high sensitivity and dynamic range. | Mass spectrometer, proteomics, proteins, clinical biomarker discovery, single-cell analysis, | Commercially available | https://raw.githubusercontent.com/SciCrunch/RRID-Instruments/refs/heads/main/PDF/SCR_028684.pdf | Model_Number_Thermo_Scientific_Orbitrap_Astral | https://documents.thermofisher.com/TFS-Assets/CMD/Specification-Sheets/ps-001797-ms-orbitrap-astral-ps001797-en.pdf | SCR_028684 | , Thermo Scientific™ Orbitrap™ Astral | 2026-08-08 12:08:27 | 0 | |||||||
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Buxco FinePointe Inhalation Software Resource Report Resource Website |
Buxco FinePointe Inhalation Software (RRID:SCR_028683) | software resource | Software for collecting, analyzing, and reporting life science data. Used to control inhalation exposure systems, track real-time animal respiration, and calculate precise delivered drug doses in pre-clinical research. It automates aerosol delivery, monitors lung function data, and manages experimental protocols. | control inhalation exposure systems, track real-time animal respiration, calculate precise delivered drug doses, automate aerosol delivery, monitors lung function data, manages experimental protocols, | Restricted | https://support.datasci.com/hc/en-us/article_attachments/360100396374, https://support.datasci.com/hc/en-us/article_attachments/1500001560141 | SCR_028683 | 2026-08-08 12:08:33 | 0 | ||||||||||
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Diagenode: Bioruptor Pico sonicator Resource Report Resource Website |
Diagenode: Bioruptor Pico sonicator (RRID:SCR_028774) | instrument resource | Ultrasonic shearing instrument used to fragment chromatin, shear DNA and RNA, and lyse cells. | Ultrasonic shearing, fragment chromatin, shear DNA and RNA, lyse cells, | Commercially available | https://raw.githubusercontent.com/SciCrunch/RRID-Instruments/refs/heads/main/PDF/SCR_028774.pdf | SCR_028774 | 2026-08-08 12:08:34 | 0 | ||||||||||
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MaineHealth; Portland; United States Resource Report Resource Website |
MaineHealth; Portland; United States (RRID:SCR_028781) | institution | Health care organization in Maine, serving communities across Maine and New Hampshire. Includes MaineHealth Institute for Research to support research at MaineHealth ranging from basic laboratory-based research through translational research, which works to apply basic discoveries to medical problems, to clinical research, which studies the direct application of new drugs, devices and treatment protocols to patients, to health services research which seeks to use research methods to help improve and evaluate health care delivery programs and new technologies. | Health care organization, health care research, | is parent organization of: MaineHealth Institute for Research Small Animal Imaging Core Facility | , GRID grid.429380.4, ISNI 0000 0004 0455 8490 | https://ror.org/017xncd55 | SCR_028781 | 2026-08-08 12:08:35 | 0 | |||||||||
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SPAdes Resource Report Resource Website 100+ mentions |
SPAdes (RRID:SCR_000131) | SPAdes | software toolkit, software resource | Software package for assembling single cell genomes and mini metagenomes. Uses short read sets as input. Used for genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. Works with Illumina or IonTorrent reads and can provide hybrid assemblies using PacBio, Oxford Nanopore and Sanger reads. Intended for small genomes like bacterial or fungal., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | assembler, single, cell, small, genome, short, read, data |
is used by: shovill is listed by: OMICtools is listed by: Debian is listed by: SoftCite is related to: rnaSPAdes is related to: rnaQUAST has parent organization: Saint Petersburg Academic University; Saint Petersburg; Russia works with: Illumina: iSeq 100 Sequencing System |
Government of the Russian Federation ; NCRR P41 RR024851 |
PMID:24093227 PMID:22506599 DOI:10.1089/cmb.2012.0021 |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01502 | https://sources.debian.org/src/spades/ | http://bioinf.spbau.ru/spades/ | SCR_000131 | SPAdes Genome Assembler | 2026-08-09 09:02:54 | 108 | |||
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DrugSim2DR Resource Report Resource Website 1+ mentions |
DrugSim2DR (RRID:SCR_024564) | simulation software, software application, software resource | Software R package to predict drug functional similarity to drug repurposing. | predict drug functional similarity, similarity to drug repurposing, | is listed by: CRAN | Free, Available for download, Freely available | SCR_024564 | 2026-08-09 09:08:30 | 1 | ||||||||||
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Japan Society for the Promotion of Science Resource Report Resource Website 10+ mentions |
Japan Society for the Promotion of Science (RRID:SCR_001085) | JSPS | regional funding resource, group, funding resource | Research and outreach organization dedicated to promoting science, research and education. The society has four main objectives, including building international cooperative networks, enhancing education and research at universities, building evidence-based science-promotion systems and creating diverse world level knowledge. | research, science, promotion, japan, education | nlx_151882 | SCR_001085 | 2026-08-09 09:03:08 | 49 | ||||||||||
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ASTRAL-Pro Resource Report Resource Website 1+ mentions |
ASTRAL-Pro (RRID:SCR_024520) | simulation software, software application, software resource | Software tool for species tree reconstruction from multi-copy gene family trees.Used for estimating unrooted species tree given set of unrooted gene trees and is statistically consistent under the multi-species coalescent model. ASTRAL-pro extends ASTRAL to allow multi-copy genes. ASTRAL-Pro 2, ultrafast and memory efficient version of ASTRAL-Pro that adopts placement based optimization algorithm for significantly better scalability without sacrificing accuracy. | species tree reconstruction, reconstruction from multi-copy gene family trees | is listed by: SoftCite | PMID:32886770 | Free, Available for download, Freely available | SCR_024520 | ASTRAL for PaRalogs and Orthologs, ASTRAL-Pro 2 | 2026-08-09 09:09:04 | 3 | ||||||||
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CpGassoc Resource Report Resource Website 1+ mentions |
CpGassoc (RRID:SCR_000320) | software toolkit, software resource | Software R package to test association between methylation at CpG sites across genome and phenotype of interest, adjusting for any relevant covariates. Can perform standard analyses of large datasets without need to manually input data. Can handle mixed effects models with chip or batch entering model as random intercept. Includes tools to apply quality control filters, perform permutation tests, and create QQ plots, manhattan plots, and scatterplots for individual CpG sites. | control filters, permutation test, qq plots, manhattan plots, scatterplots, phenotype, sequence analysis software, cpg |
is listed by: OMICtools is listed by: CRAN |
PMID:22451269 | Free, Available for download, Freely available | OMICS_00793 | SCR_000320 | 2026-08-09 09:02:57 | 1 | ||||||||
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GenePaint E15 Atlas Resource Report Resource Website |
GenePaint E15 Atlas (RRID:SCR_002786) | GenePaint Map E15.5 | data or information resource, atlas, reference atlas | Abbreviated reference atlas for the Embryonic 15.5 post conception day mouse. All sections were nissl stained and digitized. To assist in the initial identification of sites of gene expression sites, maps of brains are available for E15.5, P7 and the adult. These maps depict the boundaries of major brain regions (cortex, thalamus, striatum, globus pallidus, ventral striatum, septum, basal forebrain, hippocampus, midbrain, pons, medulla, cerebellum) and also show the more prominent nerve tracts. Maps are most efficiently used by placing the window depicting the map of interest next to the gene expression image. Browsing between planes of sectioning is permitted thus allowing the most appropriate plane to be selected. The annotation of anatomical details such as brain nuclei is currently beyond the scope of the GenePaint database. Hence, such information on the anatomy of the brain and embryo should be obtained from published atlases of mouse anatomy (Kaufman, 1995; Paxinos and Franklin, 2001; Jacobowitz and Abbott, 1997; Schambra et al., 1992; Valverde1998). | expression, gene, gene expression, anatomical, anatomy, basal forebrain, brain, cerebellum, cortex, developmental, digitized, globus pallidus, hippocampus, map, medulla, midbrain, mouse, nerve, nissl staining protocol, nucleus, pons, prenatal, region, septum, striatum, thalamus, tract, ventral striatum, image, nissl stain, embryonic mouse, thalamus, nerve tract, development |
is related to: GenePaint P7 Atlas is related to: GenePaint P56 Mouse Atlas has parent organization: GenePaint |
Free, Freely available | nif-0000-24447 | SCR_002786 | GenePaint E15.5 Mouse Atlas | 2026-08-09 09:03:36 | 0 | |||||||
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Rat Hippocampus Atlas Resource Report Resource Website 1+ mentions |
Rat Hippocampus Atlas (RRID:SCR_005552) | Rat Hippocampus Atlas | data or information resource, atlas, reference atlas | An interactive reference atlas providing a systematic overview of cyto- and chemoarchectonical features of the hippocampus proper, fasciola, and associated parahippocampal cortices. This atlas system has been developed to serve the need to integrate detailed descriptions of structures and criteria defining boundaries and atlas images in which the underlying histological features can be explored. Features * Alphabetical and hierarchical overview of 18 hippocampal structures * Detailed, illustrated descriptions of 63 boundaries * Interactive image repository with ~100 coronal histological images stained for NeuN, calbindin, and parvalbumin * Triple image viewer in which differently stained neighboring sections can be interactively compared * Graphical overlay of substructures based on described boundary criteria * Bidirectional links between structure descriptions and image repository The atlas is based on histological material from an adult Long Evans rat, stained for NeuN, calbindin, and parvalbumin. The system is intended for researchers working in the field, as well as students interested in this brain region. The atlas is accessed through the structure index or image viewer. Re-use of data from this repository is allowed provided that reference is given to the publication. | rat, hippocampus, adult rat, long evans rat, hippocampus proper, fasciola, parahippocampal cortex, neuroanatomy, histology |
is related to: Temporal-Lobe: Hippocampal - Parahippocampal Neuroanatomy of the Rat has parent organization: University of Oslo; Oslo; Norway |
University of Oslo; Oslo; Norway ; Research Council of Norway ; International Neuroinformatics Coordinating Facility ; Norwegian Node |
PMID:21519393 | nlx_144643 | SCR_005552 | 2026-08-09 09:04:07 | 4 | |||||||
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SRI24 Atlas: Normal Adult Brain Anatomy Resource Report Resource Website 10+ mentions |
SRI24 Atlas: Normal Adult Brain Anatomy (RRID:SCR_002551) | SRI24 Atlas, SRI24, sri24-atlas | data or information resource, atlas, reference atlas | An MRI-based atlas of normal adult human brain anatomy, generated by template-free nonrigid registration from images of 24 normal control subjects. The atlas comprises T1, T2, and PD weighted structural MRI, tissue probability maps (GM, WM, CSF), maximum-likelihood tissue segmentation, DTI-based measures (FA, MD, longitudinal and transversal diffusivity), and two labels maps of cortical regions and subcortical structures. The atlas is provided at 1mm isotropic image resolution in Analyze, NIFTI, and Nrrd format. We are also providing an experimental packaging for use with SPM8. | analyze, model, magnetic resonance, nifti, nrrd, neuroanatomy, adult human, brain, mri, dti |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Stanford Research Institute International |
Normal | NIAAA AA005965; NIAAA AA012888; NIAAA AA017347; NIAAA AA017168; NIA AG017919 |
PMID:20017133 | Free, Available for download, Freely available | nlx_155957 | SCR_002551 | sri24-atlas - MRI-based brain atlas of normal adult human brain anatomy, SRI24 Multi-Channel Atlas of Normal Adult Human Brain Structure | 2026-08-09 09:03:36 | 10 | ||||
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GenePaint P7 Atlas Resource Report Resource Website |
GenePaint P7 Atlas (RRID:SCR_002787) | GenePaint Map P7 | data or information resource, atlas, reference atlas | Abbreviated reference atlas for the P56 mouse. All sections were nissl stained and digitized. To assist in the initial identification of sites of gene expression sites, maps of brains are available for E15.5, P7 and the adult. These maps depict the boundaries of major brain regions (cortex, thalamus, striatum, globus pallidus, ventral striatum, septum, basal forebrain, hippocampus, midbrain, pons, medulla, cerebellum) and also show the more prominent nerve tracts. Maps are most efficiently used by placing the window depicting the map of interest next to the gene expression image. Browsing between planes of sectioning is permitted thus allowing the most appropriate plane to be selected. The annotation of anatomical details such as brain nuclei is currently beyond the scope of the GenePaint database. Hence, such information on the anatomy of the brain and embryo should be obtained from published atlases of mouse anatomy (Kaufman, 1995; Paxinos and Franklin, 2001; Jacobowitz and Abbott, 1997; Schambra et al., 1992; Valverde1998). | gene, anatomical, anatomy, annotation, atlas, basal forebrain, brain, cerebellum, cortex, developmental, digitized, globus pallidus, hippocampus, map, medulla, midbrain, mouse, nerve, nissl staining protocol, nucleus, pons, region, septum, stained, striatum, thalamus, tract, ventral striatum, image, gene expression, young mouse |
is related to: GenePaint E15 Atlas is related to: GenePaint P56 Mouse Atlas is related to: GenePaint P56 Mouse Atlas has parent organization: GenePaint |
Free, Freely available | nif-0000-24449 | SCR_002787 | GenePaint Mouse Brain Map P7, GenePaint P7 Atlas | 2026-08-09 09:03:38 | 0 | |||||||
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UNC Human Brain Atlas Resource Report Resource Website 1+ mentions |
UNC Human Brain Atlas (RRID:SCR_002606) | UNC Human Brain Atlas | data or information resource, atlas, reference atlas | Human brain atlases for adult, pediatric and elderly populations, by iterative joint deformable registration of training datasets into a single unbiased average image. Atlases packages include T1-weighted images, tissue priors (WM,GM,CSF), lobar parcellation maps and subcortical structures. Current available atlases: * Adult atlas: Symmetric atlas generated from 50+ healthy adult subjects (20-59 year old). * UNC-MNI Pediatric 1-year-old atlas: Symmetric atlas generated from 104 1-year-old subjects, combining children at high familial risk of autism and controls. * Pediatric 4-year-old atlas: Symmetric atlas generated from 10 4-year-old healthy subjects. * Elderly atlas: Atlas generated from 27 healthy elderly subjects (60+ years old). Additional information and acknowledgment for their usage can be found by clicking on the release notes. | atlas data, magnetic resonance, nrrd, adult human, young human, pediatric, infant, late adult human, brain |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: INCF Software Center is related to: NeoSegPipeline has parent organization: University of North Carolina at Chapel Hill; North Carolina; USA |
Free, Available for download, Freely available | nlx_156009 | SCR_002606 | 2026-08-09 09:03:30 | 5 |
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