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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
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calciumImagingAnalysis Resource Report Resource Website 1+ mentions |
calciumImagingAnalysis (RRID:SCR_021153) | data analysis software, data processing software, software application, software resource, software toolkit | Software package for analyzing one and two photon calcium imaging datasets.Can be used to create GUI-less, command line ready analysis pipelines. Supports Neurodata Without Borders data standard for reading/writing cell-extraction (e.g. outputs of PCA-ICA, CELLMax, CNMF, CNMF-E, EXTRACT, etc.). Supports reading and writing NWB movie files with continued integration planned. Supports most major imaging movie file formats: HDF5, NWB, AVI, ISXD [Inscopix], and TIFF. | Photon calcium imaging datasets analysis, command line ready analysis pipelines, Neurodata Without Borders data standard |
uses: MATLAB is listed by: Neurodata Without Borders |
Free, Available for download, Freely available | https://www.nwb.org/tools/ | SCR_021153 | SciCrunch Registry | CIAtah | 2026-10-10 12:41:25 | 2 | ||||||||
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Innovadyne Technologies: Nanodrop 2 Pipetting System Resource Report Resource Website |
Innovadyne Technologies: Nanodrop 2 Pipetting System (RRID:SCR_021033) | instrument resource | Liquid handling system designed for high precision pipetting. | Commercially available | SCR_021033 | SciCrunch Registry | 2026-10-10 12:41:24 | 0 | ||||||||||||
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NWBwidgets Resource Report Resource Website 1+ mentions |
NWBwidgets (RRID:SCR_021154) | software resource | of widgets for visualization NWB data in Jupyter notebook. Widgets allow you to navigate through hierarchical structure of NWB file and visualize specific data elements. Designed to work with NWB 2.0 files and to be easy to extend. | visualization NWB data, Jupyter notebook, widgets library, NWB file hierarchical structure, | is listed by: Neurodata Without Borders | Free, Available for download, Freely available | https://www.nwb.org/tools/ | SCR_021154 | SciCrunch Registry | 2026-10-10 12:41:18 | 3 | |||||||||
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Driftage Resource Report Resource Website 1+ mentions |
Driftage (RRID:SCR_021031) | 1d time-series analysis software, 2d time-series analysis software, code testing framework, data analysis software, data processing software, software application, software development tool, software resource, time-series analysis software | Software tool as modular multi agent framework to detect concept drifts from batch or streaming data. | Concept Drift, Data Drift, Anomaly Detection, Time Series, Multi-agent Systems, detect concept drifts | Free, Available for download, Freely available | SCR_021031 | SciCrunch Registry | 2026-10-10 12:41:44 | 1 | |||||||||||
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CaImAn Resource Report Resource Website 1+ mentions |
CaImAn (RRID:SCR_021152) | data analysis software, data processing software, software application, software resource | Software Python toolbox for large scale calcium imaging data analysis and behavioral analysis.Used for motion correction, source extraction, spike deconvolution, and component registration across multiple days. It is suitable for both two-photon and one-photon fluorescence microscopy data, and can be run in both batch and online modes. Contains some routines for analysis of behavior from video cameras. | Calcium imaging data analysis, behavioral analysis, motion correction, source extraction, spike deconvolution, photon fluorescence microscopy data | Free, Available for download, Freely available | https://caiman.readthedocs.io/en/master/Overview.html, https://www.nwb.org/tools/ | SCR_021152 | SciCrunch Registry | 2026-10-10 12:41:46 | 9 | ||||||||||
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Phantom: Miro C110 camera Resource Report Resource Website |
Phantom: Miro C110 camera (RRID:SCR_021081) | instrument resource | Small, sturdy camera with all standard Phantom features and image quality. Memory can be partitioned up to 63 times to deliver images from 1.3 Mpx sensor with 12-bit depth and tightly packed 5.6 micron pixel size. Miro C110 is capable of 1295 fps at 720p HD and up to 52445 fps at reduced resolutions. | small camera, Phantom, image quality, instrument, equipment, USEDit | Commercially available | Model_Number_Micro_C110 | SCR_021081 | SciCrunch Registry | Phantom Miro C110 | 2026-10-10 12:41:45 | 0 | |||||||||
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BioSpherix: C Shuttle Glove Box hood Resource Report Resource Website |
BioSpherix: C Shuttle Glove Box hood (RRID:SCR_021082) | C-Shuttle | instrument resource | Oxygen controlled hood for handling cells under physiologic or pathophysiologic conditions. Double door entry allows import/export of materials without perturbation of experimental conditions. Optional control of carbon dioxide as well. Receives C-Chamber Incubator Subchamber to transfer cells without exposure to room air. | BioSpherix, Physioxia, Physioxic, Hypoxia, Hypoxic, Glove box, oxygen, cell culture hood, carbon dioxide, instrument, equipment, USEDit | Commercially available | https://raw.githubusercontent.com/SciCrunch/RRID-Instruments/refs/heads/main/PDF/SCR_021082.pdf | SCR_021082 | SciCrunch Registry | BioSpherix C-Shuttle Glove Box, Hypoxic Glove Box, C-Shuttle laboratory glove box | 2026-10-10 12:41:25 | 0 | ||||||||
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Anton Paar: MCR501 rheometer Resource Report Resource Website 1+ mentions |
Anton Paar: MCR501 rheometer (RRID:SCR_021122) | instrument resource | Stress controlled rheometer.THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 19,2026. | Stress controlled rheometer, rheometer, instrument, equipment, USEDit | is organization facet of: Anton Paar | THIS RESOURCE IS NO LONGER IN SERVICE. | https://raw.githubusercontent.com/SciCrunch/RRID-Instruments/refs/heads/main/PDF/SCR_021122.pdf | Model_Number_MCR501 | SCR_021122 | SciCrunch Registry | SMaRT – MCR501, , Modular Compact Rheometer 501, SMaRT – MCR501 (Anton Paar) | 2026-10-10 12:41:46 | 1 | |||||||
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SCIGA Resource Report Resource Website 10+ mentions |
SCIGA (RRID:SCR_021002) | data analysis software, data processing software, software application, software resource, software toolkit | Software Perl toolkit for 10X single cell immunoglobulin repertoires analysis. Uses raw reads or output of Cellranger as input and performs reads quality control, immunoglobulin sequence assembly, sequence annotation, heavy- and light- chain pairing, computing statistics and visualizing. | 10X single cell immunoglobulin repertoires analysis, quality control, immunoglobulin sequence assembly, sequence annotation, heavy and light chain pairing, computing statistics, visualizing. | Free, Available for download, Freely available | biotools:sciga | https://bio.tools/sciga | SCR_021002 | SciCrunch Registry | SCIGA_v1.0.0.tar.gz | 2026-10-10 12:41:23 | 10 | ||||||||
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ALLMAP Resource Report Resource Website 1+ mentions |
ALLMAP (RRID:SCR_021120) | software resource | Software tool for computing scaffold ordering that maximizes colinearity across collection of maps including genetic, physical or comparative maps into final chromosome build. Robust scaffold ordering based on multiple maps. ALLMAPS is robust against common mapping errors, and generates sequences that are maximally concordant with input maps. Used in building high quality genome assemblies. | Computing scaffold ordering, colinearity across map collection maximization, final chromosome build, robust scaffold ordering, multiple maps, common mapping errors, genome assemblies | Gordon and Betty Moore Foundation ; National Science Foundation |
DOI:10.1186/s13059-014-0573-1 | Free, Available for download, Freely available | SCR_021120 | SciCrunch Registry | 2026-10-10 12:41:24 | 1 | |||||||||
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Allen Mouse Reference Atlas Ontology Resource Report Resource Website 1+ mentions |
Allen Mouse Reference Atlas Ontology (RRID:SCR_021000) | controlled vocabulary, data or information resource, ontology | Developed for Allen Reference Atlas and follows terminology from Brain Maps: Structure for the Rat Brain (Swanson, 2004, 2018). The ontology has been subsequently extended and revised to also serve as structure ontology for Allen Mouse Common Coordinate Framework.Defines hierarchical partonomy of anatomical structures of adult mouse brain. At top level, brain is divided into gray matter, fiber tracts and ventricular systems. Gray matter is subdivided into cerebrum, brain stem, and cerebellum, which are themselves organized into subregions in hierarchical tree. | structure ontology, brain structure, ontology, hierarchical partonomy, anatomical structures |
is used by: Allen Mouse Brain Common Coordinate Framework is used by: Early Postnatal Developmental Mouse Brain Atlas has parent organization: Allen Institute for Brain Science |
PMID:32386544 | Free, Freely available | SCR_021000 | SciCrunch Registry | 2026-10-10 12:41:44 | 5 | |||||||||
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SYCAMORE Resource Report Resource Website 1+ mentions |
SYCAMORE (RRID:SCR_021117) | data access protocol, software resource, web service | Web browser based application that facilitates construction, simulation and analysis of kinetic models in systems biology. Allows database supported modelling, basic model checking and estimation of unknown kinetic parameters based on protein structures. Integrates different online applications as well as locally installed software. Provides user guidance for sequence of steps associated with model building, model checking, simulation and analysis of results. | Systems biology computational analysis, modeling research environment, kinetic models analysis, kinetic models construction, kinetic models simulation, systems biology, protein structures, kinetic parameters |
has parent organization: Heidelberg Institute for Theoretical Studies; Heidelberg; Germany has parent organization: Heidelberg University; Baden-Wurttemberg; Germany |
German Ministry of Education and Research ; Klaus Tschira Foundation |
PMID:18463116 | Free, Freely available | SCR_021117 | SciCrunch Registry | SYstems biology Computational Analysis and MOdeling Research Environment | 2026-10-10 12:41:25 | 1 | |||||||
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BioSpherix: OxyCycler GT4181CN Controller Resource Report Resource Website |
BioSpherix: OxyCycler GT4181CN Controller (RRID:SCR_021113) | GT4181CN | instrument resource | Carbon Monoxide, Nitric Oxide, O2, and CO2 controller with limit control of relative humidity and monitoring of temperature conditions when used in combination with C-Chamber incubator subchamber from BioSpherix. Features secondary monitors for both Carbon Monoxide and Nitric Oxide and may be used in combination with I-Hood Incubator Hood from BioSpherix to ventilate fumes. | Carbon Monoxide, Nitric Oxide, O2, CO2, controller, instrument, equipment, USEDit | Commercially available | https://raw.githubusercontent.com/SciCrunch/RRID-Instruments/refs/heads/main/PDF/SCR_021113.pdf | SCR_021113 | SciCrunch Registry | Carbon Monoxide, CO2, OxyCycler GT4181CN Dynamic O2, OxyCycler GT4181CN, and Nitric Oxide Subchamber Cell Culture System | 2026-10-10 12:41:46 | 0 | ||||||||
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Abricate Resource Report Resource Website 1000+ mentions |
Abricate (RRID:SCR_021093) | data analysis software, data processing software, software application, software resource | Software tool for mass screening of contigs for antimicrobial and virulence genes. Mass screening of contigs for antimicrobial resistance or virulence genes. It comes bundled with multiple databases: NCBI, CARD, ARG-ANNOT, Resfinder, MEGARES, EcOH, PlasmidFinder, Ecoli_VF and VFDB. | contigs mass screening, antimicrobial genes, virulence genes, antimicrobial genes contigs, virulence genes contigs, FASEB list | Free, Available for download, Freely available | SCR_021093 | SciCrunch Registry | ABRicate | 2026-10-10 12:41:17 | 1355 | ||||||||||
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PySyft Resource Report Resource Website 10+ mentions |
PySyft (RRID:SCR_021012) | software resource | Software Python library for secure and private Deep Learning. Decouples private data from model training, using Federated Learning, Differential Privacy, and Encrypted Computation and Homomorphic Encryption within main deep learning frameworks. Used for computing on data you do not own and cannot see. | Private Deep Learning, deep learning, decouples private data, unseen data computing |
is related to: PyTorch is related to: tensorflow |
Free, Available for download, Freely available | SCR_021012 | SciCrunch Registry | 2026-10-10 12:41:24 | 11 | ||||||||||
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xiNET Resource Report Resource Website 10+ mentions |
xiNET (RRID:SCR_021010) | data access protocol, data processing software, data visualization software, software application, software resource, web service | Open source web based visualization tool for exploring crosslinking mass spectrometry results. Displays residue resolution positional information including linkage sites and linked peptides, all types of crosslinking reaction product, ambiguous results and additional sequence information such as domains. | Crosslinking mass spectrometry data visualization, linkage sites, linked peptides, crosslinking reaction product display, crosslink network maps, maps with residue resolution | Wellcome Trust | PMID:25648531 | Free, Available for download, Freely available | http://github.com/colin-combe/crosslink-viewer | SCR_021010 | SciCrunch Registry | Crosslink Network Maps With Residue Resolution | 2026-10-10 12:41:21 | 20 | |||||||
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Thermo Fisher: Applied Biosystems: QuantStudio 12K Flex RealTime PCR System Resource Report Resource Website 10+ mentions |
Thermo Fisher: Applied Biosystems: QuantStudio 12K Flex RealTime PCR System (RRID:SCR_021098) | instrument resource | System can simultaneously run up to four 3072 reaction QuantStudio 12K Flex OpenArray plates in about four hours. When combined with the QuantStudio 12K Flex OpenArray AccuFill System, can produce up to 110000 data points or more in 8 hour day. Has touch screen interface and comprehensive software analysis tools for gene expression, genotyping, and digital PCR increase productivity. Has five interchangable block formats including: OpenArray plate, TaqMan Array card, 384-well, and 96-well (0.1 and 0.2 mL). | Real Time PCR System, QuantStudio 12K Flex OpenArray, instrument, equipment, USEDit | uses: Applied Biosystems QuantStudio 12K Flex RT PCR Software | Commercially available | SCR_021098 | SciCrunch Registry | QuantStudio 12K Flex Real-Time PCR System | 2026-10-10 12:41:23 | 16 | |||||||||
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BioSpherix: ProOx C21 Controller Resource Report Resource Website 1+ mentions |
BioSpherix: ProOx C21 Controller (RRID:SCR_021131) | C21 | instrument resource | Compact O2 and CO2 Subchamber Controller used together with C-Chamber Incubator Subchamber from BioSpherix or chambers from other manufacturers. | Compact controller, Oxygen controller, CO2 controller, Subchamber Controller, BioSpherix, instrument, equipment, USEDit | Commercially Available | https://raw.githubusercontent.com/SciCrunch/RRID-Instruments/refs/heads/main/PDF/SCR_021131.pdf | Model_Number_ProOx C21 | SCR_021131 | SciCrunch Registry | ProOx C21, ProOx C21 Oxygen and Carbon Dioxide Subchamber Controller | 2026-10-10 12:41:17 | 1 | |||||||
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Biofactoid Resource Report Resource Website 1+ mentions |
Biofactoid (RRID:SCR_021011) | data access protocol, data or information resource, knowledge environment resource, portal, project portal, software resource, web service | Web tool for creating digital profile of scientific discoveries in article and connecting them to related research. Authors describe molecular interactions supported by their results, letting researchers explore first hand account of article findings and connect to related articles and knowledge. Web based system for scientists to compose structured representation of networks of interactions between genes, their products, and chemical compounds, represented using power of formal ontology. | Knowledge management, molecular interactions, pathway, compose network structured representation, digital profile, connect related articles, formal ontology |
is related to: Biological Pathways Exchange is related to: Biological Pathways Exchange has parent organization: University of Toronto; Ontario; Canada has parent organization: Harvard University; Cambridge; United States has parent organization: University of Oregon; Oregon; USA |
DARPA Big Mechanism ; NHGRI U41HG006623 |
Free, Freely available | SCR_021011 | SciCrunch Registry | 2026-10-10 12:41:44 | 1 | |||||||||
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Applied Biosystems QuantStudio 12K Flex RT PCR Software Resource Report Resource Website 1+ mentions |
Applied Biosystems QuantStudio 12K Flex RT PCR Software (RRID:SCR_021096) | data acquisition software, data analysis software, data processing software, software application, software resource | Software supports QuantStudio12K Flex Real Time PCR System to open and analyze experiments. Enables to set up experiments, send experiments to instrument, control thermal cycling process in instrument, collect data and analyze collected data. | control instrument thermal cycling process, data collection, data analysis, QuantStudio12K Flex Real Time PCR System support | is used by: Thermo Fisher: Applied Biosystems: QuantStudio 12K Flex RealTime PCR System | Restricted | SCR_021096 | SciCrunch Registry | QuantStudio 12K Flex Real Time PCR Software, Applied Biosystems QuantStudio 12K Flex RT PCR Software | 2026-10-10 12:41:25 | 5 |
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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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