Searching the RRID Resource Information Network
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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.
https://www.openicpsr.org/openicpsr/covid19
Repository for data examining social, behavioral, public health, and economic impact of novel coronavirus global pandemic. Free self publishing option for any researcher who wants to share data related to COVID-19. Deposits should include all data, annotated program code, command files, and documentation necessary to understand data collection and/or replicate research findings.
Proper citation: COVID-19 Data Repository (RRID:SCR_019105) Copy
https://dknet.org/rin/rrid-report
dkNET service that assists researchers in preparing authentication plans for cell lines or antibodies to comply with NIH Submission Policy when submitting proposal or publication. Automated tool to enable researchers to create customized report based on key biological resources they plan to use. These customized reports provide additional information such as known problems with particular cell line or antibody.
Proper citation: Authentication Reports (RRID:SCR_019226) Copy
https://github.com/slzarate/parliament2
Software tool to identify structural variants in given sample relative to reference genome. Runs combination of tools to generate structural variant calls on whole genome sequencing data.
Proper citation: Parliament2 (RRID:SCR_019187) Copy
Portal for human electrophysiological data, supports, sharing and in depth analysis of identified human neuroelectromagnetic brain data including scalp EEG, its magnetic counterpart, MEG, and, intracranial iEEG and ECoG. Open access EEG and MEG data archives, analysis, and visualization. Neuroelectromagnetic data, tools, and compute resource.
Proper citation: NEMAR (RRID:SCR_019100) Copy
https://github.com/dmnfarrell/epitopepredict
Open source software tool as programmatic framework and command line tool designed to aid process of MHC binding prediction. Provides access to multiple binding prediction algorithms under single interface and scales for whole genomes using multiple target MHC alleles.Software should be run on Linux operating system. Ubuntu is recommended but most major distributions will be fine. Windows is not supported.
Proper citation: epitopepredict (RRID:SCR_019221) Copy
https://delaney.shinyapps.io/CAIRN/
Web tool to graph all copy number alterations present in segment file. Custom data is permitted. Allows to display copy number alterations which overlap user specified region, to quantify number of amplified CNAs and deleted CNAs. Visualization tool to explore copy number alterations discovered in published cancer datasets. Intended to help oncology community observe of relative rates of amplification, deletion, and mutation of interesting genes and regions.
Proper citation: CAIRN (RRID:SCR_019101) Copy
http://synaptosoft.com/MiniAnalysis/ABFUtility.html
Software tool to convert data files from Mac program such as Igor and Pulse or John Dempster CDR, WinTida, to ABF formats and analyze them with Mini Analysis Program.
Proper citation: ABF Utility (RRID:SCR_019222) Copy
Web platform for electronic data capture by OpenClinica, LLC. Used as clinical trial management system.
Proper citation: OpenClinica (RRID:SCR_019223) Copy
http://www.neuro.uni-jena.de/cat/
Software toolbox as extension to SPM12 to provide computational anatomy. This covers diverse morphometric methods such as voxel based morphometry, surface based morphometry, deformation based morphometry, and region or label based morphometry.
Proper citation: Computational Anatomy Toolbox for SPM (RRID:SCR_019184) Copy
https://CRAN.R-project.org/package=tidyverse
Software tool as collection of R packages designed for data science which share underlying design philosophy, grammar, and data structures. Packages work in harmony because they share common data representations and API design. Used in everyday data analyses.
Proper citation: tidyverse (RRID:SCR_019186) Copy
https://sils.fnwi.uva.nl/bcb/objectj/
Software tool used for non destructive marking and linked results in ImageJ. Integrates image analysis across many images or stacks into single project file.
Proper citation: ObjectJ (RRID:SCR_019190) Copy
https://CRAN.R-project.org/package=NBR
Software tool as implementation of network based statistics toolbox in R. Includes mixed effects models.
Proper citation: Network-Based R-Statistics (RRID:SCR_019114) Copy
Interactive database of software tools for analysis of long read sequencing data.Catalogue of long-read sequencing data analysis tools. Catalogue of downstream analysis tools of real and synthetic long-read technologies.
Proper citation: long-read-tools (RRID:SCR_019116) Copy
https://www.ebi.ac.uk/pdbe/emdb/empiar/
Public archive for raw electron microscopy image data. Resource for raw 2D electron microscopy images. Used to browse, upload and download raw images to build 3D structure. Provides access to raw data to facilitate methods development and validation. Complements Electron Microscopy Data Bank where 3D volumes are stored, and uses Aspera platform for data transfers.
Proper citation: Electron Microscopy Public Image Archive (RRID:SCR_019237) Copy
https://run.biosimulations.org
Web tool for executing broad range of modeling studies and visualizing their results. Provides web interface for reusing any model. Models, simulations, and visualizations are available under licenses specified for each resource.
Proper citation: runBioSimulations (RRID:SCR_019110) Copy
https://raw.githubusercontent.com/SciCrunch/RRID-Instruments/refs/heads/main/PDF/SCR_019231.pdf
HoloMonitor live cell imaging and analysis system by Phase Holographic Imaging PHI AB. Contains small, digital live cell, quantitative phase imaging microscope HoloMonitor M4 designed to operate constantly inside incubator and HoloMonitor cell imaging software App Suite or Hstudio to continuously monitor and quantitatively analyze both individual cells and cell populations over time without any cellular labels or stains. Microscope can operate in cell incubator, hypoxia chamber or on lab bench.
Proper citation: Phase Holographic Imaging: HoloMonitor live cell imaging and analysis system (RRID:SCR_019231) Copy
Web tool as collection of containerized biosimulation tools that provide consistent interfaces and guide to choosing simulator. Helps to find simulation tools that have capabilities, including supported modeling frameworks, simulation algorithms, and modeling formats, needed for specific modeling projects.
Proper citation: BioSimulators (RRID:SCR_019111) Copy
https://jtremblay.github.io/amplicontagger.html
Software tool as rRNA marker gene amplicon pipeline coded in python framework that enables fine tuning and integration of virtually any potential rRNA gene amplicon bioinformatic procedure. Designed to work within HPC environment, supporting complex network of job dependencies with smart restart mechanism in case of job failure or parameter modifications.
Proper citation: AmpliconTagger (RRID:SCR_019112) Copy
https://www.elektralabs.com/solutions/education
Free curriculum, resources, and research for those considering incorporation of remote health monitoring.
Proper citation: Elektra Academy (RRID:SCR_019234) Copy
https://trials.bgcarlisle.com/
Software tool to download and parse information from ClinicalTrials.gov at the time of search to populate the graph of clinical trials. FDA information is updated weekly from Drugs at FDA dataset and FDA postmarketing commitment data set.
Proper citation: Clinical Trials Viewer (RRID:SCR_019230) Copy
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