Searching the RRID Resource Information Network
Are you sure you want to leave this community? Leaving the community will revoke any permissions you have been granted in this community.
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 | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
Human Brain Atlas Resource Report Resource Website 1+ mentions |
Human Brain Atlas (RRID:SCR_006131) | Human Brain Atlas | data or information resource, video resource, atlas | A labeled three-dimensional atlas of the human brain created from MRI images. In conjunction are presented anatomically labeled stained sections that correspond to the three-dimensional MRI images. The stained sections are from a different brain than the one which was scanned for the MRI images. Also available the major anatomical features of the human hypothalamus, axial sections stained for cell bodies or for nerve fibers, at six rostro-caudal levels of the human brain stem; images and Quicktime movies. The MRI subject was a 22-year-old adult male. Differing techniques used to study the anatomy of the human brain all have their advantages and disadvantages. Magnetic resonance imaging (MRI) allows for the three-dimensional viewing of the brain and structures, precise spatial relationships and some differentiation between types of tissue, however, the image resolution is somewhat limited. Stained sections, on the other hand, offer excellent resolution and the ability to see individual nuclei (cell stain) or fiber tracts (myelin stain), however, there are often spatial distortions inherent in the staining process. The nomenclature used is from Paxinos G, and Watson C. 1998. The Rat Brain in Stereotaxic Coordinates, 4th ed. Academic Press. San Diego, CA. 256 pp | human, adult, mri, fiber stain, anatomy, normal, neuroanatomy, nissl stain, image, brainstem, cell body, nerve fiber, brain, coronal, sagittal, horizontal, 3d model, montage, weil, hypothalamus |
is used by: NIF Data Federation has parent organization: Michigan State University; Michigan; USA |
NSF IBN 0131267; NSF 0131826; NSF 0131028 |
Copyrighted, Public, Request that you secure their permission, Acknowledgement required | nif-0000-00088 | SCR_006131 | MSU Brain Biodiversity Bank - Human Brain Atlas, Michigan State University Brain Biodiversity Bank - Human Brain Atlas | 2026-08-10 09:32:45 | 3 | ||||||
|
RIKEN integrated database of mammals Resource Report Resource Website |
RIKEN integrated database of mammals (RRID:SCR_006890) | RIKEN integrated database of mammals | data or information resource, portal, database |
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 16, 2019. A database that integrates not only RIKEN''''s original large-scale mammalian databases, such as FANTOM, the ENU mutagenesis program, the RIKEN Cerebellar Development Transcriptome Database and the Bioresource Database, but also imported data from public databases, such as Ensembl, MGI and biomedical ontologies. Our integrated database has been implemented on the infrastructure of publication medium for databases, termed SciNetS/SciNeS, or the Scientists'''' Networking System, where the data and metadata are structured as a semantic web and are downloadable in various standardized formats. The top-level ontology-based implementation of mammal-related data directly integrates the representative knowledge and individual data records in existing databases to ensure advanced cross-database searches and reduced unevenness of the data management operations. Through the development of this database, we propose a novel methodology for the development of standardized comprehensive management of heterogeneous data sets in multiple databases to improve the sustainability, accessibility, utility and publicity of the data of biomedical information. |
integration, network, standardization, biomedical, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: Functional Annotation of the Mammalian Genome is related to: Cerebellar Development Transcriptome Database is related to: Ensembl is related to: Mouse Genome Informatics (MGI) is related to: OBO has parent organization: RIKEN Yokohama Institute; Kanagawa; Japan |
Japanese Ministry of Education Culture Sports Science and Technology MEXT | PMID:21076152 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_151886, biotools:riken | https://bio.tools/riken | SCR_006890 | 2026-08-10 09:32:58 | 0 | |||||
|
XSEDE - Extreme Science and Engineering Discovery Environment Resource Report Resource Website 10+ mentions |
XSEDE - Extreme Science and Engineering Discovery Environment (RRID:SCR_006091) | XSEDE | data or information resource, portal | XSEDE is a single virtual system that scientists can use to interactively share computing resources, data and expertise. People around the world use these resources and services things like supercomputers, collections of data and new tools to improve our planet. XSEDE resources may be broadly categorized as follows: High Performance Computing, High Throughput Computing, Visualization, Storage, and Data Services. Many resources provide overlapping functionality across categories. Scientists, engineers, social scientists, and humanists around the world - many of them at colleges and universities - use advanced digital resources and services every day. Things like supercomputers, collections of data, and new tools are critical to the success of those researchers, who use them to make our lives healthier, safer, and better. XSEDE integrates these resources and services, makes them easier to use, and helps more people use them. XSEDE supports 16 supercomputers and high-end visualization and data analysis resources across the country. Digital services, meanwhile, provide users with seamless integration to NSF''s high-performance computing and data resources. XSEDE''s integrated, comprehensive suite of advanced digital services will federate with other high-end facilities and with campus-based resources, serving as the foundation for a national cyberinfrastructure ecosystem. Common authentication and trust mechanisms, global namespace and filesystems, remote job submission and monitoring, and file transfer services are examples of XSEDE''s advanced digital services. XSEDE''s standards-based architecture allows open development for future digital services and enhancements. XSEDE also provides the expertise to ensure that researchers can make the most of the supercomputers and tools. | data sharing, computing, supercomputer, data, tool, visualization, data analysis, cyberinfrastructure, digital service, high performance computing, high throughput computing, visualization, storage, data service |
is related to: Neuroscience Gateway has parent organization: San Diego Supercomputer Center |
NSF OCI-1053575 | nlx_151554, grid.501421.3 | https://ror.org/05524hb64 | SCR_006091 | XSEDE - Extreme Science Engineering Discovery Environment, Extreme Science and Engineering Discovery Environment | 2026-08-10 09:32:45 | 29 | ||||||
|
epigenomix Resource Report Resource Website 1+ mentions |
epigenomix (RRID:SCR_006407) | epigenomix | software application, data processing software, software resource | Software package for the integrative analysis of microarray based gene expression and histone modification data obtained by ChIP-seq. The package provides methods for data preprocessing and matching as well as methods for fitting bayesian mixture models in order to detect genes with differences in both data types. | epigenetic, gene expression, microarray, histone modification, chip-seq, classification, differential expression, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor |
PMID:24403540 | GNU Lesser General Public License, v3 | biotools:epigenomix, OMICS_02205 | https://bio.tools/epigenomix | SCR_006407 | epigenomix - Epigenetic and gene expression data normalization and integration with mixture models | 2026-08-10 09:32:49 | 2 | |||||
|
The Surf-Hippo Neuron Simulation System Resource Report Resource Website 1+ mentions |
The Surf-Hippo Neuron Simulation System (RRID:SCR_007257) | software application, data processing software, software resource | The Surf-Hippo neuron simulator is used to investigate morphologically and biophysically detailed compartmental models of single neurons and networks of neurons. Surf-Hippo allows ready construction of cells and networks using built-in functions and various anatomical file formats (Neurolucida, NTS and others). Surf-Hippo is a public domain package, written in Lisp, and runs under Unix and Linux. | nif-0000-00170 | SCR_007257 | Surf-Hippo | 2026-08-10 09:33:05 | 1 | |||||||||||
|
Cellpack Resource Report Resource Website 1+ mentions |
Cellpack (RRID:SCR_006831) | cellPack | software application, data processing software, software resource | A specialized version of autoPack designed to pack biological components together. The current version is optimized to pack molecules into cells with biologically relevant interactions to populate massive cell models with atomic or near-atomic details. Components of the algorithm pack transmembrane proteins and lipids into bilayers, globular molecules into compartments defined by the bilayers (or as exteriors), and fibrous components like microtubules, actin, and DNA. | 3d packing software, pack, molecule, cell |
is related to: Autopack has parent organization: Autopack |
QB3 at UCSF Fellowship ; NSF 07576; NCRR P41 RR08605 |
GNU Lesser General Public License | nlx_151792 | https://sites.google.com/site/autofill21/, http://code.google.com/p/autofill/ | SCR_006831 | 2026-08-10 09:33:02 | 9 | ||||||
|
SOAPaligner/soap2 Resource Report Resource Website 100+ mentions |
SOAPaligner/soap2 (RRID:SCR_005503) | SOAPaligner, SOAP2 | software application, data processing software, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 12,2024. Updated version of SOAP software for short oligonucleotide alignment that features in super fast and accurate alignment for huge amounts of short reads generated by Illumina/Solexa Genome Analyzer., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | next generation sequencing, alignment, short read, oligonucleotide, single-read, pair-end, resequencing, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SOAP |
PMID:19497933 DOI:10.1093/bioinformatics/btn025 |
THIS RESOURCE IS NO LONGER IN SERVICE | biotools:soap2 | https://bio.tools/soap2, https://sources.debian.org/src/soapaligner/ | SCR_005503 | 2026-08-10 09:32:34 | 325 | ||||||
|
British National Formulary Resource Report Resource Website 1+ mentions |
British National Formulary (RRID:SCR_008176) | data or information resource, portal | The BNF aims to provide prescribers, pharmacists and other healthcare professionals with sound up-to-date information about the use of medicines. The BNF provides ready access to key information on the selection, prescribing, dispensing and administration of medicines. Medicines that are generally prescribed in the UK are covered and those considered less suitable for prescribing are clearly identified. | drug, administration, clinical, dispensing, health care, manufacturer, medical, medicine, pharmaceutical, prescribing, product, regulatory, selection | nif-0000-21065 | SCR_008176 | BNF | 2026-08-10 09:33:25 | 6 | ||||||||||
|
LONI Inspector Resource Report Resource Website 1+ mentions |
LONI Inspector (RRID:SCR_004923) | LONI Inspector | software application, data processing software, software resource | A Java application for reading, displaying, searching, comparing, and exporting metadata from medical image files: AFNI, ANALYZE, DICOM, ECAT, GE, Interfile, MINC, and NIFTI. | analyze, dicom, java, minc, magnetic resonance, nifti, os independent, win32 (ms windows), workflow |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Laboratory of Neuro Imaging |
NIBIB 9P41EB015922-15; NCRR 2-P41-RR-013642-15 |
LONI Software License | nlx_155785 | http://www.nitrc.org/projects/inspector | http://www.loni.ucla.edu/Software/LONI-Inspector | SCR_004923 | 2026-08-10 09:32:26 | 3 | |||||
|
Functional Analysis of Diffusion Tensor Resource Report Resource Website 1+ mentions |
Functional Analysis of Diffusion Tensor (RRID:SCR_008888) | FADTTS | software application, data processing software, software resource | Pipeline developed for delineating the association between multiple diffusion properties along major white matter fiber bundles with a set of covariates of interest, such as age, diagnostic status and gender, and the structure of the variability of these white matter tract properties in various diffusion tensor imaging studies. FADTTS can be used to facilitate understanding of normal brain development, the neural bases of neuropsychiatric disorders, and the joint effects of environmental and genetic factors on white matter fiber bundles. The advantages of FADTTS compared with the other existing approaches are that they are capable of modelling the structured inter-subject variability, testing the joint effects, and constructing their simultaneous confidence bands. | genomic analysis, diffusion tensor imaging |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Spatial Statistical Parametric Mapping |
Academic Free License | nlx_151351 | SCR_008888 | Functional Analysis of Diffusion Tensor Tract Statistics | 2026-08-10 09:33:35 | 3 | |||||||
|
Neuroscience Gateway Resource Report Resource Website 10+ mentions |
Neuroscience Gateway (RRID:SCR_008915) | NSG | data or information resource, project portal, portal, software resource | Web portal that allows free access to supercomputing resources for large scale modeling and data processing. Portal facilitates access and use of National Science Foundation (NSF) High Performance Computing (HPC) resources by neuroscientists. | Large, scale, modeling, data, computing, neuroscience, neuron, BRAIN Initiative |
is recommended by: BRAIN Initiative lists: ModelRun is related to: XSEDE - Extreme Science and Engineering Discovery Environment is related to: NEURON is related to: GENESIS Neural Database and Modelers Workspace has parent organization: San Diego Supercomputer Center has parent organization: Neuroscience Information Framework has parent organization: Yale School of Medicine; Connecticut; USA |
NSF 1458840; NSF 1458495; BBSRC N005236; NIBIB R01 EB023297; NSF 1339856; NSF 1146949 |
Free, Freely available | nlx_151553, SCR_015767 | http://www.nitrc.org/projects/nsg/ | SCR_008915 | Neuroscience Gateway - A Portal for Computational Neuroscience, Neuroscience Gateway, Neuroscience Gateway (NSG) Portal | 2026-08-10 09:33:40 | 25 | |||||
|
Medscape App for iPhone and iPod touch Resource Report Resource Website |
Medscape App for iPhone and iPod touch (RRID:SCR_010610) | software application, mobile app, software resource | Free medical app for comprising a drug reference, drug interaction checker, disease and condition reference, procedures and protocols and specialty-focused Medical News * Drug Reference: Search prescribing and safety information for over 8,000 brand, generic and OTC drugs, herbals and supplements * Drug Interaction Checker: Check mild interactions to serious contraindications for any combination of drugs, herbals and supplements * Disease & Condition Reference: Review the latest in-depth clinical information for 4,000+ diseases and conditions (enhanced with images and videos) *Procedures & Protocols: Follow detailed stepbystep instructions for 600+ clinical procedures, including 80+ widely used Tables & Protocols * Specialty-focused Medical News: Read in-depth medical news articles daily in 30 specialty areas | iphone | Free | nlx_55618 | SCR_010610 | Medscape App | 2026-08-10 09:34:02 | 0 | |||||||||
|
Agency for Science Technology and Research Resource Report Resource Website 1+ mentions |
Agency for Science Technology and Research (RRID:SCR_011085) | institution, funding resource | Agency drives mission oriented research that advances scientific discovery and technological innovation. We play a key role in nurturing and developing talent and leaders for our Research Institutes, the wider research community, and industry.Our research creates economic growth and jobs for Singapore. As Science and Technology Organisation, we bridge gap between academia and industry in terms of research and development. |
is parent organization of: Genome Institute of Singapore; Singapore; Singapore is parent organization of: Defensins Knowledgebase is parent organization of: Bioinformatics Institute; Singapore; Singapore is parent organization of: Institute of Molecular and Cell Biology; Singapore; Singapore |
nlx_27227 | http://www.a-star.edu.sg/AgencyforScienceTechnologyandResearch/tabid/36/Default.aspx | SCR_011085 | A*STAR, A*STAR Singapore | 2026-08-10 09:34:10 | 6 | |||||||||
|
COILS: Prediction of Coiled Coil Regions in Proteins Resource Report Resource Website 100+ mentions |
COILS: Prediction of Coiled Coil Regions in Proteins (RRID:SCR_008440) | software application, data processing software, software resource | COILS is a program that compares a sequence to a database of known parallel two-stranded coiled-coils and derives a similarity score. By comparing this score to the distribution of scores in globular and coiled-coil proteins, the program then calculates the probability that the sequence will adopt a coiled-coil conformation. | software, prediction, database, sequence, coil, globular, protein, probability, bio.tools, FASEB list |
is listed by: 3DVC is listed by: Debian is listed by: bio.tools is listed by: OMICtools |
DOI:10.1126/science.252.5009.1162 | biotools:ncoils, OMICS_07850, nif-0000-30263 | https://bio.tools/ncoils, https://sources.debian.org/src/ncoils/ | https://sources.debian.org/src/ncoils/ | SCR_008440 | COILS Server | 2026-08-10 09:33:29 | 169 | ||||||
|
Graphtools Resource Report Resource Website 1+ mentions |
Graphtools (RRID:SCR_009490) | Graphtools | software application, data processing software, software resource | A set of MATLAB scripts for analysis of networks derived from neuroimaging data. Some of these scripts are entirely original, while some are adapted (or just copied) from the Brain Connectivity Toolbox (https://sites.google.com/a/brain-connectivity-toolbox.net/bct) The source code is available via git: git clone ssh://user | magnetic resonance, matlab |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: Brain Connectivity Toolbox |
BSD License | nlx_155638 | SCR_009490 | 2026-08-10 09:33:44 | 4 | ||||||||
|
Argonne National Laboratory Labs and Facilities Resource Report Resource Website 1+ mentions |
Argonne National Laboratory Labs and Facilities (RRID:SCR_011062) | Argonne Labs & Facilities, Argonne Labs and Facilities | data or information resource, portal | Argonne National Laboratory, located just outside of Chicago, is one of the U.S. Department of Energy''s largest national laboratories for scientific and engineering research to solve most important challenges in energy, environment and national security. Programmatic activities cover all aspects of innovation ecology including basic research, technology development and prototype development and testing. We regularly work with industry through exclusive licensing, joint research and variety of other mechanisms to transfer our inventions to marketplace. |
is listed by: ScienceExchange is related to: UChicago IGSB Next Generation Sequencing Core has parent organization: Argonne National Laboratory |
SciEx_9914 | http://www.scienceexchange.com/facilities/argonne-national-laboratory | SCR_011062 | Argonne National Laboratory Labs & Facilities | 2026-08-10 09:34:09 | 2 | ||||||||
|
Omics Discovery Index Resource Report Resource Website 10+ mentions |
Omics Discovery Index (RRID:SCR_010494) | OmicsDI, DDI, DDICC | data or information resource, portal, database | Portal for dataset discovery across a heterogeneous, distributed group of transcriptomics, genomics, proteomics and metabolomics data resources. These resources span eight repositories in three continents and six organisations, including both open and controlled access data resources. | dataset search, knowledge framework, knowledge discovery |
is affiliated with: MetabolomeXchange is affiliated with: ProteomeXchange has parent organization: University of California at San Diego; California; USA is parent organization of: Integrated Datasets |
NIA 1U24AI117966-01; NIGMS 1U54GM114833-01 |
Free, Public | nlx_158507, SCR_014747 | SCR_010494 | Omics Discovery Index (OmicsDI) | 2026-08-10 09:34:00 | 33 | ||||||
|
Subread Resource Report Resource Website 1000+ mentions |
Subread (RRID:SCR_009803) | software application, data processing software, software resource | Software package for high-performance read alignment, quantification and mutation discovery.General purpose read aligner which can be used to map both genomic DNA-seq reads and RNA-seq reads. Subread aligner as fast, accurate and scalable read mapping by seed-and-vote.These programs were also implemented in Bioconductor R package Rsubread. | read alignment, DNA-seq reads mapping, RNA-seq reads mapping, mutation discovery, , bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: Rsubread has parent organization: University of Melbourne; Victoria; Australia |
Australian National Health and Medical Research Council ; Victorian State Government Operational Infrastructure Support ; Australian Government |
PMID:23558742 | Free, Freely available | OMICS_01255, biotools:subread | https://bio.tools/subread, https://sources.debian.org/src/subread/ | SCR_009803 | 2026-08-10 09:33:54 | 2138 | ||||||
|
GRETNA Resource Report Resource Website 100+ mentions |
GRETNA (RRID:SCR_009487) | GRETNA | software application, data processing software, software resource | A graph theoretical network analysis toolbox which allows researchers to perform comprehensive analysis on the topology of brain connectome by integrating the most of network measures studied in current neuroscience field. | computational neuroscience, eeg, meg, electrocorticography, magnetic resonance, pet, spect |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is affiliated with: Functional Connectivity Analysis Tool for near-infrared spectroscopy data |
GNU General Public License | nlx_155634 | SCR_009487 | 2026-08-10 09:33:42 | 493 | ||||||||
|
LONI Java Image I/O Plugins Resource Report Resource Website |
LONI Java Image I/O Plugins (RRID:SCR_008277) | software application, data processing software, software resource | Decoders and encoders written in Java for the AFNI, ANALYZE, DICOM, ECAT, GE, MINC, NIFTI and other neuroimaging file formats.The plugins use Java Image I/O interfaces to read and write metadata and image data and can read and write AFNI, ANALYZE 7.5, DICOM, ECAT 7.2, GE 5.0, INTERFILE (including hrrt), MINC, NIFTI, and UCLA PACS file formats. All source code is provided and usage examples are included. | plugin, MRI, software, visualization, data processing |
is related to: Laboratory of Neuro Imaging has parent organization: University of Southern California; Los Angeles; USA |
NIBIB 9P41EB015922-15; NCRR 2-P41-RR-013642-15 |
Available for educational and research purposes only | nif-0000-23320 | SCR_008277 | 2026-08-10 09:33:30 | 0 |
Can't find your Tool?
We recommend that you click next to the search bar to check some helpful tips on searches and refine your search firstly. Alternatively, please register your tool with the SciCrunch Registry by adding a little information to a web form, logging in will enable users to create a provisional RRID, but it not required to submit.
Welcome to the RRID Resources search. From here you can search through a compilation of resources used by RRID and see how data is organized within our community.
You are currently on the Community Resources tab looking through categories and sources that RRID has compiled. You can navigate through those categories from here or change to a different tab to execute your search through. Each tab gives a different perspective on data.
If you have an account on RRID then you can log in from here to get additional features in RRID such as Collections, Saved Searches, and managing Resources.
Here is the search term that is being executed, you can type in anything you want to search for. Some tips to help searching:
If you are logged into RRID you can add data records to your collections to create custom spreadsheets across multiple sources of data.
Here are the facets that you can filter the data by.
If you have any further questions please check out our FAQs Page to ask questions and see our tutorials. Click this button to view this tutorial again.
