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 | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
Neurogrid Resource Report Resource Website 10+ mentions |
Neurogrid (RRID:SCR_005024) | Neurogrid | instrument resource | A specialized hardware platform that will perform cortex-scale emulations while offering software-like flexibility. With sixteen 12x14 sq-mm chips (Neurocores) assembled on a 6.5x7.5 sq-in circuit board that can model a slab of cortex with up to 16x256x256 neurons - over a million! The chips are interconnected in a binary tree by 80M spike/sec links. An on-chip RAM (in each Neurocore) and an off-chip RAM (on a daughterboard, not shown) softwire vertical and horizontcal cortical connections, respectively. It provides an affordable option for brain simulations that uses analog computation to emulate ion-channel activity and uses digital communication to softwire synaptic connections. These technologies impose different constraints, because they operate in parallel and in serial, respectively. Analog computation constrains the number of distinct ion-channel populations that can be simulatedunlike digital computation, which simply takes longer to run bigger simulations. Digital communication constrains the number of synaptic connections that can be activated per secondunlike analog communication, which simply sums additional inputs onto the same wire. Working within these constraints, Neurogrid achieves its goal of simulating multiple cortical areas in real-time by making judicious choices. | simulation, neuron, cortex, synapse, analog vlsi, instrument, equipment, hardware | has parent organization: Stanford University; Stanford; California | NSF ; NIH |
PMID:17959490 | nlx_97879 | SCR_005024 | 2026-08-15 11:22:57 | 14 | |||||||
|
SMART Resource Report Resource Website 5000+ mentions |
SMART (RRID:SCR_005026) | SMART | database, production service resource, data analysis service, web service, data or information resource, data access protocol, software resource, service resource, analysis service resource | Software tool for identification and annotation of genetically mobile domains and analysis of domain architectures. | extracellular, gene, genetic, genetically, genome, architecture, chromatin, domain, mobile, phyletic, protein, proteome, signaling, structure, taxonomic, tertiary, bio.tools, FASEB list |
is used by: Mutation Annotation and Genomic Interpretation is listed by: bio.tools is listed by: Debian is related to: Eukaryotic Linear Motif is related to: Conserved Domain Database is related to: GOTaxExplorer has parent organization: EMBL - Bork Group |
European Union | PMID:18978020 PMID:16381859 PMID:14681379 PMID:10592234 PMID:9847187 PMID:9600884 |
Free, Freely available | nif-0000-03471, biotools:smart | http://smart.embl-heidelberg.de/, https://bio.tools/smart | SCR_005026 | Simple Modular Architecture Research Tool | 2026-08-15 11:23:10 | 8432 | ||||
|
UPARSE Resource Report Resource Website 1000+ mentions |
UPARSE (RRID:SCR_005020) | UPARSE | software resource | An Operational Taxonomic Unit (OTU) clustering software for 16S and other marker genes. Highly accurate OTU sequences and improved diversity measures. | is listed by: OMICtools | PMID:23955772 | OMICS_01449 | SCR_005020 | 2026-08-15 11:23:05 | 4687 | |||||||||
|
Chicken Gene Nomenclature Consortium Resource Report Resource Website 1+ mentions |
Chicken Gene Nomenclature Consortium (RRID:SCR_004966) | CGNC | database, data repository, standard specification, storage service resource, data or information resource, international standard specification, service resource, narrative resource | International group of researchers interested in providing standardized gene nomenclature for chicken genes. A Chicken Gene Annotation Tool is available from CGNC-UK which assigns chicken nomenclature based on predicted orthology to human genes. The CGNC-US database includes CGNC-UK information and adds manually biocurated from biocurators and interested contributors. A Human Chicken Ortholog Predictions Search is available. Both resources are part of a united CGNC effort and nomenclature data is shared and co-ordinated between these two resources. They strongly encourage researchers with domain knowledge to participate in this nomenclature effort by requesting a login and providing gene nomenclature for their genes of interest. Please contact them for further information or assistance. The AGNC works in conjunction with public resources such as NCBI and Ensembl and in consultation with existing nomenclature committees, including the Chicken Gene Nomenclature Committee (CGNC). The Avian and Chicken nomenclature efforts are co-ordinated and chicken data is shared between these two groups. | orthology, ortholog, human, gene, nomenclature, prediction | has parent organization: Mississippi State University; Mississippi; USA | PMID:19607656 | Account required, The community can contribute to this resource | nlx_93177 | http://www.agnc.msstate.edu/Default.aspx | SCR_004966 | 2026-08-15 11:23:04 | 1 | ||||||
|
BioVision Resource Report Resource Website 10000+ mentions |
BioVision (RRID:SCR_005057) | commercial organization | An Antibody supplier, THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_152316 | SCR_005057 | 2026-08-15 11:23:06 | 14127 | |||||||||||
|
University of Kerala; Kerala; India Resource Report Resource Website 1+ mentions |
University of Kerala; Kerala; India (RRID:SCR_005059) | University of Kerala | university | University of Kerala, formerly the University of Travancore, is an affiliating university located in Thiruvananthapuram, capital of the state of Kerala, India. | is parent organization of: TheScienceJobs.com | nlx_144191, grid.413002.4, Wikidata:Q1552247, ISNI:0000 0001 2179 5111, Crossref funder ID:100007779 | https://ror.org/05tqa9940 | SCR_005059 | University of Travancore | 2026-08-15 11:22:58 | 1 | ||||||||
|
CARMA Resource Report Resource Website 50+ mentions |
CARMA (RRID:SCR_004999) | CARMA | software resource | A software pipeline for characterizing the taxonomic composition and genetic diversity of short-read metagenomes. The software was originally designed for the analysis of environmental metagenomes obtained by the ultra-fast 454 pyrosequencing system. | metagenome, phylogenetic, dna fragment, dna, classification |
is listed by: OMICtools has parent organization: Bielefeld University; North Rhine-Westphalia; Germany |
PMID:18285365 | Acknowledgement requested | OMICS_01451 | SCR_004999 | CARMA - Characterizing Short Read Metagenomes | 2026-08-15 11:23:04 | 88 | ||||||
|
SMD Resource Report Resource Website 10+ mentions |
SMD (RRID:SCR_004987) | SMD | database, data repository, production service resource, storage service resource, data analysis service, data or information resource, service resource, analysis service resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on December 17, 2021. Database to store, annotate, view, analyze and share microarray data. It provides registered users access to their own data, provides users access to public data, and tools with which to analyze those data, to any public user anywhere in the world. The GenePattern software package has been incorporated directly into SMD, providing access to many new analysis tools, as well as a plug-in architecture that allows users to directly integrate and share additional tools through SMD. This extension is available with the SMD source code that is fully and freely available to others under an Open Source license, enabling other groups to create a local installation of SMD with an enriched data analysis capability. SMD search options allow the user to Search By Experiments, Search By Datasets, or Search By Gene Names. Web services are provided using common standards, such as Simple Object Access Protocol (SOAP). This enables both local and remote researchers to connect to an installation of the database and retrieve data using pre-defined methods, without needing to resort to use of a web browser. | data set, microarray, gene, image, gene expression, adenovirus disease, apoptosis, leukemia, source code, web service |
is listed by: 3DVC is listed by: re3data.org is listed by: OMICtools is related to: Longhorn Array Database is related to: Tuberculosis Database has parent organization: Princeton University; New Jersey; USA is parent organization of: SOURCE |
NCI ; Howard Hughes Medical Institute ; Stanford University School of Medicine; California; USA ; NHGRI R01 HG003469 |
PMID:18953035 PMID:17182626 PMID:15608265 PMID:12519956 PMID:11125075 |
Public, Open-source license, The community can contribute to this resource, Acknowledgement requested, THIS RESOURCE IS NO LONGER IN SERVICE | nlx_94141, OMICS_00870, r3d100010555 | https://doi.org/10.17616/R3DW40 | http://genome-www.stanford.edu/microarray/, http://smd.stanford.edu/ | SCR_004987 | Stanford Microarray Database | 2026-08-15 11:23:09 | 12 | |||
|
MiTCR Resource Report Resource Website 10+ mentions |
MiTCR (RRID:SCR_004989) | MiTCR | software resource | An open source software package aimed at extraction of information on repertoire of T-cell clones from Next Generation Sequencing (NGS) data. It is designed with the knowledge of the critical challenges arising in everyday processing of immunological data. | next generation sequencing | is listed by: OMICtools | PMID:23892897 | Apache License | OMICS_00003 | SCR_004989 | MiTCR - T-cell receptor repertoire analysis software | 2026-08-15 11:23:04 | 37 | ||||||
|
MIP Scaffolder Resource Report Resource Website 1+ mentions |
MIP Scaffolder (RRID:SCR_005072) | MIP Scaffolder | software resource | A software program for scaffolding contigs produced by fragment assemblers using mate pair data such as those generated by ABI SOLiD or Illumina Genome Analyzer. | scaffolding, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of Helsinki; Helsinki; Finland |
OMICS_00044, biotools:mip_scaffolder | https://bio.tools/mip_scaffolder | SCR_005072 | 2026-08-15 11:22:58 | 1 | ||||||||
|
Scarpa Resource Report Resource Website 10+ mentions |
Scarpa (RRID:SCR_005073) | Scarpa | software resource | A stand-alone scaffolding tool for NGS data. It can be used together with virtually any genome assembler and any NGS read mapper that supports SAM format. Other features include support for multiple libraries and an option to estimate insert size distributions from data. | scaffolding |
is listed by: OMICtools has parent organization: University of Toronto; Ontario; Canada |
PMID:23274213 | GNU General Public License | OMICS_00047 | SCR_005073 | SCARPA: scaffolding reads with practical algorithms, Scaffolding Reads with Practical Algorithms | 2026-08-15 11:23:06 | 13 | ||||||
|
NIH Neuroscience Microarray Consortium Resource Report Resource Website 1+ mentions |
NIH Neuroscience Microarray Consortium (RRID:SCR_004930) | database, production service resource, data repository, storage service resource, data analysis service, data or information resource, service resource, analysis service resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented on April 24, 2012. (no longer being funded) The NIH Microarray Consortium provides for-fee services to a community of NIH grantees, together with a more limited set of services to the public. The primary goal of this consortium is to move basic and translational research forward through acquisition and dissemination of high quality genomic data. This site includes a repository of microarray data sets and offers one-click links to public projects. These datasets were generated by various researchers on these platforms: Affymetrix, Agilent, Ambion, cDNA, Illumina, and Operon. The species currently covered are: Arabidopsis, Bovine, chicken, C. Elegans, Drosophila, Human, Macaca mulatta (Rhesus macaque), Mouse, Rat, Songbird, Xenopus, Yeast, and zebra finch. Basic search functions allows users to choose multiple options for finding the projects that interest them, and raw data files can also be downloaded after user registration. Web-based data analysis tools are also available. Scientists can analyze microarray data from the consortium repository or investigators can upload outside data for analysis. | arabidopsis, bos taurus, chicken, caenorhabditis elegans, drosophila, human, rhesus monkey, mouse, rat, songbird, xenopus, yeast, zebra finch |
is used by: NIF Data Federation is related to: Songbird Brain Transcriptome Database has parent organization: National Institutes of Health |
NIH Blueprint for Neuroscience Research | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-00074 | http://arrayconsortium.tgen.org, http://np2.ctrl.ucla.edu/np2/home.do | SCR_004930 | NIH Neuroscience Microarray Consortium | 2026-08-15 11:22:55 | 4 | ||||||
|
German Federal Ministry of Education and Research Resource Report Resource Website 100+ mentions |
German Federal Ministry of Education and Research (RRID:SCR_005066) | BMBF | government granting agency | SCR_005066 | Bundesministerium für Bildung und Forschung, Federal Ministry of Education and Research, Federal Ministry of Education and Research (Germany) | 2026-08-15 11:23:06 | 137 | ||||||||||||
|
Alzheimer's and Dementia Resource Center Resource Report Resource Website 100+ mentions |
Alzheimer's and Dementia Resource Center (RRID:SCR_004924) | ADRC | biomaterial supply resource, tissue bank, material resource, brain bank | The Alzheimer's and Dementia Resource Center (ADRC) facilitates tissue donations for the Brain Bank Research Program in order to help find better treatments, more diagnostic tools and a cure for Alzheimer's disease and dementia. The Brain Bank Program is administered by Mount Sinai Medical Center in Miami Beach and under contract with the Florida Department of Elder Affairs. ADRC also provides caregivers with the educational resources, spiritual comfort and emotional support. The ADRC facilitates training for professional caregivers that meets requirements for the Florida Department of Elder Affairs. | alzheimer's disease, dementia, brain, tissue, brain bank, caregiver, educational resource, patient support | is listed by: One Mind Biospecimen Bank Listing | Alzheimer's disease, Dementia | Public, Registration and pre-registration required to access the brain bank | nlx_143948 | SCR_004924 | alzheimer's disease, tissue, brain, patient support, educational resource, caregiver, dementia, brain bank | 2026-08-15 11:23:07 | 421 | ||||||
|
PhenomeBLAST Ontology Resource Report Resource Website 1+ mentions |
PhenomeBLAST Ontology (RRID:SCR_005139) | PHENOMEBLAST | ontology, data or information resource, controlled vocabulary | A cross-species phenotype and anatomy ontology resulting from combining available anatomy and phenotype ontologies and their definitions. The ontology includes phenotype definitions for yeast, mouse, fish, worm, fly and human phenotypes and diseases. | owl | is listed by: BioPortal | nlx_157549 | SCR_005139 | 2026-08-15 11:23:08 | 1 | |||||||||
|
T-lex Resource Report Resource Website 1+ mentions |
T-lex (RRID:SCR_005134) | T-lex | software resource | Software package for fast and accurate discovery, annotation, re-annotation and population analysis of Transposable Elements using Next-Generation Sequencing data. | transposable element, next-generation sequencing, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Stanford University; Stanford; California has parent organization: SourceForge |
GNU General Public License | biotools:t-lex2, OMICS_00121 | https://bio.tools/t-lex2 | SCR_005134 | T-lex package | 2026-08-15 11:23:08 | 4 | ||||||
|
PoPoolation TE Resource Report Resource Website 1+ mentions |
PoPoolation TE (RRID:SCR_005131) | PoPoolation TE | software resource | A quick and simple pipeline for the analysis of transposable element (TE) insertions in (natural) populations using next generation sequencing. It calculates TE insertion frequencies for TEs that are present in the reference genome as well as for novel TE insertions. PoPoolation TE requires paired-end reads from a pooled population, a reference sequence and transposable element sequences (fasta-file). | next generation sequencing, transposable element, insertion frequency, genomics, population genetics, illumina |
is listed by: OMICtools has parent organization: Google Code |
PMID:22291611 | Acknowledgement requested, New BSD License | OMICS_00119 | SCR_005131 | 2026-08-15 11:23:08 | 1 | |||||||
|
Alfred P. Sloan Foundation Resource Report Resource Website 50+ mentions |
Alfred P. Sloan Foundation (RRID:SCR_005099) | Sloan Foundation | institution | The Alfred P. Sloan Foundation is a philanthropic, not-for-profit grantmaking institution based in New York City. Established in 1934 by Alfred Pritchard Sloan Jr., then-President and Chief Executive Officer of the General Motors Corporation, the Foundation makes grants in support of original research and education in science, technology, engineering, mathematics and economic performance. * Promotes research in science, technology, engineering, mathematics, and economic performance * Offers two-year long research fellowships for early career researchers | grant, fellowship |
is related to: MIT Center for Biomedical Innovation is parent organization of: Datahub |
grid.453006.4, Crossref funder ID: 100000879, ISNI: 0000 0004 0508 3060, nlx_144112 | https://ror.org/052csg198 | SCR_005099 | 2026-08-15 11:22:59 | 56 | ||||||||
|
Eurexpress Resource Report Resource Website 1+ mentions |
Eurexpress (RRID:SCR_005093) | Eurexpress | database, expression atlas, data or information resource, image collection, atlas | Genome transcriptome atlas by RNA in situ hybridization on sagittal sections of developing mouse at embryonic day 14.5. Consists of searchable database of annotated images that can be interactively viewed. Anatomy based expression profiles for coding genes and microRNAs, tissue specific genes. Expression data generated by using human and murine tissue arrays. | Genome, transcriptome, atlas, RNA, in situ, hybrydization, sagittal, section, developing, mouse, embryo, expression, gene |
is listed by: GUDMAP Ontology is listed by: NIDDK Information Network (dkNET) is related to: EMAGE Gene Expression Database is related to: aGEM has parent organization: Telethon Institute of Genetics and Medicine; Naples; Italy |
European Union ; VI Framework ; Telethon Foundation ; Swiss National Science Foundation ; Max Planck Society ; MRC ; Association pour la Recherche sur le Cancer ; Ingenio 2010 MEuropean Union |
PMID:21267068 | nif-0000-00243 | http://www.eurexpress.org/ee/databases/anatomy/treeFrames.jsp, http://www.eurexpress.org/ee/ | SCR_005093 | Eurexpress atlas, Transcriptome Atlas Database for Mouse Embryo | 2026-08-15 11:23:12 | 3 | |||||
|
BEERS Resource Report Resource Website 10+ mentions |
BEERS (RRID:SCR_005090) | BEERS | software resource | A simulation engine for generating RNA-Seq data that was designed to benchmark RNA-Seq alignment algorithms and also algorithms that aim to reconstruct different isoforms and alternate splicing from RNA-Seq data. By default BEERS simulates either mouse or human paired-end RNA-Seq data modeled on the illumina platform. It starts with a large number of gene models (approx 500K) taken from about ten different published annotation efforts, and then chooses a fixed number of these genes at random (30,000 by default). This avoids biasing for or against any particular set of annotations. BEERS then introduces substitutions, indels, alternate spice forms, sequencing errors, and intron signal. BEERS can also simulate strand specific reads. BEERS does not simulate quality scores. There are four configuration files required, these are available for human and mouse. BEERS can also be configured to use any set of gene models. Pre-built indexes for human refseq are given. Using these indexes will generate a much tamer set of transcripts. BEERS is written in perl. | perl, rna-seq |
is listed by: OMICtools has parent organization: University of Pennsylvania Perelman School of Medicine; Pennsylvania; USA |
PMID:21775302 | OMICS_01364 | SCR_005090 | Benchmarker for Evaluating the Effectiveness of RNA-Seq Software (BEERS), Benchmarker for Evaluating the Effectiveness of RNA-Seq Software | 2026-08-15 11:22:58 | 22 |
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.
