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Resource Name Proper Citation Abbreviations Resource Type Description Keywords Resource Relationships Related Condition Funding Defining Citation Availability Specification URL Alternate IDs Alternate URLs Old URLs Parent Organization Resource ID Synonyms Record Last Update Mentions Count
GENCODE
 
Resource Report
Resource Website
5000+ mentions
Rating or validation data
GENCODE (RRID:SCR_014966) data or information resource, dataset, portal, project portal Human and mouse genome annotation project which aims to identify all gene features in the human genome using computational analysis, manual annotation, and experimental validation. human, mouse, genome, annotation, sequence, gene features, bio.tools is listed by: Debian
is listed by: bio.tools
is affiliated with: ENCODE
NHGRI 5U54HG004555;
Wellcome Trust WT098051
PMID:22955987 Free biotools:GENCODE https://bio.tools/GENCODE SCR_014966 ENCODE 2026-09-19 12:56:04 8811
IITC Incapacitance Meter
 
Resource Report
Resource Website
IITC Incapacitance Meter (RRID:SCR_016143) resource Hardware that is used to test and assess pain and inflammation of the hind limbs on mice and rats. Dynamic weight bearing enables the test to be implemented on both limbs, while inflicting less stress on the subject animal. hardware, equipment, instrument, pain, inflammation, mice, rat, limb PMID:28326938 Commercially available SCR_016143 The IITC Incapacitance Test Meter, Incapacitance Meter 2026-09-19 12:53:18 0
Enhancer Trap Line Browser
 
Resource Report
Resource Website
Enhancer Trap Line Browser (RRID:SCR_003592) Enhancer Trap Line Browser atlas, data or information resource, database THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 6, 2023. Database and atlas of transgenic mouse lines that are generated by random insertion of enhancer trap probes. The trapped lines have highly restricted expression of tet transcription activator (some lines also have Cre DNA recombinase), which enables genetic manipulations in specific cell types. sagittal, coronal, gene, image, enhancer trap, piggybac transposon, probe, tet enahcer trap is related to: UCSC Genome Browser
is related to: Mouse Genome Informatics (MGI)
is related to: Allen Mouse Brain Reference Atlas
has parent organization: Brandeis University; Massachusetts; USA
THIS RESOURCE IS NO LONGER IN SERVICE nlx_157737 SCR_003592 2026-09-19 12:56:40 0
FIDEA
 
Resource Report
Resource Website
1+ mentions
FIDEA (RRID:SCR_004187) FIDEA analysis service resource, data analysis service, production service resource, service resource A web server for the functional interpretation of differential expression analysis. It can: * Calculate overrepresentation statistics using KEGG, Interpro, Gene Ontology Molecular Function, Gene Ontology Biological Process, Gene Ontology Cellular Component and GoSlim classifications; * Analyze down-regulated and up-regulated DE genes separately or together as a single set; * Provide interactive graphs and tables that can be modified on the fly according to user defined parameters; the user can set a fold change filter and interactively see the effects on the gene set under examination; * Output publication-ready plot of the graph; * Compare the results of several experiments in any combination. is listed by: OMICtools
has parent organization: Sapienza University of Rome; Rome; Italy
PMID:23754850 Public, Free, Acknowledgement requested OMICS_01539 SCR_004187 Functional Interpretation of Differential Expression Analysis 2026-09-19 12:56:42 9
Pain Genes database
 
Resource Report
Resource Website
10+ mentions
Pain Genes database (RRID:SCR_004771) PainGenesdb data or information resource, database Database of genes regulated by pain derived from published manuscripts describing results of pain-relevant knockout studies. The database has two levels of exploration: across-gene and within-gene. The across-gene level, the PainGenesdbSelector, is encountered first. All genes in the database can be accessed and sorted by their gene name, protein name, common names and acronyms, or genomic position (by navigating a graphic representation of the mouse genome). The gene and protein names can be selected from an alphabetical list, or by typing a text string into a search box. knock out mouse, pain sensation, mice, mutant, knockout, gene, genome, protein has parent organization: McGill University; Montreal; Canada Pain Louise Edwards Foundation PMID:17574758 nlx_77039, r3d100012129 https://doi.org/10.17616/R3WP95 SCR_004771 PainGenes DB 2026-09-19 12:56:46 16
Information Hyperlinked Over Proteins
 
Resource Report
Resource Website
10+ mentions
Information Hyperlinked Over Proteins (RRID:SCR_004829) iHOP data or information resource, database, service resource Information system that provides a network of concurring genes and proteins extends through the scientific literature touching on phenotypes, pathologies and gene function. It provides this network as a natural way of accessing millions of PubMed abstracts. By using genes and proteins as hyperlinks between sentences and abstracts, the information in PubMed can be converted into one navigable resource, bringing all advantages of the internet to scientific literature research. Moreover, this literature network can be superimposed on experimental interaction data (e.g., yeast-two hybrid data from Drosophila melanogaster and Caenorhabditis elegans) to make possible a simultaneous analysis of new and existing knowledge. The network contains half a million sentences and 30,000 different genes from humans, mice, D. melanogaster, C. elegans, zebrafish, Arabidopsis thaliana, yeast and Escherichia coli. phenotype, gene, protein, interaction, pathology, physiology, gene network, network, literature, gene function, text-mining, bio.tools is listed by: OMICtools
is listed by: Debian
is listed by: bio.tools
is related to: PubMed
has parent organization: Autonomous University of Madrid; Madrid; Spain
European Union IST-2001- 32688;
European Union QLRT-2001-00015
PMID:15226743 Creative Commons Attribution-NoDerivs License, Works v3 biotools:ihop, nif-0000-00232, OMICS_01185 https://bio.tools/ihop SCR_004829 iHOP - Information Hyperlinked over Proteins 2026-09-19 12:56:47 24
mouseMAP
 
Resource Report
Resource Website
mouseMAP (RRID:SCR_004784) MouseMAP analysis service resource, data analysis service, production service resource, service resource In collaboration with several research groups at Jackson Laboratory, we mapped the tissue-specific functional relationship networks in the laboratory mouse by simulating the natural tissue specificity realized by differential protein expression between tissues. MouseMAP is an interface that allows browsing networks of different tissues and the comparison between them. The current version of MouseMAP includes one global network as an extension of mouseNET (http://mousenet.princeton.edu) and 107 tissue-specific networks organized into 15 different major body systems. The interface has the following features (their usage are detailed in Help and FAQ page): 1. Single graph query with one or multiple genes of interests. 2. Expansion/shrinking of query results through edge or node cutoffs. 3. Comparison of local networks between different tissues. 4. Dynamic generation of figure legend to facilitate manuscript writing. network, visualization, mouse, gene is related to: MouseNET
has parent organization: Princeton University; New Jersey; USA
nlx_143914 SCR_004784 mouseMAP: Tissue-specific functional networks for the laboratory mouse 2026-09-19 12:56:46 0
MethylomeDB
 
Resource Report
Resource Website
1+ mentions
MethylomeDB (RRID:SCR_005583) MethylomeDB data or information resource, database A database containing genome-wide brain DNA methylation profiles for human and mouse brains. The DNA methylation profiles were generated by Methylation Mapping Analysis by Paired-end Sequencing (Methyl-MAPS) method and analyzed by Methyl-Analyzer software package. The methylation profiles cover over 80% CpG dinucleotides in human and mouse brains in single-CpG resolution. The integrated genome browser (modified from UCSC Genome Browser allows users to browse DNA methylation profiles in specific genomic loci, to search specific methylation patterns, and to compare methylation patterns between individual samples. Two species were included in the Brain Methylome Database: human and mouse. Human postmortem brain samples were obtained from three distinct cortical regions, i.e., dorsal lateral prefrontal cortex (dlPFC), ventral prefrontal cortex (vPFC), and auditory cortex (AC). Human samples were selected from our postmortem brain collection with extensive neuropathological and psychopathological data, as well as brain toxicology reports. The Department of Psychiatry of Columbia University and the New York State Psychiatric Institute have assembled this brain collection, where a validated psychological autopsy method is used to generate Axis I and II DSM IV diagnoses and data are obtained on developmental history, history of psychiatric illness and treatment, and family history for each subject. The mouse sample (strain 129S6/SvEv) DNA was collected from the entire left cerebral hemisphere. The three human brain regions were selected because they have been implicated in the neuropathology of depression and schizophrenia. Within each cortical region, both disease and non-psychiatric samples have been profiled (matching subjects by age and sex in each group). Such careful matching of subjects allows one to perform a wide range of queries with the ability to characterize methylation features in non-psychiatric controls, as well as detect differentially methylated domains or features between disease and non-psychiatric samples. A total of 14 non-psychiatric, 9 schizophrenic, and 6 depression methylation profiles are included in the database. brain, dna methylation, dorsal lateral prefrontal cortex, ventral prefrontal cortex, auditory cortex, bio.tools is listed by: OMICtools
is listed by: Debian
is listed by: bio.tools
has parent organization: Columbia University; New York; USA
NIH ;
NHGRI HG002915;
NIMH MH074118
PMID:22140101 OMICS_01843, biotools:methylomedb, nlx_146210 https://bio.tools/methylomedb SCR_005583 MethylomeDB - the Brain Methylome Database, Brain Methylome Database 2026-09-19 12:56:52 1
High Resolution Mouse Brain Atlas
 
Resource Report
Resource Website
10+ mentions
High Resolution Mouse Brain Atlas (RRID:SCR_006063) High Resolution Mouse Brain Atlas atlas, data or information resource 2D mouse brain atlas of high quality coronal Nissl- and myelin-stained sections with labels, 3D images of hippocampal formation and limited other brain structures. The data for this digital atlas are based on the Atlas of the Mouse Brain and Spinal Cord, authored by Richard L. Sidman, Jay. B. Angevine and Elizabeth Taber Pierce, published as a hard cover book by Harvard University Press in 1971 and currently out of print. C57BL/6J strain adult specimens were used in creating the atlas. adult mouse, hippocampal formation, image, leaf lumina camera, mouse, normal, nuclei of the limbic thalamus, c57bl/6, nissel, myelin, neuroanatomy, olfactory bulb, frontal pole, pyriform cortex, septo-striatal, septo-diencephalic, rostral diencephalon, caudal diencephalon, rostral cerebellum, caudal cerebellum, medula, spinal cord, diencephalon, cerebellum, mesencephalon has parent organization: Harvard University; Cambridge; United States Human Brain Project ;
NINDS RO1 NS36041
nif-0000-00087 SCR_006063 2026-09-19 12:56:55 28
Unified Human Interactome
 
Resource Report
Resource Website
10+ mentions
Unified Human Interactome (RRID:SCR_005805) UniHI data or information resource, database A database of human molecular interaction networks that integrates human protein-protein and transcriptional regulatory interactions from 15 distinct resources and aims to give direct and easy access to the integrated data set and to enable users to perform network-based investigations. The database includes tools (i) to search for molecular interaction partners of query genes or proteins in the integrated dataset, (ii) to inspect the origin, evidence and functional annotation of retrieved proteins and interactions, (iii) to visualize and adjust the resulting interaction network, (iv) to filter interactions based on method of derivation, evidence and type of experiment as well as based on gene expression data or gene lists and (v) to analyze the functional composition of interaction networks. molecular interaction network, interactome, protein, protein interaction network, protein interaction, pathway, function, visualization, protein-protein interaction, transcriptional regulatory interaction, network is listed by: OMICtools
has parent organization: University of Algarve; Faro; Portugal
PMID:24214987
PMID:22218860
PMID:18984619
PMID:17158159
Public, Non-commercial OMICS_01911, nif-0000-03609 http://www.mdc-berlin.de/unihi SCR_005805 2026-09-19 12:56:54 20
FuncAssociate: The Gene Set Functionator
 
Resource Report
Resource Website
10+ mentions
FuncAssociate: The Gene Set Functionator (RRID:SCR_005768) FuncAssociate analysis service resource, data analysis service, production service resource, service resource A web-based tool that accepts as input a list of genes, and returns a list of GO attributes that are over- (or under-) represented among the genes in the input list. Only those over- (or under-) representations that are statistically significant, after correcting for multiple hypotheses testing, are reported. Currently 37 organisms are supported. In addition to the input list of genes, users may specify a) whether this list should be regarded as ordered or unordered; b) the universe of genes to be considered by FuncAssociate; c) whether to report over-, or under-represented attributes, or both; and d) the p-value cutoff. A new version of FuncAssociate supports a wider range of naming schemes for input genes, and uses more frequently updated GO associations. However, some features of the original version, such as sorting by LOD or the option to see the gene-attribute table, are not yet implemented. Platform: Online tool gene, gene ontology, statistical analysis, web service, bio.tools is listed by: Gene Ontology Tools
is listed by: OMICtools
is listed by: bio.tools
is listed by: Debian
is related to: Gene Ontology
has parent organization: Roth Laboratory
NIH ;
Canadian Institute for Advanced Research ;
NINDS NS054052;
NINDS NS035611;
NHLBI HL081341;
NHGRI HG0017115;
NHGRI HG004233;
NHGRI HG003224
PMID:19717575
PMID:14668247
Free for academic use, Acknowledgement requested biotools:funcassociate, OMICS_02264, nlx_149233 http://llama.mshri.on.ca/cgi/func/funcassociate, https://bio.tools/funcassociate SCR_005768 2026-09-19 12:56:53 36
ADGO
 
Resource Report
Resource Website
1+ mentions
ADGO (RRID:SCR_006343) ADGO analysis service resource, data analysis service, production service resource, service resource A web-based tool that provides composite interpretations for microarray data comparing two sample groups as well as lists of genes from diverse sources of biological information. It provides multiple gene set analysis methods for microarray inputs as well as enrichment analyses for lists of genes. It screens redundant composite annotations when generating and prioritizing them. It also incorporates union and subtracted sets as well as intersection sets. Users can upload their gene sets (e.g. predicted miRNA targets) to generate and analyze new composite sets. microarray, gene, annotation, bio.tools is listed by: OMICtools
is listed by: Debian
is listed by: bio.tools
PMID:21624890 Acknowledgement requested OMICS_02229, biotools:adgo https://bio.tools/adgo SCR_006343 2026-09-19 12:56:57 3
Recombinase (cre) Activity
 
Resource Report
Resource Website
10+ mentions
Recombinase (cre) Activity (RRID:SCR_006585) Recombinase Activity data or information resource, database Curated data about all recombinase-containing transgenes and knock-ins developed in mice providing a comprehensive resource delineating known activity patterns and allows users to find relevant mouse resources for their studies. cre, recombinase, transgene, knock-in, allele, expression, activity pattern, mutagenesis, promoter, driver, image, tissue, specificity assay is related to: International Mouse Strain Resource
is related to: CREATE
is related to: JAX Cre Repository
is related to: Allen Institute for Brain Science
is related to: CRE Driver Network
is related to: Pleiades Promoter Project: Genomic Resources Advancing Therapies for Brain Disorders
is related to: EUCOMMTOOLS
has parent organization: Mouse Genome Informatics (MGI)
European Union HEALTH-F4-2009-223487;
NCRR RR03 2656;
NICHD HD062499
SCR_017520, nlx_152803 http://www.creportal.org/ SCR_006585 Cre Portal 2026-09-19 12:56:59 22
Tuberculosis Database
 
Resource Report
Resource Website
50+ mentions
Tuberculosis Database (RRID:SCR_006619) TBDB data or information resource, database Database providing integrated access to genome sequence, expression data and literature curation for Tuberculosis (TB) that houses genome assemblies for numerous strains of Mycobacterium tuberculosis (MTB) as well assemblies for over 20 strains related to MTB and useful for comparative analysis. TBDB stores pre- and post-publication gene-expression data from M. tuberculosis and its close relatives, including over 3000 MTB microarrays, 95 RT-PCR datasets, 2700 microarrays for human and mouse TB related experiments, and 260 arrays for Streptomyces coelicolor. (July 2010) To enable wide use of these data, TBDB provides a suite of tools for searching, browsing, analyzing, and downloading the data. genomic, protein, blast, genome, gene, systems biology, gene expression, microarray, comparative analysis, regulatory network, metabolic network, epitope, expression profile, rt-pcr, gene regulation, genome browser, FASEB list is listed by: re3data.org
is related to: SMD
is related to: BioCyc
has parent organization: Broad Institute
has parent organization: Stanford University School of Medicine; California; USA
Tuberculosis Bill and Melinda Gates Foundation PMID:20488753
PMID:18835847
Acknowledgement requested, Public, (Published data) nif-0000-03537, r3d100010930 https://doi.org/10.17616/R39G8F SCR_006619 TB Database, TBDatabase 2026-09-19 12:56:59 64
Integrated Gene-Disease Interaction
 
Resource Report
Resource Website
Integrated Gene-Disease Interaction (RRID:SCR_006173) data or information resource, database Virtual database currently indexing interaction between genes and diseases from Online Mendelian Inheritance in Man (OMIM) and Comparative Toxicogenomics Database (CTD). gene, phenotype, disease, interaction, integrated, database is used by: NIF Data Federation
is related to: OMIM
is related to: Comparative Toxicogenomics Database (CTD)
has parent organization: Integrated
NIDA ;
NIH Blueprint for Neuroscience Research
Data are licensed by their respective owners, Use and distribution is subject to the Terms of Use by the original resource nlx_151674 https://legacy.neuinfo.org/mynif/search.php?q=*&t=indexable&list=cover&nif=nlx_154697-7 http://neuinfo.org/nif/nifgwt.html?query=nlx_151674, https://www.neuinfo.org/mynif/search.php?q=*&t=indexable&nif=nlx_151674-1, https://neuinfo.org/mynif/search.php?q=*&t=indexable&list=cover&nif=nlx_154697-7 SCR_006173 Gene-Disease Interaction, NIF Integrated Gene-Disease Interaction, Integrated GDI, NIF Integrated Gene-Disease Interaction View, NIF Gene-Disease Interaction, Integrated Gene-Disease Interaction View 2026-09-19 12:56:56 0
PITA
 
Resource Report
Resource Website
1000+ mentions
PITA (RRID:SCR_010853) PITA data or information resource, data set Catalogs of predicted microRNA targets in worm (based on ce6 genome assembly), fly (dm3), mouse (mm9) and human (hg18). We follow standard seed parameter settings and consider seeds of length 6-8 bases, beginning at position 2 of the microRNA. No mismatches or loops are allowed, but a single G:U wobble is allowed in 7- or 8-mers. In genes missing a 3' UTR annotation, 500 bp (fly), 800 bp (human and mouse) or 300 bp (worm) downstream of the annotated end of the coding sequence were used as the predicted UTR. For each organism, a catalog with zero flank and with a flank of 3 and 15 bases upstream and downstream. is listed by: OMICtools OMICS_00412 SCR_010853 2026-09-19 12:58:56 1079
Retinal wave repository
 
Resource Report
Resource Website
Retinal wave repository (RRID:SCR_010462) Retinal wave repository data or information resource, data set A subset of the CARMEN repository, a curated set of data and code of multielectrode array recordings of spontaneous activity in developing mouse and ferret retina. The data have been annotated with minimal metadata and converted into HDF5 (Hierarchical data format, version 5) including the essential features of the recordings, such as developmental age, and genotype. All code and tools used in the analyses are also fully available for reuse, giving the ability to regenerate each figure and table and know exactly how the results were calculated, adding confidence in the research output and allowing others to easily build upon previous work. The addition of published data to the repository is encouraged. hdf5, development, neural circuit, retina, eye, multielectrode, array recording, spontaneous activity, reproducible research, retinal wave, electrophysiology, multielectrode array, developmental age, genotype has parent organization: GigaScience
has parent organization: Code Analysis Repository and Modelling for e-Neuroscience
has parent organization: University of Cambridge; Cambridge; United Kingdom
Developing retina, Aging EPSRC EP/E002331/1;
BBSRC BB/H023577/1;
BBSRC BB/I000984/1;
Wellcome Trust 083205/B/07/Z
PMID:24666584 Registration required, (CARMEN), Acknowledgement required, The community can contribute to this resource nlx_157664 http://www.damtp.cam.ac.uk/user/eglen/waverepo/ SCR_010462 A data repository and analysis framework for spontaneous neural activity recordings in developing retina 2026-09-19 12:58:56 0
CU Denver iPSC Core
 
Resource Report
Resource Website
CU Denver iPSC Core (RRID:SCR_012176) CU Denver iPSC Core access service resource, core facility, service resource The new iPSC Core generates custom-designed iPSCs from mouse and human cells, including disease-specific human iPSCs. iPSCs from other species are currently under development. The Core is currently using both lentiviral- and sendai viral vector systems to deliver reprogramming factors to cells. Both systems are efficient, with the latter system having the advantage to generate iPSCs with a non-DNA-integrating vector system. is listed by: ScienceExchange
is related to: University of Colorado Denver Labs and Facilities
has parent organization: University of Colorado Denver; Colorado; USA
SciEx_10241 SCR_012176 University of Colorado Denver iPS Core, University of Colorado Denver iPSC Core, CU Denver iPS Core, University of Colorado Denver Induced Pluripotent Stem Cell Core 2026-09-19 12:59:04 0
CU Denver Transgenic and Gene Targeting Core
 
Resource Report
Resource Website
CU Denver Transgenic and Gene Targeting Core (RRID:SCR_012177) CU Denver Transgenic and Gene Targeting Core access service resource, core facility, service resource THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 22,2024. Transgenic and Gene Targeting Core is a full-service facility designed to assist you in generating genetically engineered mouse models for biomedical research. Our services include gene targeting in embryonic stem cells, the generation of ES cell-derived knockout and knockin mice, transgenic mice (conventional and BAC transgenic mice) and the cryo-preservation of mouse lines. The latter service is of particular importance for investigators that have long-term projects with non-commercial mouse lines. Changes in the genetic make-up of your mouse lines that occur spontaneously over time (gene drift) and disease outbreaks can significantly affect the outcome of your research. It is therefore advisable to preserve your mouse lines, providing you with a backup of your valuable research tools. We currently offer both embryo cryopreservation as well as sperm cryopreservation for this purpose. is listed by: ScienceExchange
is related to: University of Colorado Denver Labs and Facilities
has parent organization: University of Colorado Denver; Colorado; USA
THIS RESOURCE IS NO LONGER IN SERVICE SciEx_10246 SCR_012177 University of Colorado Denver Transgenic and Gene Targeting Core 2026-09-19 12:59:04 0
HNDC NeuroBehavior Laboratory Core
 
Resource Report
Resource Website
1+ mentions
HNDC NeuroBehavior Laboratory Core (RRID:SCR_012396) HNDC NeuroBehavior Laboratory Core access service resource, core facility, service resource Core facility that provides the following services: Surgery/necropsy service. Mouse models have become a popular and successful approach to elucidating the physiological and pathological roles of individual genes and are truly crucial to accelerate the development of effective treatments and cures for Alzheimer''''s, Parkinson''''s, ALS, MS and other neurodegenerative diseases. The increasing demand for mouse behavioral studies within the neuroscience community has led the Harvard NeuroDiscovery Center to develop a major new, state of the art mouse behavior laboratory, located in the Longwood medical area and carefully designed to meet the exacting standards required for this type of work. The NeuroBehavior Laboratory (NBL) will provide the Harvard community and other investigators access to a broad range of reliable behavioral/cognitive tests necessary to analyze and interpret the impact of a genetic, surgical or pharmacologic manipulation on specific behaviors. They can provide: * Assistance with experimental design. * Support for grant applications that have a significant component of mouse neurobehavioral research. * Full, fee-for-service, mouse behavioral testing services. * Training in all aspects of mouse neurobehavioral testing. * Assistance with data analysis and interpretation. small animal surgery is listed by: ScienceExchange
is listed by: Eagle I
is related to: Harvard NeuroDiscovery Center Labs and Facilities
has parent organization: Harvard Medical School; Massachusetts; USA
SciEx_13134 http://harvard.eagle-i.net/i/0000012c-e5df-4802-2162-17a280000000, http://www.scienceexchange.com/facilities/neurobehavior-laboratory-core SCR_012396 Harvard NeuroDiscovery Center - NeuroBehavior Laboratory, Harvard NeuroDiscovery Center NeuroBehavior Laboratory Core 2026-09-19 12:59:08 3

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