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 | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
Cell Centered Database Resource Report Resource Website 10+ mentions |
Cell Centered Database (RRID:SCR_002168) | CCDB | data or information resource, data repository, database, image repository, service resource, storage service resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented June 5, 2017. It has been merged with Cell Image Library. Database for sharing and mining cellular and subcellular high resolution 2D, 3D and 4D data from light and electron microscopy, including correlated imaging that makes unique and valuable datasets available to the scientific community for visualization, reuse and reanalysis. Techniques range from wide field mosaics taken with multiphoton microscopy to 3D reconstructions of cellular ultrastructure using electron tomography. Contributions from the community are welcome. The CCDB was designed around the process of reconstruction from 2D micrographs, capturing key steps in the process from experiment to analysis. The CCDB refers to the set of images taken from microscope the as the Microscopy Product. The microscopy product refers to a set of related 2D images taken by light (epifluorescence, transmitted light, confocal or multiphoton) or electron microscopy (conventional or high voltage transmission electron microscopy). These image sets may comprise a tilt series, optical section series, through focus series, serial sections, mosaics, time series or a set of survey sections taken in a single microscopy session that are not related in any systematic way. A given set of data may be more than one product, for example, it is possible for a set of images to be both a mosaic and a tilt series. The Microscopy Product ID serves as the accession number for the CCDB. All microscopy products must belong to a project and be stored along with key specimen preparation details. Each project receives a unique Project ID that groups together related microscopy products. Many of the datasets come from published literature, but publication is not a prerequisite for inclusion in the CCDB. Any datasets that are of high quality and interest to the scientific community can be included in the CCDB. | electron microscope, light microscopy, electron tomography, electron microscopy, image, cell, microscopy, tomography |
is used by: NIF Data Federation is used by: Integrated Datasets is listed by: re3data.org is related to: Cell Image Library (CIL) is related to: Cell Image Library (CIL) is related to: Whole Brain Catalog is related to: Integrated Manually Extracted Annotation has parent organization: University of California at San Diego; California; USA has parent organization: University of California; San Diego;National Center for Microscopy and Imaging Research - NCMIR is parent organization of: Subcellular Anatomy Ontology is parent organization of: CCDB Image Converter is parent organization of: Jinx is parent organization of: WebImageBrowser is parent organization of: Image Workflow is parent organization of: Animal Imaging Database |
PMID:18054501 PMID:12160711 |
Free, Freely available | nif-0000-00007, r3d100000018 | SCR_002168 | CCDB, Cell-Centered Database | 2026-09-05 06:24:44 | 31 | ||||||
|
Genevestigator Resource Report Resource Website 100+ mentions |
Genevestigator (RRID:SCR_002358) | Genevestigator | analysis service resource, commercial organization, data analysis service, data or information resource, database, production service resource, service resource | A high performance search engine for gene expression that integrates thousands of manually curated public microarray and RNAseq experiments and nicely visualizes gene expression across different biological contexts (diseases, drugs, tissues, cancers, genotypes, etc.). There are two basic analysis approaches: # for a gene of interest, identify which conditions affect its expression. # for condition(s) of interest, identify which genes are specifically expressed in this/these conditions. Genevestigator builds on the deep integration of data, both at the level of data normalization and on the level of sample annotations. This deep integration allows scientists to ask new types of questions that cannot be addressed using conventional tools. | gene, genetic, animal, development, disease, meta-analysis, regulation, stage, microarray, rnaseq, visualization, gene expression, disease, drug, tissue, cancer, genotype, pharma, biomedical, conditions, genotype, anatomy, neoplasm, chemical, hormone, infection, model organism, organ, cell type, cell line, target, biomarker, similarity, FASEB list | is parent organization of: RefGenes | 4 products:, Free, Free for academic use, Account required, Paid subscription, Local installation | nif-0000-21172, OMICS_00763 | SCR_002358 | 2026-09-05 06:24:47 | 407 | ||||||||
|
Ear Lab Resource Report Resource Website |
Ear Lab (RRID:SCR_002531) | Earlab | data or information resource, laboratory portal, organization portal, portal | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 13, 2026. Computationally oriented experimental laboratory interested in the encoding of auditory information in the cerebral cortex and brainstem, and in the mechanisms of tinnitus and the effect of various drugs (Lidocaine, steroids, anti-oxidants) in relieving noise trauma induced tinnitus. The ferret (Mustela putorius) and the rat serve as their system model. Through chronic implants, they obtain electrophysiological data from awake behaving animals in order to investigate the response properties and functional organization of the auditory system, both in health and after noise trauma that induces tinnitus in rats. Projects: * Response Modulation to Ongoing Broadband Sounds in Primary Auditory Cortex * Neuronal Response Characteristics in the Inferior Colliculus of the Awake Ferret and Rat * Spectro-Temporal Representation of Feature Onsets in Primary Auditory Cortex * Targeting the changes in inferior colliculus induced by tinnitus | ear, auditory, cerebral cortex, behavior, health, noise, trauma, research, engineering, primary auditory cortex, neuron, brainstem, tinnitus, drug, lidocaine, steroid, anti-oxidant, computation, auditory system, sound, mustela putorius, inferior colliculus | has parent organization: University of Maryland; Maryland; USA | Tinnitus, Healthy | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-00404 | SCR_002531 | the ear lab | 2026-09-05 06:24:49 | 0 | ||||||
|
Kidney and Urinary Pathway Knowledge Base Resource Report Resource Website 1+ mentions |
Kidney and Urinary Pathway Knowledge Base (RRID:SCR_001746) | KUPKB | analysis service resource, data analysis service, data or information resource, data repository, data set, production service resource, service resource, storage service resource | A collection of omics datasets (mRNA, proteins and miRNA) that have been extracted from PubMed and other related renal databases, all related to kidney physiology and pathology giving KUP biologists the means to ask queries across many resources in order to aggregate knowledge that is necessary for answering biological questions. Some microarray raw datasets have also been downloaded from the Gene Expression Omnibus and analyzed by the open-source software GeneArmada. The Semantic Web technologies, together with the background knowledge from the domain's ontologies, allows both rapid conversion and integration of this knowledge base. SPARQL endpoint http://sparql.kupkb.org/sparql The KUPKB Network Explorer will help you visualize the relationships among molecules stored in the KUPKB. A simple spreadsheet template is available for users to submit data to the KUPKB. It aims to capture a minimal amount of information about the experiment and the observations made. | kidney, urinary, urine, pathway, molecule, visualizer, gene, protein, mirna, metabolite, mrna, microarray, ortholog, rdf, renal cell, anatomy, animal model, disease, sparql, proteomics, ontology, biomarker, gene expression, physiology, pathology |
is related to: NIDDK Information Network (dkNET) is related to: Gene Expression Omnibus is related to: Gene Ontology is related to: KEGG has parent organization: University of Manchester; Manchester; United Kingdom has parent organization: National Institute of Health and Medical Research; Rennes; France |
Kidney disease | European Union ; FP7 ; ICT-2007.4.4 e-LICO project |
PMID:21624162 | THIS RESOURCE IS NO LONGER IN SERVICE. | nlx_154134 | http://www.e-lico.eu/kupkb | SCR_001746 | Kidney & Urinary Pathway Knowledge Base | 2026-09-05 06:24:38 | 2 | |||
|
Connectome Mapping Toolkit Resource Report Resource Website 10+ mentions |
Connectome Mapping Toolkit (RRID:SCR_001644) | Connectome Mapping Toolkit | data management software, data or information resource, data processing software, data set, image analysis software, image processing software, software application, software resource, software toolkit | A Python-based open source toolkit for magnetic resonance connectome mapping, data management, sharing, visualization and analysis. The toolkit includes the connectome mapper (a full DMRI processing pipeline), a new file format for multi modal data and metadata, and a visualization application. | magnetic resonance, connectome, mapping, data management, data sharing, visualization, analysis, connectome mapper, processing pipeline, python, connectomics, multi-modal, network analysis, neuroimaging, neuroinformatics tool, mri, knowledge-base, semantic, technology, mapping, source code |
is related to: Diffusion MRI of Traumatic Brain Injury has parent organization: University of Lausanne; Lausanne; Switzerland has parent organization: Ecole Polytechnique Federale de Lausanne; Lausanne; Switzerland is parent organization of: Connectome Viewer |
Swiss National Science Foundation 33CM30-124089 | PMID:21713110 | Free, Available for download, Freely available | nlx_153920 | http://www.cmtk.org/, http://www.connectome.ch/ | SCR_001644 | 2026-09-05 06:24:37 | 10 | |||||
|
Diabetes Disease Portal Resource Report Resource Website |
Diabetes Disease Portal (RRID:SCR_001660) | Diabetes Disease Portal | data or information resource, data set, disease-related portal, portal, topical portal | An integrated resource for information on genes, QTLs and strains associated with diabetes. The portal provides easy acces to data related to both Type 1 and Type 2 Diabetes and Diabetes-related Obesity and Hypertension, as well as information on Diabetic Complications. View the results for all the included diabetes-related disease states or choose a disease category to get a pull-down list of diseases. A single click on a disease will provide a list of related genes, QTLs, and strains as well as a genome wide view of these via the GViewer tool. A link from GViewer to GBrowse shows the genes and QTLs within their genomic context. Additional pages for Phenotypes, Pathways and Biological Processes provide one-click access to data related to diabetes. Tools, Related Links and Rat Strain Models pages link to additional resources of interest to diabetes researchers. | gene, quantitative trait locus, strain, diabetic complication, genome, gviewer, genomic, phenotype, pathway, biological process, chromosome, visualization, molecular function, cellular component, synteny |
is related to: NIDDK Information Network (dkNET) is related to: Gene Ontology has parent organization: Rat Genome Database (RGD) |
Type 1 diabetes, Type 2 diabetes, Diabetes, Obesity, Hyperlipidemia, Metaboic disease, Hypertension | Free, Freely Available | nlx_153942 | http://rgd.mcw.edu/rgdCuration/?module=portal&func=show&name=diabetes | SCR_001660 | 2026-09-05 06:24:37 | 0 | ||||||
|
Rat Resource and Research Center Resource Report Resource Website 100+ mentions |
Rat Resource and Research Center (RRID:SCR_002044) | NRRRC, RRRC, NCRR RRRC | biomaterial supply resource, cell repository, material resource, organism supplier | Supplies biomedical investigators with rat models, embryonic stem cells, related reagents, and protocols they require for their research. In addition to repository, cryostorage and distribution functions, RRRC can facilitate acquisition of rat strains from other international repositories as well as provide consultation and technical training to investigators using rat models. | RIN, Resource Information Network, embryo, gamete, animal, drug, biomedical, cryopreserved, disease, genome, genotyping, germplasma, human, hybrid, inbred, infectious, molecular, mutant, nuclear, ovarian, pathogen, rat, research, tissue, rat model, embryonic stem cell, reagent, protocol, cell line, stem cell, strain, database, catalog, RRID Community Authority |
is listed by: One Mind Biospecimen Bank Listing is listed by: Resource Information Network is related to: One Mind Biospecimen Bank Listing has parent organization: University of Missouri; Missouri; USA |
NCRR P40 RR016939; NIH Office of the Director P40 OD011062 |
Free | nif-0000-12085 | http://www.nrrrc.missouri.edu/ | SCR_002044 | National Rat Resource Research Center, National Center for Research Resources, Rat Resource & Research Center, Rat Resource and Research Center, Rat Resource Research Center, NCRR | 2026-09-05 06:24:43 | 230 | |||||
|
InteroPorc Resource Report Resource Website 1+ mentions |
InteroPorc (RRID:SCR_002067) | InteroPorc | analysis service resource, data analysis service, data analysis software, data or information resource, data processing software, database, production service resource, service resource, software application, software resource, source code | Automatic prediction tool to infer protein-protein interaction networks, it is applicable for lots of species using orthology and known interactions. The interoPORC method is based on the interolog concept and combines source interaction datasets from public databases as well as clusters of orthologous proteins (PORC) available on Integr8. Users can use this page to ask InteroPorc for all species present in Integr8. Some results are already computed and users can run InteroPorc to investigate any other species. Currently, the following databases are processed and merged (with datetime of the last available public release for each database used): IntAct, MINT, DIP, and Integr8. | orthology, prediction, protein interaction, tool, sequenced genome, proteinprotein interaction, inferred interaction, molecular interaction, interaction, protein, bio.tools |
is listed by: bio.tools is listed by: Debian is related to: Integr8 : Access to complete genomes and proteomes is related to: IntAct is related to: MINT is related to: Database of Interacting Proteins (DIP) is related to: PSICQUIC Registry has parent organization: CEA; Gif sur Yvette; France |
European Union FELICS 021902 RII3; Marie Curie Fellowship ; French National Agency of Research ANR Biosys06_134823 SULFIRHOM; French Atomic Energy Commission |
PMID:18508856 | Open unspecified license, Acknowledgement requested | nif-0000-20816, biotools:interoporc | https://bio.tools/interoporc | SCR_002067 | InteroPorc: Automatic molecular interaction predictions, Automatic molecular interaction predictions | 2026-09-05 06:24:43 | 6 | ||||
|
MONARCH Initiative Resource Report Resource Website 10+ mentions |
MONARCH Initiative (RRID:SCR_000824) | Monarch | data or information resource, database | Repository of information about model organisms, in vitro models, genes, pathways, gene expression, protein and genetic interactions, orthology, disease, phenotypes, publications, and authors, and ability to navigate multi-scale spatial and temporal phenotypes across in vivo and in vitro model systems in context of genetic and genomic data, using semantics and statistics. Discovery system provides basic and clinical science researchers, informaticists, and medical professionals with integrated interface and set of discovery tools to reveal genetic basis of disease, facilitate hypothesis generation, and identify novel candidate drug targets. Database that indexes authoritative information on experimental models of disease from MGI, RGD and ZFIN. | disease, animal model, phenotype, model organism, in vitro model, gene, pathway, gene expression, protein interaction, genetic interaction, orthology, disease, publication, author, genetic, genomic, model system, genotype, drug, in vivo model |
uses: Animal QTLdb uses: Ensembl Variation uses: Human Phenotype Ontology is used by: NIF Data Federation is related to: Mouse Genome Informatics (MGI) is related to: Rat Genome Database (RGD) is related to: Zebrafish Information Network (ZFIN) is related to: openSNP is related to: Ancora is related to: PhenoGen Informatics is related to: Lifespan Observations Database has parent organization: Oregon Health and Science University; Oregon; USA is parent organization of: monarch-ontologies |
NIH Office of the Director R24 OD011883 | PMID:26269093 | Free, Freely available | r3d100011594, nlx_152525, SCR_001373, nlx_152748 | https://orip.nih.gov/comparative-medicine/programs/genetic-biological-and-information-resources, https://doi.org/10.17616/R31M09 | SCR_000824 | MONARCH Integrated Disease Model, MONARCH Integrated Disease Models View, MONARCH Disease Models View, The MONARCH Initiative | 2026-09-05 06:24:26 | 13 | ||||
|
MPO Resource Report Resource Website 10+ mentions |
MPO (RRID:SCR_004855) | MPO, MP | controlled vocabulary, data or information resource, ontology | Community ontology to provide standard terms for annotating mammalian phenotypic data. It has a hierarchical structure that permits a range of detail from high-level, broadly descriptive terms to very low-level, highly specific terms. This range is useful for annotating phenotypic data to the level of detail known and for searching for this information using either broad or specific terms as search criteria. Your input is welcome. | mus, phenotype, obo |
is used by: NIF Data Federation is listed by: BioPortal is related to: Rat Genome Database (RGD) is related to: MouseBook is related to: Neurocarta is related to: phenomeNET has parent organization: OBO has parent organization: Mouse Genome Informatics (MGI) |
PMID:17989687 | The community can contribute to this resource | nlx_83784 | http://obofoundry.org/cgi-bin/detail.cgi?id=mammalian_phenotype, http://purl.bioontology.org/ontology/MP | SCR_004855 | Mammalian Phenotype Ontology | 2026-09-05 06:25:25 | 19 | |||||
|
Hippocampus 3D Model Resource Report Resource Website 1+ mentions |
Hippocampus 3D Model (RRID:SCR_005083) | Hippocampus 3D Model | data or information resource, data set, image collection, video resource | Data files for a high resolution three dimensional (3D) structure of the rat hippocampus reconstructed from histological sections. The data files (supplementary data for Ropireddy et al., Neurosci., 2012 Mar 15;205:91-111) are being shared on the Windows Live cloud space provided by Microsoft. Downloadable data files include the Nissl histological images, the hippocampus layer tracings that can be visualized alone or superimposed to the corresponding Nissl images, the voxel database coordinates, and the surface rendering VRML files. * Hippocampus Nissl Images: The high resolution histological Nissl images obtained at 16 micrometer inter-slice distance for the Long-Evans rat hippocampus can be downloaded or directly viewed in a browser. This dataset consists of 230 jpeg images that cover the hippocampus from rostral to caudal poles. This image dataset is uploaded in seven parts as rar files. * Hippocampus Layer Tracings: The seven hippocampus layers ''ML, ''GC'', ''HILUS'' in DG and ''LM'', ''RAD'', ''PC'', ''OR'' in CA were segmented (traced) using the Reconstruct tool which can be downloaded from Synapse web. This tool outputs all the tracings for each image in XML format. The XML tracing files for all these seven layers for each of the above Nissl images are zipped into one file and can be downloaded. * Hippocampus VoxelDB: The 3D hippocampus reconstructed is volumetrically transformed into 16 micrometer sized voxels for all the seven layers. Each voxel is reported according to multiple coordinate systems, namely in Cartesian, along the natural hippocampal dimensions, and in reference to the canonical brain planes. The voxel database file is created in ascii format. The single voxel database file was split into three rar archive files. Please note that the three rar archive files should be downloaded and decompressed in a single directory in order to obtain the single voxel data file (Hippocampus-VoxelDB.txt). * 3D Surface Renderings: This is a rar archive file with a single VRML file containing the surface rendering of DG and CA layers. This VRML file can be opened and visualized in any VRML viewer, e.g. the open source software view3dscene. * 3D Hippocampus Movie: This movie contains visualization of the 3D surface renderings of CA (blue) and DG (red) inner and outer boundaries; neuronal embeddings of DG granule and CA pyramidal dendritic arbors; potential synapses between CA3b interneuron axon and pyramidal dendrite, and between CA2 pyramidal axon and CA pyramidal dendrites. | rat, hippocampus, long evans rat, nissl, reconstruction, model, nissl staining, histology, tracing, voxel, surface rendering | has parent organization: Computational Neuroanatomy Group | NIH ; Office of Naval Research MURI N00014-10-1-0198; NINDS NS39600; NINDS NS058816 |
PMID:22245503 | nlx_144141 | SCR_005083 | 2026-09-05 06:25:29 | 2 | |||||||
|
Blue Brain Project Resource Report Resource Website 10+ mentions |
Blue Brain Project (RRID:SCR_002994) | Blue Brain | data or information resource, portal, topical portal | A Swiss-led project with the aim of reverse engineering the mammalian brain and achieving a complete virtual human brain. The researchers have demonstrated the validity of their method by developing a realistic model of a rat cortical column, consisting of about 10,000 neurons. The eventual goal is to simulate systems of millions and hundreds of millions of neurons. The virtual brain will be an exceptional tool giving neuroscientists a new understanding of the brain and a better understanding of neurological diseases. In five years of work, Henry Markram's team has perfected a facility that can create realistic models of one of the brain's essential building blocks. This process is entirely data driven and essentially automatically executed on the supercomputer. Meanwhile the generated models show a behavior already observed in years of neuroscientific experiments. These models will be basic building blocks for larger scale models leading towards a complete virtual brain. | brain, neuron, microcircuit, simulation, cortex, cortical column, model |
is related to: NeuroCurator has parent organization: Ecole Polytechnique Federale de Lausanne; Lausanne; Switzerland is parent organization of: ChannelPedia provides: Blue Brain Cell Atlas |
Neurological disease | nif-0000-30208 | SCR_002994 | Bluebrain | 2026-09-05 06:24:56 | 22 | |||||||
|
Gene Expression Profiling in Spinal Cord Injury Resource Report Resource Website 100+ mentions |
Gene Expression Profiling in Spinal Cord Injury (RRID:SCR_003260) | data or information resource, data set, database | Database which provides on-line searching of microarray datasets generated from rat spinal cord after contusion injury. Both the primary injury site and a site 5 mm distal to the injury site were assayed. Tissue was obtained from Long Evans rats subject to spinal cord contusion injury using the MASCIS impactor (formerly known as the NYU impactor). RNA expression was assayed at the site of injury and distal to the site of injury using the Affymetrix Rat Neuro U34 chip. | database, spinal cord, contusion, microarray data, FASEB list | has parent organization: Rutgers University; New Jersey; USA | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-00011 | SCR_003260 | 2026-09-05 06:25:00 | 394 | |||||||||
|
Retinal Degeneration Rat Model Resource Resource Report Resource Website 10+ mentions |
Retinal Degeneration Rat Model Resource (RRID:SCR_003311) | Retinal Degeneration Rat Model Resource | biomaterial supply resource, material resource, organism supplier | Supplier of fully penetrant rat models of the retinitis pigmentosa type of inherited retinal degeneration, including the following models: * Mutant rhodopsin transgenic rats ** P23H mutant rhodopsin transgenic rats -Three lines with different rates of photoreceptor degeneration ** S334ter mutant rhodopsin transgenic rats -Five lines with different rates of photoreceptor degeneration * RCS (Royal College of Surgeons) rats with inherited retinal dystrophy ** RCS pink-eyed inbred strain ** RCS pigmented congenic strain with slowed rate of retinal dystrophy ** RCS congenic control strains of both pigmentation types, wild-type at the retinal dystrophy (Mertk) genetic locus The resource has been supported by the National Eye Institute (NEI) for the past 19 years to produce and distribute breeding pairs of these animal models to vision scientists. Thus, the following apply: * Request for rats requires only a 1-page letter/e-mail addressing 4 questions * No charge for the animals or tissues (except for shipping costs) * No Material Transfer Agreement (MTA) required * No collaboration requirement (in most cases) The resource usually provides multiple breeding pairs of the rats to vision scientists to generate breeding stock. It can also provide extra animals to breed for immediate experimental work, animals of specific ages (depending upon availability), animals with prior exposure to different lighting conditions, eyes taken at specific ages instead of rats for pilot studies and other experiments (fresh, frozen, dissected in specific ways, or fixed with special fixatives or by different methods), or other tissues (e.g., liver, spleen, brain, testis, etc.) prepared different ways. | mutant rhodopsin transgenic rat, p23h mutant rhodopsin transgenic rat, s334ter mutant rhodopsin transgenic rat, rcs inbred, congenic strain, retinitis pigmentosa, retinal degeneration, retinal dystrophy, vision, rat, eye, transgenic rat, retina, model organism, mutant rat |
is listed by: One Mind Biospecimen Bank Listing has parent organization: UCSF School of Medicine; California; USA |
Retinitis pigmentosa | NIH Blueprint for Neuroscience Research ; NEI |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-00188 | SCR_003311 | NEI Retinal Degeneration Rat Model Resource | 2026-09-05 06:25:01 | 23 | |||||
|
GeneInfoViz Resource Report Resource Website |
GeneInfoViz (RRID:SCR_005680) | GeneInfoViz | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource | GeneInfoViz is a web based tool for batch retrieval of gene function information, visualization of GO structure and construction of gene relation networks. It takes a input list of genes in the form of LocusLink ID, UniGeneID, gene symbol, or accession number and returns their functional genomic information. Based on the GO annotations of the given genes, GeneInfoViz allows users to visualize these genes in the DAG structure of GO, and construct a gene relation network at a selected level of the DAG. Platform: Online tool | gene network, gene ontology, visualization, gene, ontology or annotation browser |
is listed by: Gene Ontology Tools is related to: Gene Ontology has parent organization: University of Tennessee Health Science Center; Tennessee; USA |
PMID:15724283 | Free for academic use | nlx_149121 | SCR_005680 | GeneInfoViz: Constructing and Visualizing Gene Relation Networks | 2026-09-05 06:25:39 | 0 | ||||||
|
EthoVision XT Resource Report Resource Website 100+ mentions |
EthoVision XT (RRID:SCR_000441) | EthoVision XT | software resource | Video tracking software that tracks and analyzes the behavior, movement, and activity of any animal. | behavior, tracking | has parent organization: Noldus | rid_000100 | SCR_000441 | 2026-09-05 06:24:19 | 368 | |||||||||
|
GeneCodis Resource Report Resource Website 100+ mentions |
GeneCodis (RRID:SCR_006943) | GeneCodis | analysis service resource, data access protocol, data analysis service, production service resource, service resource, software resource, web service | Web-based tool for the ontological analysis of large lists of genes. It can be used to determine biological annotations or combinations of annotations that are significantly associated to a list of genes under study with respect to a reference list. As well as single annotations, this tool allows users to simultaneously evaluate annotations from different sources, for example Biological Process and Cellular Component categories of Gene Ontology., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | functional analysis, gene, annotation, statistical analysis, functional genomics, 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 is related to: KEGG has parent organization: Spanish National Research Council; Madrid; Spain |
Juan de la Cierva research program ; Spanish Minister of Science and Innovation BIO2010-17527; Government of Madrid P2010/BMD-2305 |
PMID:22573175 PMID:19465387 PMID:17204154 |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02221, biotools:genecodis3, nlx_149254 | https://bio.tools/genecodis3 | SCR_006943 | Gene annotations co-ocurrence discovery, GeneCodis - Gene annotations co-ocurrence discovery | 2026-09-05 06:30:00 | 353 | ||||
|
CRCNS Resource Report Resource Website 100+ mentions |
CRCNS (RRID:SCR_005608) | CRCNS | collaborative tool, data or information resource, data repository, funding resource, service resource, storage service resource | Website for brain experimental data and other resources such as stimuli and analysis tools. Provides marketplace and discussion forum for sharing tools and data in neuroscience. Data repository and collaborative tool that supports integration of theoretical and experimental neuroscience through collaborative research projects. CRCNS offers funding for new class of proposals focused on data sharing and other resources. | collaborative research, data sharing, computational model, brain, computational neuroscience, data set, FASEB list |
is used by: NIF Data Federation is used by: DataLad is used by: Integrated Datasets is recommended by: National Library of Medicine is listed by: DataCite is related to: Integrated Manually Extracted Annotation has parent organization: University of California at Berkeley; Berkeley; USA has parent organization: University of California; California; USA |
NIH ; NSF 0636838; NSF IIS-0749049 |
PMID:18259695 | Free, Freely available | nif-0000-00255, r3d100011269 | https://api.datacite.org/dois?prefix=10.6080, https://doi.org/10.17616/R31S7P | SCR_005608 | CRCNS Data sharing, Collaborative Research in Computational Neuroscience - Data sharing, Collaborative Research in Computational Neuroscience, CRCNS - Data sharing | 2026-09-05 06:29:58 | 123 | ||||
|
GeneMerge Resource Report Resource Website 10+ mentions |
GeneMerge (RRID:SCR_005744) | GeneMerge | analysis service resource, data analysis service, production service resource, service resource, software application, software resource | THIS RESOURCE IS NO LONGER IN SERVCE, documented September 2, 2016. Web-based and standalone application that returns a wide range of functional genomic data for a given set of study genes and provides rank scores for over-representation of particular functions or categories in the data. It uses the hypergeometric test statistic which returns statistically correct results for samples of all sizes and is the #2 fastest GO tool available (Khatri and Draghici, 2005). GeneMerge can be used with any discrete, locus-based annotation data, including, literature references, genetic interactions, mutant phenotypes as well as traditional Gene Ontology queries. GeneMerge is particularly useful for the analysis of microarray data and other large biological datasets. The big advantage of GeneMerge over other similar programs is that you are not limited to analyzing your data from the perspective of a pre-packaged set of gene-association data. You can download or create gene-association files to analyze your data from an unlimited number of perspectives. Platform: Online tool, Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible | gene, genomics, functional genomic data, analysis, post-genomic analysis, data mining, hypothesis testing, statistical analysis, slimmer-type tool, term enrichment, text mining, false discovery rate, bonferroni correction, false discovery rate and bonferroni correction, perl, microarray |
is listed by: Gene Ontology Tools is related to: Gene Ontology has parent organization: Harvard University; Cambridge; United States |
PMID:12724301 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_149203 | http://genemerge.cbcb.umd.edu/ | SCR_005744 | 2026-09-05 06:29:59 | 26 | ||||||
|
Synapse Resource Report Resource Website 1000+ mentions |
Synapse (RRID:SCR_006307) | Synapse | data or information resource, data repository, database, service resource, storage service resource | A cloud-based collaborative platform which co-locates data, code, and computing resources for analyzing genome-scale data and seamlessly integrates these services allowing scientists to share and analyze data together. Synapse consists of a web portal integrated with the R/Bioconductor statistical package and will be integrated with additional tools. The web portal is organized around the concept of a Project which is an environment where you can interact, share data, and analysis methods with a specific group of users or broadly across open collaborations. Projects provide an organizational structure to interact with data, code and analyses, and to track data provenance. A project can be created by anyone with a Synapse account and can be shared among all Synapse users or restricted to a specific team. Public data projects include the Synapse Commons Repository (SCR) (syn150935) and the metaGenomics project (syn275039). The SCR provides access to raw data and phenotypic information for publicly available genomic data sets, such as GEO and TCGA. The metaGenomics project provides standardized preprocessed data and precomputed analysis of the public SCR data. | data sharing, collaboration, data management, analysis, genome, phenotype, crowd sourcing, open data, provenance, resource management, annotation, authoring, markup, r, python, java, command-line, cloud, FASEB list |
is used by: NF Data Portal is listed by: FORCE11 is listed by: DataCite is listed by: re3data.org is related to: clearScience is related to: Exemplar Microscopy Images of Tissues has parent organization: Sage Bionetworks |
Cancer, Normal, Cardiovascular disease, Floppy hat syndrome | Life Sciences Discovery Fund ; NCI ; NHLBI ; Alfred P. Sloan Foundation |
The community can contribute to this resource | nlx_151983, DOI:10.17616/R3B934, r3d100011894, DOI:10.7303 | https://doi.org/10.17616/R3B934, https://doi.org/10.48550/arxiv.1506.00272, https://doi.org/10.7303/, https://dx.doi.org/10.7303, https://doi.org/10.17616/R3B934 | SCR_006307 | 2026-09-05 06:30:00 | 1104 |
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 NIF Resources search. From here you can search through a compilation of resources used by NIF and see how data is organized within our community.
You are currently on the Community Resources tab looking through categories and sources that NIF 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 NIF then you can log in from here to get additional features in NIF 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 NIF 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.
Welcome to the Neuroscience Information Framework Project, designed to serve the biomedical research community. NIF maintains the largest searchable collection of neuroscience data, the largest catalog of biomedical resources, and the largest ontology for neuroscience on the web. We welcome all feedback and suggestions and are actively looking for resource providers to make their resources accessible through NIF. Learn about the tools available to help you share your data and discover a dynamic inventory of Web-based neuroscience resources.
