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SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.

(last updated: Oct 12, 2019)

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Resource NameResource TypeDescriptionKeywordsResource IDProper CitationParent OrganizationRelated ConditionFunding AgencyRelationReferenceWebsite StatusAlternate IDsAlternate URLsOld URLs
Diffusion MRI of Traumatic Brain InjuryResource, topical portal, portal, data or information resourceProject to define a roadmap for diffusion MR imaging of traumatic brain imaging and design an infrastructure to implement the recommendations and tested to ensure feasibility, disseminate results, and facilitate deployment and adoption. The research roadmap and infrastructure development will concentrate on three areas: 1) standardization of diffusion imaging methodology, 2) trial design and patient selection for acute or chronic therapy, and 3) development of multi-center collaborations and repositories for evaluating whether advanced diffusion imaging does improve decision making and TBI patients' outcomes. # DTI MRI reproducability: One of the major areas of investigation in this project is to study the reproducibility of data acquisition and image analysis algorithms. Understanding reproducibility defines a base level of deviation from which scans can be analyzed with statistical significance. As part of this work they are also developing site qualification criteria with the intention of setting limits on the MR system minimal performance for acceptable use in TBI evaluation. # Infrastructure for image storage, analysis and visualization: There is a continuing need to refine and extend software methods for diffusion MRI data analysis and visualization. Not only to translate tools into clinical practice, but also to encourage continuation of the innovation and development of new tools and techniques. To deliver upon these goals they are designing and implementing a storage and computational infrastructure to provide access to shared datasets and intuitive interfaces for analysis and visualization through a variety of tools. A strong emphasis has been placed on providing secure data sharing and the ability to add community defined common data elements. The infrastructure is built upon a Software-as-a-Service model, in which tools are hosted and managed remotely allowing users access through well-defined interfaces. The final service will also facilitate composition or orchestration of workflows composed of different analysis and processing tasks (for example using LONI or XNAT pipelines) with the ultimate goal of providing automated no-click evaluations of diffusion MRI data. # Tool development: The final aspect of this project aims to facilitate and encourage tool development and contribution. By providing access to open datasets, they will create a platform on which tool developers can compare and improve and their tools. When tools are sufficiently mature they can be exposed in the infrastructure mentioned above and used by researchers and other developers.diffusion tensor imaging, diffusion mri, standard specification, image repository, analysis, visualization, data sharing, common data element, service resource, data setSCR_001637(Diffusion MRI of Traumatic Brain Injury, RRID:SCR_001637)University of Chicago; Illinois; USA Traumatic brain injuryNINDSrelated to: vIST/e, Camino, DTI and Fibertools Software Package, Diffusion Tensor Imaging ToolKit, ExploreDTI, Connectome Mapping Toolkit, TORTOISE, MITK Diffusion, MRtrix, MIPAV: Medical Image Processing and Visualization, DTI Blog, FSLLast checked upnlx_153906
National Sleep Research Resource (NSRR) Resource, organization portal, service resource, portal, storage service resource, data repository, data or information resourceSystem for sharing sleep data. Organization portal that aggregates, harmonizes, and organizes sleep and clinical data from individuals studied as part of cohort studies or clinical trials and provides suite of tools to facilitate data exploration and data visualization. National Heart, Lung, and Blood Institute resource designed to provide big data resources to sleep research community.sleep, clinical, data, cohort, study, trial, dataset, visualization, explorationSCR_016576(National Sleep Research Resource (NSRR) , RRID:SCR_016576)sleep apneaNHLBIrecommended by: National Library of Medicine, BRAIN Initiative, lists: Apnea, Bariatric surgery, and CPAP study, Sleep Heart Health Study, Honolulu-Asia Aging Study of Sleep Apnea, Cleveland Family Study, Cleveland Children's Sleep and Health Study, Best Apnea Interventions for Research (BestAIR) sleep studyPMID:29860441Last checked downhttps://sleepdata.org/share, https://sleepdata.org/datasets
Renal Disease PortalResource, disease-related portal, data set, topical portal, portal, data or information resourceAn integrated resource for information on genes, QTLs and strains associated with a variety of kidney and renal system conditions such as Renal Hypertension, Polycystic Kidney Disease and Renal Insufficiency, as well as Kidney Neoplasms.gene, quantitative trait locus, strain, renal hypertension, kidney neoplasm, phenotype, pathway, biological process, disease, kidney, genome, gviewer, chromosome, molecular function, cellular component, visualization, syntenySCR_009030(Renal Disease Portal, RRID:SCR_009030)Rat Genome Database (RGD) Renal disease, Renal hypertension, Polycystic kidney disease, Renal insufficiency, Kidney neoplasm, Diabetes Insipidus, Hyperoxaluria, Renal hypertension, Nephritis, Nephrocalcinosis, Nephrolithiasis, Nephrosis, Renal Fibrosis, Inborn Error of Renal Tubular Transport, Uremiarelated to: NIDDK Information Network, Gene Ontology, submitted by: NIDDK Information NetworkLast checked upnlx_153941
USC Multimodal Connectivity DatabaseResource, service resource, data or information resource, data repository, storage service resource, databaseWeb-based repository and analysis site for connectivity matrices that have been derived from neuroimaging data including different imaging modalities, subject groups, and studies. Users can analyze connectivity matrices that have been shared publicly and upload their own matrices to share or analyze privately.fmri, dti, dsi, mri, eeg, meg, data set, image, computational hosting, connectivity, neuroimaging, data sharing, brain, rendering, diffusion-weighted mri, functional connectivity, graph theory, resting-state fmri, structural connectivity, image display, magnetic resonance, python, rendering, visualization, connectivity matrix, network, brain network, matrix, de-identified, male, female, apoe, child, adultSCR_012809(USC Multimodal Connectivity Database, RRID:SCR_012809)MGH-USC Human Connectome Project Normal, Lesioned, Attention deficit-hyperactivity disorder, Autism Spectrum Disorder, Obsessive-Compulsive Disorder, BDD, APOE 4/4, APOE 3/4, APOE 3/3, Alzheimer's diseaseNIA, NIDA, NIH Blueprint for Neuroscience Research, NRSAused by: NIF Data Federation, listed by: NeuroImaging Tools and Resources Collaboratory (NITRC)References (2)Last checked upnlx_83091http://www.nitrc.org/projects/umcdhttp://jessebrown.webfactional.com/welcome/default/index
CCHMC Pediatric Brain TemplatesResource, atlas, image collection, reference atlas, data or information resourceBrain imaging data collected from a large population of normal, healthy children that have been used to construct pediatric brain templates, which can be used within statistical parametric mapping for spatial normalization, tissue segmentation and visualization of imaging study results. The data has been processed and compiled in various ways to accommodate a wide range of possible research approaches. The templates are made available free of charge to all interested parties for research purposes only. When processing imaging data from children, it is important to take into account the fact that the pediatric brain differs significantly from the adult brain. Therefore, optimized processing requires appropriate reference data be used because adult reference data will introduce a systematic bias into the results. We have shown that, in the in the case of spatial normalization, the amount of non-linear deformation is dramatically less when a pediatric template is used (left, see also HBM 2002; 17:48-60). We could also show that tissue composition is substantially different between adults and children, and more so the younger the children are (right, see also MRM 2003; 50:749-757). We thus believe that the use of pediatric reference data might be more appropriate.brain, child, human, normal, pediatric, spatial normalization, template, tissue segmentation, visualization, young human, neuroimagingSCR_003276(CCHMC Pediatric Brain Templates, RRID:SCR_003276)Normal, Healthyrelated to: SPMLast checked upnif-0000-01274
MGH-USC Human Connectome ProjectResource, production service resource, image collection, material service resource, data set, instrument manufacture, service resource, data or information resourceA multi-center project comprising two distinct consortia (Mass. Gen. Hosp. and USC; and Wash. U. and the U. of Minn.) seeking to map white matter fiber pathways in the human brain using leading edge neuroimaging methods, genomics, architectonics, mathematical approaches, informatics, and interactive visualization. The mapping of the complete structural and functional neural connections in vivo within and across individuals provides unparalleled compilation of neural data, an interface to graphically navigate this data and the opportunity to achieve conclusions about the living human brain. The HCP is being developed to employ advanced neuroimaging methods, and to construct an extensive informatics infrastructure to link these data and connectivity models to detailed phenomic and genomic data, building upon existing multidisciplinary and collaborative efforts currently underway. Working with other HCP partners based at Washington University in St. Louis they will provide rich data, essential imaging protocols, and sophisticated connectivity analysis tools for the neuroscience community. This project is working to achieve the following: 1) develop sophisticated tools to process high-angular diffusion (HARDI) and diffusion spectrum imaging (DSI) from normal individuals to provide the foundation for the detailed mapping of the human connectome; 2) optimize advanced high-field imaging technologies and neurocognitive tests to map the human connectome; 3) collect connectomic, behavioral, and genotype data using optimized methods in a representative sample of normal subjects; 4) design and deploy a robust, web-based informatics infrastructure, 5) develop and disseminate data acquisition and analysis, educational, and training outreach materials.human, structural, functional, neural, white matter, fiber, brain, in vivo, genomic, neuroimaging, visualization, neuroanatomy, genotype, connectivity, connectivity model, neural pathway, phenomic, connectomics, quantification, scanner, eeg, meg, shape analysis, spatial transformation, diffusion spectrum, q-ball, tensor metric, fiber tracking, connectome, behavior, scanner, web resource, diffusion spectrum, q-ball, tensor metric, quantification, shape analysis, spatial transformation, fiber trackingSCR_003490(MGH-USC Human Connectome Project, RRID:SCR_003490)Laboratory of Neuro Imaging , NIH Human Connectome Project , Harvard Medical School; Massachusetts; USA NormalNIH, NIH Blueprint for Neuroscience Researchlisted by: NeuroImaging Tools and Resources Collaboratory (NITRC), BiositemapsLast checked upnif-0000-35789http://www.nitrc.org/projects/hcp_mgh-ucla
BraineacResource, software resource, web application, data or information resource, databaseDatabase for the UK Brain Expression Consortium (UKBEC) dataset that comprises of brains from individuals free of neurodegenerative disorders. The aim of Braineac is to release to the scientific community a valid instrument to investigate the genes and SNPs associated with neurological disorders.neurodegenerative, brain, disorder, mrna, dna, eqtl, snp, gene, visualization, expressionSCR_015888(Braineac, RRID:SCR_015888)UK Brain Expression Consortium Normalsubmitted by: Neuroscience Information FrameworkPMID:25174004Last checked down
InnateDBResource, data analysis service, production service resource, analysis service resource, database, service resource, data or information resourcePublicly available database of the genes, proteins, experimentally-verified interactions and signaling pathways involved in the innate immune response of humans, mice and bovines to microbial infection. The database captures coverage of the innate immunity interactome by integrating known interactions and pathways from major public databases together with manually-curated data into a centralized resource. The database can be mined as a knowledgebase or used with the integrated bioinformatics and visualization tools for the systems level analysis of the innate immune response. Although InnateDB curation focuses on innate immunity-relevant interactions and pathways, it also incorporates detailed annotation on the entire human, mouse and bovine interactomes by integrating data (178,000+ interactions & 3,900+ pathways) from several of the major public interaction and pathway databases. InnateDB also has integrated human, mouse and bovine orthology predictions generated using Ortholgue software. Ortholgue uses a phylogenetic distance-based method to identify possible paralogs in high-throughput orthology predictions. Integrated human and mouse conserved gene order and synteny information has also been determined to provide further support for orthology predictions. InnateDB Capabilities: * View statistics for manually-curated innate immunity relevant molecular interactions. New manually curated interactions are submitted weekly. * Search for genes and proteins of interest. * Search for experimentally-verified molecular interactions by gene/protein name, interaction type, cell type, etc. * Search genes/interactions belonging to 3,900 pathways. * Visualize interactions using an intuitive subcellular localization-based layout in Cerebral. * Upload your own list of genes along with associated gene expression data (from up to 10 experimental conditions) to interactively analyze this data in a molecular interaction network context. Once you have uploaded your data, you will be able to interactively visualize interaction networks with expression data overlaid; carry out Pathway, Gene Ontology and Transcription Factor Binding Site over-representation analyses; construct orthologous interaction networks in other species; and much more. * Access curated interaction data via a dedicated PSICQUIC webservice.gene, immune response, pathway, protein, signaling pathway, interaction, immune, signaling response, gene, orthology prediction, orthology, ortholg, annotation, interactome, gene expression, molecule, protein-protein interaction, molecular interaction, visualization, nucleic acid-protein, nucleic acid, network, web service, transcription factor binding site, software resourceSCR_006714(InnateDB, RRID:SCR_006714)Simon Fraser University; British Columbia; Canada , University of British Columbia; British Columbia; Canada Microbial infection, Allergy, AsthmaAllerGen, European Union, Michael Smith Foundation for Health Research, Teagascrelated to: IMEx - The International Molecular Exchange Consortium, Interaction Reference Index, ConsensusPathDB, IMEx - The International Molecular Exchange Consortium, PSICQUIC Registry, PSICQUIC, Gene Ontology, IntAct, listed by: re3data.org, works_with: IMEx - The International Molecular Exchange ConsortiumReferences (2)Last checked upnif-0000-20808
SumsDBResource, data analysis service, database, analysis service resource, production service resource, service resource, storage service resource, atlas, image repository, data repository, data or information resourceTHIS RESOURCE IS NO LONGER IN SERVICE, documented on May 11, 2016. Repository of brain-mapping data (surfaces and volumes; structural and functional data) derived from studies including fMRI and MRI from many laboratories, providing convenient access to a growing body of neuroimaging and related data. WebCaret is an online visualization tool for viewing SumsDB datasets. SumsDB includes: * data on cerebral cortex and cerebellar cortex * individual subject data and population data mapped to atlases * data from FreeSurfer and other brainmapping software besides Caret SumsDB provides multiple levels of data access and security: * Free (public) access (e.g., for data associated with published studies) * Data access restricted to collaborators in different laboratories * Owner-only access for work in progress Data can be downloaded from SumsDB as individual files or as bundles archived for offline visualization and analysis in Caret WebCaret provides online Caret-style visualization while circumventing software and data downloads. It is a server-side application running on a linux cluster at Washington University. WebCaret "scenes" facilitate rapid visualization of complex combinations of data Bi-directional links between online publications and WebCaret/SumsDB provide: * Links from figures in online journal article to corresponding scenes in WebCaret * Links from metadata in WebCaret directly to relevant online publications and figuressegmentation, volume, neuroimaging, brain, fmri, stereotaxic foci, stereotaxic coordinate, brain-mapping, foci, structural mri, mri, cerebral cortex, cerebellar cortex, afni brik, analyze, atlas, nifti, registration, rendering, spatial transformation, surface analysis, surface rendering, visualization, volume rendering, brain mapping, neuroanatomySCR_002759(SumsDB, RRID:SCR_002759)Washington University School of Medicine in St. Louis; Missouri; USA Mental disease, Neurological disorder, NormalHuman Brain Project, NASA, National Partnership for Advanced Computational Infrastructure, NCI, NIMH, NLM, NSFrelated to: Computerized Anatomical Reconstruction and Editing Toolkit, Integrated Manually Extracted Annotation, used by: NIF Data Federation, listed by: Biositemaps, NeuroImaging Tools and Resources Collaboratory (NITRC), re3data.orgLast checked downnif-0000-00016http://brainvis.wustl.edu/wiki/index.php/Sums:About http://www.nitrc.org/projects/sumsdb
Psychiatric Genomics ConsortiumResource, organization portal, computational hosting, production service resource, analysis service resource, consortium, service resource, portal, data analysis service, storage service resource, data repository, community building portal, data or information resourceConsortium conducting meta-analyses of genome-wide genetic data for psychiatric disease. Focused on autism, attention-deficit hyperactivity disorder, bipolar disorder, major depressive disorder, schizophrenia, anorexia nervosa (AN), Tourette syndrome (TS), and obsessive-compulsive disorder (OCD). Used to investigate common single nucleotide polymorphisms (SNPs) genotyped on commercial arrays, structural variation (copy number variation) and uncommon or rare genetic variation. To participate you are asked to upload data from your study to central computer used by this consortium. Genetic Cluster Computer serves as data warehouse and analytical platform for this study . When data from your study have been incorporated, account will be provided on central server and access to all GWAS genotypes, phenotypes, and meta-analytic results relevant to deposited data and participation aims. NHGRI GWAS Catalog contains updated information about all GWAS in biomedicine, and is usually excellent starting point to find comprehensive list of studies. Files can be obtained by any PGC member for any disease to which they contributed data. These files can also be obtained by application to NIMH Genetics Repository. Individual-level genotype and phenotype data requires application, material transfer agreement, and informed consent consideration. Some datasets are also in controlled-access dbGaP and Wellcome Trust Case-Control Consortium repositories. PGC members can also receive back cleaned and imputed data and results for samples they contributed to PGC analyses.structural variation, genetic variation, single nucleotide polymorphism, attention deficit-hyperactivity disorder, bipolar disorder, schizophrenia, mental disease, one mind ptsd, data sharing, visualization, genome-wide association study, genomic, genotype, phenotype, psychiatry, gwas, copy number variationSCR_004495(Psychiatric Genomics Consortium, RRID:SCR_004495)University of North Carolina at Chapel Hill; North Carolina; USA Mental disease, Attention deficit-hyperactivity disorder, Bipolar Disorder, Schizophrenia, Major Depressive Disorder, Autism, Cross-disorderHersenstichting Nederland, Netherlands Genetic Cluster Computer, NIMHrelated to: Ricopili, GWAS: Catalog of Published Genome-Wide Association Studies, NCBI database of Genotypes and Phenotypes, Wellcome Trust Case Control ConsortiumReferences (5)Last checked downnlx_143769https://pgc.unc.edu/
NephromineResource, data or information resource, databaseA growing database of publicly available renal gene expression profiles, a sophisticated analysis engine, and a powerful web application designed for data mining and visualization of gene expression. It provides unique access to datasets from the Personalized Molecular Nephrology Research Laboratory incorporating clinical data which is often difficult to collect from public sources and mouse data.kidney, gene expression, visualization, clinical, expression profile, gene, mouse model, microarraySCR_003813(Nephromine, RRID:SCR_003813) Life Technologies , University of Michigan; Michigan; USA Kidney disease, Healthy, Lupus nephritis, Chronic kidney disease, Diabetic nephropathylisted by: NIDDK Information NetworkLast checked upnlx_158114
SynSysNetResource, data or information resource, databaseA curated database for synaptic proteins that provides adequate definitions of pre- and post-synaptic proteins, proteins present in sub-domains of the synapse, e.g. the synaptic vesicle and associated proteins, lipid rafts and postsynaptic density. In addition to data that was and will be gathered from the experiments conducted within SynSys - A European expertise Network on building the synapse, they have extracted and manually curated all relevant data on these proteins from other sources and provided an ontology for these. Novel splice forms are being identified that can be matched with proteomics data. Information on proteins, their 3D structure, binding small molecules Protein-Protein-Interactions (PPIs) and Compound-Protein-Interactions are integrated. Proteins or compounds can be searched and Interactive Networks can be visualized. The point Diseases present neurological diseases, to illustrate the role of SynSysNet in the medication.gene, synapse, protein, interaction, compound, disease, structure, model, compound, protein-drug interaction, protein-protein interaction, pathway, drug-target, small molecule, interaction network, homology, drug, drug-target interaction, compound-protein interaction, visualization, proteomics, networkSCR_003180(SynSysNet, RRID:SCR_003180)Charite - Universitatsmedizin Berlin; Berlin; Germany Huntington's disease, Chorea Huntington, Epilepsy, Multiple Sclerosis, Parkinson's disease, Schizophrenia, Neurological diseaseDFG, European Union Seventh FPSYNSYSrelated to: Research Collaboratory for Structural Bioinformatics Protein Data Bank, KEGG, listed by: OMICtoolsPMID:23143269Last checked upnlx_156893, OMICS_01914
brainmap.orgResource, software resource, software application, data or information resource, databaseA community database of published functional and structural neuroimaging experiments with both metadata descriptions of experimental design and activation locations in the form of stereotactic coordinates (x,y,z) in Talairach or MNI space. BrainMap provides not only data for meta-analyses and data mining, but also distributes software and concepts for quantitative integration of neuroimaging data. The goal of BrainMap is to develop software and tools to share neuroimaging results and enable meta-analysis of studies of human brain function and structure in healthy and diseased subjects. It is a tool to rapidly retrieve and understand studies in specific research domains, such as language, memory, attention, reasoning, emotion, and perception, and to perform meta-analyses of like studies. Brainmap contains the following software: # Sleuth: database searches and Talairach coordinate plotting (this application requires a username and password) # GingerALE: performs meta-analyses via the activation likelihood estimation (ALE) method; also converts coordinates between MNI and Talairach spaces using icbm2tal # Scribe: database entry of published functional neuroimaging papers with coordinate results3d model, atlas, data management, imaging, map, neuroinformatics, warping, neuroimaging, brain, talairach, mni, java, modeling, magnetic resonance, nifti-1, ontology, os independent, pet, spect, visualization, functional neuroimaging, fmriSCR_003069(brainmap.org, RRID:SCR_003069)University of Texas Health Science Center at San Antonio; Texas; USA Healthy, DiseasedNIMHrelated to: Brede Database, uses: Scribe, listed by: NeuroImaging Tools and Resources Collaboratory (NITRC)References (3)Last checked upnif-0000-00049http://www.nitrc.org/projects/brainmap
exRNA AtlasResource, expression atlas, organization portal, data repository, application programming interface, data access protocol, production service resource, analysis service resource, database, consortium, atlas, service resource, portal, data analysis service, storage service resource, software resource, ontology, controlled vocabulary, data or information resourceSoftware tool as data and metadata repository of Extracellular RNA Communication Consortium. Atlas includes small RNA sequencing and qPCR derived exRNA profiles from human and mouse biofluids. All RNAseq datasets are processed using version 4 of exceRpt small RNAseq pipeline. Atlas accepts submissions for RNAseq or qPCR data.Differential, expression, RNA, sequencing, qPCR, data, visualization, extracellular, exRNA, atlas, repository, datasetSCR_017221(exRNA Atlas, RRID:SCR_017221)Baylor College of Medicine; Houston; Texas , exRNA gastric cancer, colon carcinoma, colorectal cancer, prostate carcinoma, pancreatic carcinoma, multiple sclerosis, glioblastoma multiforme, ulcerative colitis, Alzheimer's disease, ischemic stroke, intraparenchymal hemorrhage of brain, asthma, cardiovascular disorder, myocardial infarction, lupus, nephrotic syndrome, transplanted kidney present, liver disease, transplanted liver present, pre-eclampsia, Parkinson disease, intraventricular brain hemorrhage, subarachnoid hemorrhageAmerican Cancer Society ResearchProfessor Award, Frank McGraw Memorial Chair in CancerResearch, NCATS, NCI, NHLBI, NIA, NIDA, NIDDK, NIGMSrecommended by: National Library of Medicine, BRAIN InitiativePMID:30951672Last checked up
Diabetes Disease PortalResource, disease-related portal, data set, topical portal, portal, data or information resourceAn 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, syntenySCR_001660(Diabetes Disease Portal, RRID:SCR_001660)Rat Genome Database (RGD) Diabetes, Type 1 Diabetes, Type 2 Diabetes, Obesity, Hypertension, Insulin resistance, Hyperlipidemia, Metabolic diseaserelated to: NIDDK Information Network, Gene Ontology, submitted by: NIDDK Information NetworkLast checked upnlx_153942
Cancer Methylome SystemResource, data or information resource, databaseDatbase and web-based system for visualization and analysis of genome-wide methylation data of human cancers.gene, methylation, visualizationSCR_012013(Cancer Methylome System, RRID:SCR_012013)University of Texas Health Science Center at San Antonio; Texas; USA Cancer, NormalNCIlisted by: OMICtoolsPMID:22035855Last checked upOMICS_01836
Fred Hutchinson Cancer Research Center Co-operative Center for Excellence in Hematology Scientific Imaging Resource, service resource, resource, core facility, access service resourceScientific imaging service that serves as a centralized facility for imaging and visualization. The core facility provides access to time lapse and 3-D microscopy and quantitative autoradiography.scientific imaging service, imaging, visualization, time lapse, 3d microscopy, autoradiographySCR_015340( Fred Hutchinson Cancer Research Center Co-operative Center for Excellence in Hematology Scientific Imaging , RRID:SCR_015340)Fred Hutchinson Cancer Research Center cancerNIDDKlisted by: NIDDK Information NetworkLast checked up
FISH OracleResource, software resource, data or information resource, databaseA web-based software tool for the integrative analysis of cancer genomics data. It stores different kinds of downstream processed data from multiple samples in a single database. A powerful search interface allows to dynamically filter the data to be displayed with respect to different criteria. The combination of AJAX technology and a fast visualization engine facilitates a highly dynamic visualization for large amounts of data. FISH Oracle 2 is able to simultaneously display different data sets, thus simplifying their comparison. Filter and display options can be changed on the fly. High quality image export enables the life scientist to easily communicate the results, e.g. in presentations or publications. A comprehensive data administration assures to keep track of the data stored in the database.array cgh, snp, genomics, visualizationSCR_010927(FISH Oracle, RRID:SCR_010927)University of Hamburg; Hamburg; Germany Cancerlisted by: OMICtoolsPMID:21884636Last checked upOMICS_00721
SPIKEResource, service resource, data or information resource, databaseDatabase of curated human signaling pathways with an associated interactive software tool for analysis and dynamic visualization of pathways. Individual pathway maps can be viewed and downloaded; the entire database may be browsed, or launched via a map viewer tool that allows dynamic visualization of the database and save networks in XGMML format that can be viewed in all generic XGMML viewers. Map Topics * Cell cycle progress and check points * DNA damage response * Programmed cell death related processes * Stress-activated transcription factors * Mitogen-activated protein kinase pathways * Immune response signaling * HEarSpike: hearing related pathwaysvisualization, analysis, cellular, signaling pathway, regulatory network, function, genomic, proteomic, cell cycle, dna damage, cell death, stress, transcription factor, mitogen, protein kinase, pathway, immune response, signaling, hearing, dna damage response, programmed cell death, development, earSCR_010466(SPIKE, RRID:SCR_010466)Tel Aviv University; Ramat Aviv; Israel CancerA-T Children's Project, European Union FP7, Israel Science Foundation, Wolfson Foundationrelated to: ConsensusPathDBReferences (2)Last checked upnlx_157705
Neuroimage Analysis CenterResource, biomedical technology research center, training resourceBiomedical Technology Resource Center that develops image processing and analysis techniques for basic and clinical neurosciences. The NAC research approach emphasizes both specific core technologies and collaborative application projects. The core activity of the center is the development of algorithms and techniques for postprocessing of imaging data. New segmentation techniques aid identification of brain structures and disease. Registration methods are used for relating image data to specific patient anatomy or one set of images to another. Visualization tools allow the display of complex anatomical and quantitative information. High-performance computing hardware and associated software techniques further accelerate algorithms and methods. Digital anatomy atlases are developed for the support of both interactive and algorithmic computational tools. Although the emphasis of the NAC is on the dissemination of concepts and techniques, specific elements of the core software technologies have been made available to outside researchers or the community at large. The NAC's core technologies serve the following major collaborative projects: Alzheimer's disease and the aging brain, morphometric measures in schizophrenia and schizotypal disorder, quantitative analysis of multiple sclerosis, and interactive image-based planning and guidance in neurosurgery. One or more NAC researchers have been designated as responsible for each of the core technologies and the collaborative projects.brain, neuroimaging, image processing, image analysis, postprocessing, segmentation, registration, algorithm, technique, brain structure, visualization, neurosurgerySCR_008998(Neuroimage Analysis Center, RRID:SCR_008998)Harvard Medical School; Massachusetts; USA Alzheimer's disease, Aging, Schizophrenia, Schizotypal disorder, Multiple Sclerosis, NeurosurgeryNCRR, NIBIBLast checked upnlx_152643
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