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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
AlzSWAN Knowledge BaseResource, portal, knowledge environment, community building portal, knowledgebase, data or information resourceTHIS RESOURCE IS NO LONGER IN SERVICE, documented August 22, 2016. A community-driven knowledgebase of Alzheimer disease, in which researchers can annotate scientific claims, data, and information, putting these into the context of testable hypotheses and treatment discovery. This SWAN project adds a collection of hand-curated hypotheses to a research paper, which are then related through a set of discourse relationships. They can be browsed and relations between claims, as well as support networks for a specific claim, are made and visualized. AlzSWAN is where you explore scientific knowledge about Alzheimer disease and share your own ideas, comments and questions in a semantically structured system. AlzSWAN is enabled by Semantic Web technology, a new standard for knowledge organization and transfer on the Web. AlzSWAN organizes and manages knowledge using formal knowledge descriptions called ontologies. Using these formal knowledge descriptions, they can tie statements made in scientific publications or on the Web to scientific evidence, biological terminologies, and knowledgebases, and to claims and counterclaims made by other researchers.hypothesis, claim, research paper, relationship, semantics, annotationSCR_003017(AlzSWAN Knowledge Base, RRID:SCR_003017)Alzheimer's Research Forum Alzheimer's diseasealz.org, Ellison Medical Foundationrelated to: Semantic Web Applications in Neuromedicine (SWAN) Ontology, listed by: FORCE11PMID:17510163Last checked downnif-0000-00524
SysZNF - C2H2 Zinc Finger genesResource, data or information resource, databaseTHIS RESOURCE IS NO LONGER IN SERVCE, documented September 2, 2016. SysZNF is an information resource for C2H2 Zinc Finger genes in humans and mice. C2H2 Zinc Finger genes (C2H2-ZNF) constitute the largest class of transcription factors in humans and mouse. C2H2 zinc finger proteins primarily bind to DNA. In most cases, they attach to regions near certain genes and turn the genes on and off as needed. The researches on these genes show light on the evolution of gene regulation systems and development. Therefore, we develop SysZNF (Systematical information resource of Zinc Finger genes) to collect the information related to C2H2 Zinc Finger genes. The aim of SysZNF was to provide a user-friendly interface for rendering the information (DNA, Expression, Protein, Reference and so on) of each C2H2-ZNF (e.g., ZNF10) and to enable a comprehensive analysis of C2H2-ZNF. This project was supported by the Proteome-Center at Rostock University (PCRU) who conceives the concept of the database and Key laboratory of Systems biology at the Shanghai Institute for Biological Sciences (SIBS) who implemented the database. It is maintained jointly by PCRU and SIBS.zinc finger protein, zinc finger, cysteine, histidine, zinc ion, geneSCR_007056(SysZNF - C2H2 Zinc Finger genes, RRID:SCR_007056)University of Rostock; Mecklenburg-Vorpommern; Germany , Chinese Academy of Sciences; Beijing; China BMBF, Chinese Academy of SciencesPMID:18974185Last checked downnif-0000-03530
SCALE - Scandinavian lymphoma etiologyResource, disease-related portal, topical portal, research forum portal, biomaterial supply resource, portal, material resource, data or information resourceTHIS RESOURCE IS NO LONGER IN SERVICE, documented August 22, 2016. The original aim of this study was to increase our understanding of the etiology of malignant lymphomas, especially in view of the increasing trend in incidence. Malignant lymphoma (including non-Hodgkin lymphoma, NHL, Hodgkin lymphoma, HL, and chronic lymphocytic leukemia, CLL) constitute a heterogeneous group of malignancies with regard to histology, molecular characteristics and clinical course. Etiological factors may also vary by lymphoma subtype. The incidence of NHL, the most common lymphoma group, has increased dramatically during the past decades in Sweden and in many other Western countries. The reasons for this increase as well as for the majority of all new cases is not well understood. Well established risk factors for lymphoma overall include hereditary and acquired disorders of strong immune dysfunction such as HIV/AIDS and organ transplantation, but they explain few new cases in the population. Approach: Population-based case-control study in Sweden and Denmark. The study includes in total 3740 patients and 3187 controls in both countries recruited during the period October 1999 to October 2002. Through a rapid case ascertainment system, the cases were identified shortly after diagnosis. The controls were randomly selected from national population registers and frequency-matched to the expected number of cases by sex and age group. Both cases and controls were interviewed by telephone based on a standardized questionnaire to obtain detailed information on potential risk factors for lymphoma such as medical history including infectious diseases, drug use and blood transfusions, socio-economic factors and life-style. Blood samples were also collected and stored as serum, plasma, DNA and live lymphocytes. In addition, written questionnaires about dietary habits or work exposures were sent out in Sweden. Tumor material from the cases was re-examined and uniformly classified according to the REAL classification. Status The data collection ended in 2002 and data analysis has been ongoing since then. We have primarily analyzed a range of environmental factors in relation risk of malignant lymphoma subgroups including sun exposure, body mass index, family history of hematopoietic cancer, allergy, autoimmune disorders and mononucleosis. We have also assessed specific genetic determinants in a subgroups of patients with follicular lymphoma and controls. Study results have so far been presented in 14 publications in peer-reviewed journals. In addition to new analyses on other environmental factors, we now also work to understand genetic susceptibility and gene-environmental interaction and risk of lymphoma. Also, prognostic studies have been initiated in collaboration with other research groups with regard to in CLL, HL and T-cell lymphoma.malignant lymphoma, non-hodgkin lymphoma, hodgkin lymphoma, chronic lymphocytic leukemia, etiology, questionnaire, interview, risk factor, medical history, infectious disease, drug use, blood transfusion, socio-economic factor, life-style, environmental factor, sun exposure, body mass index, family history, hematopoietic cancer, allergy, autoimmune disorder, mononucleosis, follicular lymphoma, control, gene, lymphoma, t-cell lymphoma, genetic, tumor, environmentSCR_006041(SCALE - Scandinavian lymphoma etiology, RRID:SCR_006041)Karolisnka Biobank Malignant lymphoma, Normal control, LymphomaCancerforeningen, Danish Cancer Society, NCI, Plan Denmark, Swedish Cancer Societylisted by: One Mind Biospecimen Bank ListingLast checked downnlx_151438
DIStributions of SPINEsResource, software resource, software application, data analysis software, data processing softwareTHIS RESOURCE IS NO LONGER IN SERVICE, documented August 19, 2016. Software tool that facilitates the analysis of the 3D structure of spine insertions in dendrites, providing insight on spine distribution patterns. Dispine depends on python 2.6, PyQt4, numpy, python wrappers of VTK and pygame. If you want to test the tool, a test set is provided.spine, insertion, dendrite, distribution pattern, data set, visualization, spiny dendrite, 3d structure, spine insertionSCR_006925(DIStributions of SPINEs, RRID:SCR_006925)Polytechnic University of Madrid; Madrid; Spain Centre for Networked Biomedical Research into Neurodegenerative Diseases, Spanish Ministry of Education Science and InnovationPMID:22644869Last checked downnlx_152807
International HapMap ProjectResource, narrative resource, data or information resource, experimental protocol, databaseTHIS RESOURCE IS NO LONGER IN SERVICE, documented August 22, 2016. A multi-country collaboration among scientists and funding agencies to develop a public resource where genetic similarities and differences in human beings are identified and catalogued. Using this information, researchers will be able to find genes that affect health, disease, and individual responses to medications and environmental factors. All of the information generated by the Project will be released into the public domain. Their goal is to compare the genetic sequences of different individuals to identify chromosomal regions where genetic variants are shared. Public and private organizations in six countries are participating in the International HapMap Project. Data generated by the Project can be downloaded with minimal constraints. HapMap project related data, software, and documentation include: bulk data on genotypes, frequencies, LD data, phasing data, allocated SNPs, recombination rates and hotspots, SNP assays, Perlegen amplicons, raw data, inferred genotypes, and mitochondrial and chrY haplogroups; Generic Genome Browser software; protocols and information on assay design, genotyping and other protocols used in the project; and documentation of samples/individuals and the XML format used in the project.genetic variant, disease, genetic sequence, genetic variation, single nucleotide polymorphism, genetic diversity, dna, sequence, catalog, genome, chromosomeSCR_002846(International HapMap Project, RRID:SCR_002846)NCBI Chinese Academy of Sciences, Chinese Ministry of Science and Technology, Delores Dore Eccles Foundation, Genome Canada, Genome Quebec, Hong Kong Innovation and Technology Commission, Japanese Ministry of Education Culture Sports Science and Technology MEXT, National Natural Science Foundation of China, NIH, SNP Consortium, University Grants Committee of Hong Kong, Wellcome Trust, W. M. Keck Foundationrelated to: SNAP - SNP Annotation and Proxy Search, Haploview, NHGRI Sample Repository for Human Genetic Research, DistiLD - Diseases and Traits in LD, SNP at Ethnos, GBrowse, used by: BioSample Database at EBI, listed by: OMICtoolsLast checked downnif-0000-02940, OMICS_00273http://www.hapmap.org/http://snp.cshl.org
FSSP - Families of Structurally Similar ProteinsResource, data set, data or information resourceTHIS RESOURCE IS NO LONGER IN SERVCE, documented September 6, 2016. FSSP (families of structurally similar proteins) is a database of structural alignments of proteins in the Protein Data Bank. The database currently contains an extended structural family for each of 330 representative protein chains. Each data set contains structural alignments of one search structure with all other structurally significantly similar proteins in the representative set (remote homologs, below 30%% sequence identity), as well as all structures in the Protein Data Bank with 70-30%% sequence identity relative to the search structure (medium homologs). Very close homologs (above 70 % sequence identity) are excluded as they rarely have marked structural differences. The alignments of remote homologs are the result of pairwise all-against-all structural comparisons in the set of 330 representative protein chains. All such comparisons are based purely on the 3D co-ordinates of the proteins and are derived by automatic (objective) structure comparison programs. The significance of structural similarity is estimated based on statistical criteria. The FSSP database is available electronically and by anonymous ftp (file transfer protocol).computer algorithm, modular protein design, protein folding, protein structure alignment, protein structure, gold standardSCR_003534(FSSP - Families of Structurally Similar Proteins, RRID:SCR_003534)European Bioinformatics Institute Commission of the European Communities and Human Frontiers Science Program, EMBOPMID:1304898Last checked downnlx_10193http://www.sander.ebi.ac.uk/dali/fssp/
Gray MattersResource, narrative resource, podcast, data or information resourceTHIS RESOURCE IS NO LONGER IN SERVICE, documented on September 06, 2013. Gray Matters is a radio series on brain topics that has been produced since 1994 by Public Radio International in association with the Dana Alliance. More than 25 programs have been created on topics ranging from stress, neuroethics, learning throughout life and sports, fitness and the Brain. Dana Alliance members serve as advisers to Gray Matters programming and are interviewed during the programs. The transcripts are also available.SCR_004433(Gray Matters, RRID:SCR_004433)The Dana Foundationrelated to: Integrated Podcasts, used by: NIF Data FederationLast checked downnlx_54435
Coddle-Codons Optimized to Discover Deleterious LEsionsResource, analysis service resource, data analysis service, service resource, production service resourceTHIS RESOURCE IS NO LONGER IN SERVICE, documented August 22, 2016. Web-accessible program that identifies the region(s) of a user-selected gene and of its coding sequence (CDS) where the anticipated point mutations are most likely to result in deleterious effects on the gene's function. CODDLe separately handles 1) the prediction of changes which should truncate the protein and destabilize the RNA - nonsense changes and splice junction changes, and 2) the prediction of missense changes which should alter function of the gene product - those in conserved amino acid blocks in the CDS. Because the region(s) identified will be PCR amplified by the user and that amplicon will be used for polymorphism discovery, the application delivers primer pairs selected by Primer3 (Steve Rozen, Helen J. Skaletsky (1996,1997,1998)Primer3.) After selecting a primer pair, CODDLe returns a window with the selected amplicon and tabulates the effects of all possible polymorphisms which could be detected in that amplicon. CODDLe will not identify the regions of a gene where polymorphisms are most likely to be discovered. Others have shown that naturally occurring SNPs are found more often in the untranslated regions of a gene.codon, deleterious lesion, gene, coding, sequence, mutation, primer, protein sequence, cdna, sequence alignment, coding sequenceSCR_003003(Coddle-Codons Optimized to Discover Deleterious LEsions, RRID:SCR_003003)Fred Hutchinson Cancer Research Center DOE, Office of Energy Researchlisted by: 3DVCLast checked downnif-0000-30262
Rat Gene Symbol TrackerResource, data or information resource, databaseTHIS RESOURCE IS NO LONGER IN SERVCE, documented September 2, 2016. Database for defining official rat gene symbols. It includes rat gene symbols from three major sources: the Rat Genome Database (RGD), Ensembl, and NCBI-Gene. All rat symbols are compared with official symbols from orthologous human genes as specified by the Human Gene Nomenclature Committee (HGNC). Based on the outcome of the comparisons, a rat gene symbol may be selected. Rat symbols that do not match a human ortholog undergo a strict procedure of comparisons between the different rat gene sources as well as with the Mouse Genome Database (MGD). For each rat gene this procedure results in an unambiguous gene designation. The designation is presented as a status level that accompanies every rat gene symbol suggested in the database. The status level describes both how a rat symbol was selected, and its validity. Rat Gene Symbol Tracker approves rat gene symbols by an automatic procedure. The rat genes are presented with links to RGD, Ensembl, NCBI Gene, MGI and HGNC. RGST ensures that each acclaimed rat gene symbol is unique and follows the guidelines given by the RGNC. To each symbol a status level associated, describing the gene naming process.gene, orthology, naming, gene symbol, nomenclature, human, mouseSCR_003261(Rat Gene Symbol Tracker, RRID:SCR_003261)RatMap Erik Philip-Sorensen Foundation, Nilsson-Ehle Foundation, Sven and Lilly Lawski Foundation, Swedish MRC, SWEGENE Foundation, Wilhelm and Martina Lundgren Research Foundationrelated to: Rat Genome Database (RGD), Entrez Gene, Ensembl, Mouse Genome Informatics (MGI), HGNCPMID:18215257Last checked downnif-0000-31426
Expression ProfilerResource, analysis service resource, data analysis service, service resource, production service resourceTHIS RESOURCE IS NO LONGER IN SERVCE, documented September 2, 2016. The EP:GO browser is built into EBI's Expression Profiler, a set of tools for clustering, analysis and visualization of gene expression and other genomic data. With it, you can search for GO terms and identify gene associations for a node, with or without associated subnodes, for the organism of your choice.other analysis, cluster, analysis, visualization, gene expression, genomic, gene ontology, gene association, microarray, protein-protein interaction, geneSCR_005821(Expression Profiler, RRID:SCR_005821)European Bioinformatics Institute Estonian Science Foundation, European Union, Wellcome Trustrelated to: Gene Ontology, listed by: Gene Ontology ToolsPMID:15215431Last checked downnlx_149323
GenomEUtwinResource, disease-related portal, topical portal, database, biomaterial supply resource, research forum portal, portal, material resource, data or information resourceTHIS RESOURCE IS NO LONGER IN SERVICE, documented August 29, 2016. Study of genetic and life-style risk factors associated with common diseases based on analysis of European twins. The population cohorts used in the Genomeutwin study consist of Danish, Finnish, Italian, Dutch, English, Australian and Swedish twins and the MORGAM population cohort. This project will apply and develop new molecular and statistical strategies to analyze unique European twin and other population cohorts to define and characterize the genetic, environmental and life-style components in the background of health problems like obesity, migraine, coronary heart disease and stroke, representing major health care problems worldwide. The participating 8 twin cohorts form a collection of over 0.6 million pairs of twins. Tens of thousands of DNA samples with informed consents for genetic studies of common diseases have already been stored from these population-based twin cohorts. Studies targeted to cardiovascular traits are now being undertaken in MORGAM, a prospective case-cohort study. MORGAM cohorts include approximately 6000 individuals, drawn from population-based cohorts consisting of more than 80 000 participants who have donated DNA samples.genetic, environment, lifestyle, gene, diseaseSCR_002843(GenomEUtwin, RRID:SCR_002843)University of Helsinki; Helsinki; Finland TwinEuropean Unionrelated to: KI Biobank - TwinGene, listed by: One Mind Biospecimen Bank ListingLast checked downnif-0000-25218
BovMap DatabaseResource, service resource, data or information resource, data repository, storage service resource, databaseTHIS RESOURCE IS NO LONGER IN SERVICE, documented August 22, 2016. Database containing information on the cattle genome comprising loci list, phenes list, homology query, cattle maps, gene list, and chromosome homology. The objective of BovMap is to develop a set of anchored loci for the cattle genome map. In total, 58 clones were hybridized with chromosomes and identified loci on 22 of the 31 different bovine chromosomes. Three clones contained satellite DNA. Two or more markers were placed on 12 chromosomes. Sequencing of the microsatellites and flanking regions was performed directly from 43 cosmids, as previously reported. Primers were developed for 39 markers and used to describe the polymorphism associated with the corresponding loci. Users are also allowed to summit their own data for Bovmap. An integrated cytogenetic and meiotic map of the bovine genome has also been developed around the Bovmap database. One objective that Bovmap uses as the mapping strategy for the bovine genome uses large insert clones as a tool for physical mapping and as a source of highly polymorphic microsatellites for genetic typing.genetic, bovine, cattle, chromosome, clone, cosmid, cow, cytogenetic, dna, genome, homology, locus, meiotic, phene, polymorphism, sequence, map, geneSCR_008145(BovMap Database, RRID:SCR_008145)INRA - French National Institute for Agricultural Research; Paris; France European UnionLast checked downnif-0000-20968
eVOCResource, ontology, data or information resource, controlled vocabularyTHIS RESOURCE IS NO LONGER SUPPORTED, documented September 6, 2016. Set of orthogonal controlled vocabularies that unifies gene expression data by facilitating a link between the genome sequence and expression phenotype information. The system associates labelled target cDNAs for microarray experiments, or cDNA libraries and their associated transcripts with controlled terms in a set of hierarchical vocabularies. eVOC consists of four orthogonal controlled vocabularies suitable for describing the domains of human gene expression data including Anatomical System, Cell Type, Pathology and Developmental Stage. The four core eVOC ontologies provide an appropriate set of detailed human terms that describe the sample source of human experimental material such as cDNA and SAGE libraries. These expression terms are linked to libraries and transcripts allowing the assessment of tissue expression profiles, differential gene expression levels and the physical distribution of expression across the genome. Analysis is currently possible using EST and SAGE data, with microarray data being incorporated. The eVOC data is increasingly being accepted as a standard for describing gene expression and eVOC ontologies are integrated with the Ensembl EnsMart database, the Alternate Transcript Diversity Project and the UniProt Knowledgebase. Several groups are currently working to provide shared development of this resource such that it is of maximum use in unifying transcript expression information.mouse, mapping, cdna, development, microarray, expression, expressed sequence, anatomical system, cell type, developmental stage, experimental technique, microarray platform, pathology, pooling, tissue preparation, treatment, gene expression, genome sequence, expression phenotype, genome, sequence, phenotype, anatomical system, cell type, pathology, anatomySCR_010704(eVOC, RRID:SCR_010704)University of the Western Cape; Bellville; South Africa European Union, South African Department of Arts Culture Science and Technology, South African National Research Foundation, Wellcome Trustrelated to: OBO, Bgee: a dataBase for Gene Expression EvolutionPMID:12799354Last checked downnlx_84448
Australian Medical Bioinformatics ResourceResource, disease-related portal, topical portal, data or information resource, portal, research forum portalTHIS RESOURCE IS NO LONGER IN SERVCE, documented September 6, 2016. AMBeR's aim is to bring together Australia's unique resources for genetic epidemiology and genomics with high level expertise in bioinformatics and statistical science, conduct advanced methodological research, develop new research capacity and competitiveness in cutting-edge techniques, bring them to bear on important medical research problems, train young Australians in bioinformatics and advanced biostatistics, and transfer this expertise to the medical research community.medical, bioinformatics, statistical, science, genomics, epidemiology, research, methodological, techniques, biostatisticsSCR_008385(Australian Medical Bioinformatics Resource, RRID:SCR_008385)University of Western Australia; Perth; Australia Genomics and Proteomics Program, Medical Bioinformatics, MRC, National HealthLast checked downnif-0000-30032
CryptoBaseResource, software resourceTHIS RESOURCE IS NO LONGER AVAILABLE, documented July 19, 2016. This site is built and maintained by the Madhani Lab, Dept. of Biochemistry and Biophysics at the University of California, San FranciscoSCR_000780(CryptoBase, RRID:SCR_000780)University of California at San Francisco; California; USA Herb and Marion Sandler FoundationLast checked downnif-0000-30395http://archive.is/YgVX4
Northern Ireland Virtual Tissue ArchiveResource, narrative resource, training material, image collection, data or information resourceTHIS RESOURCE IS NO LONGER IN SERVICE, documented August 29, 2016. A pan European network for virtual tissue archiving aimed at supporting clinical trials, biomarker research, tissue microarray analysis and virtual slide based education. NIVTA has state-of-the-art digital scanning systems including an Aperio CS system, Aperio OS system (one of only two currently available in Europe) and a Hamamatsu system with fluorescent scanning capability.clinical trial, biomarker research, tissue microarray, analysis, virtual slide, tissue, archive, data resourceSCR_004452(Northern Ireland Virtual Tissue Archive, RRID:SCR_004452)Queen's University Belfast; Ireland; United Kingdom Hewlett-Packard, Queen's University Belfast; Ireland; United KingdomLast checked downnlx_44619
Short Course on the Genetics of AddictionResource, short course, training resourceTHIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. This course emphasizes genetic applications and approaches to drug addiction research through methodological instruction based on literature, data sets and informatics resources drawn from studies of addiction related phenotypes. The course includes plenary sessions on major progress in addiction genetics, and discussion sessions in which students present their work for discussion on applications of genetic methods. Students will leave the course able to design and interpret genetic and genomic studies of addiction as they relate to their specific research question, and will be able to make use of current bioinformatics resources to identify research resources and make use of public data sources in their own research.addiction, gene, genetic, genomic, addiction, drugSCR_005560(Short Course on the Genetics of Addiction, RRID:SCR_005560)Jackson Laboratory Drug addictionHoward Hughes Medical Institute, NIDALast checked downnlx_146202
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
Swami: The Next Generation Biology WorkbenchResource, service resourceTHIS RESOURCE IS NO LONGER IN SERVICE, documented August 22, 2016. The Next Generation Biology Workbench is a free resource for research and education in Bioinformatics, Genomics, Proteomics, and Phylogenetics. The NGBW is a re-engineering of the Biology Workbench which was designed by Shankar Subramaniam and his group to provide an integrated environment where tools, user data, and public data resources can be easily accessed. The NGBW is designed to be an organic tool that evolves with the needs of the Biomedical research and education communities. The Next Generation Biology Workbench (NGBW) is now available for public use, in its production release.SCR_007217(Swami: The Next Generation Biology Workbench, RRID:SCR_007217)University of California at San Diego; California; USA IBM Corporation, Microsoft Research, NIGMSLast checked downnlx_14257http://www.ngbw.org/
IndelFR - Indel Flanking Region DatabaseResource, data or information resource, databaseTHIS RESOURCE IS NO LONGER IN SERVCE, documented September 2, 2016. Indel Flanking Region Database is an online resource for indels and the flanking regions of proteins in SCOP superfamilies, including amino acid sequences, lengths, locations, secondary structure constitutions, hydrophilicity / hydrophobicity, domain information, 3D structures and so on. It aims at providing a comprehensive dataset for analyzing the qualities of amino acid insertion/deletions(indels), substitutions and the relationship between them. The indels were obtained through the pairwise alignment of homologous structures in SCOP superfamilies. The IndelFR database contains 2,925,017 indels with flanking regions extracted from 373,402 structural alignment pairs of 12,573 non-redundant domains from 1053 superfamilies. IndelFR has already been used for molecular evolution studies and may help to promote future functional studies of indels and their flanking regions.indel, flanking region, protein, structural domain, domain, protein superfamily, protein structure, insertion/deletion, insertion, deletion, protein sequence, sequence, structure, protein domainSCR_006050(IndelFR - Indel Flanking Region Database, RRID:SCR_006050)Shandong University; Shandong; China Independent Innovation Foundation of Shandong University, National Natural Science Foundation of China, Scientific Research Reward Fund for excellent Young and Middle-Aged scientists in Shandong Provincerelated to: SCOP: Structural Classification of Proteins, Research Collaboratory for Structural Bioinformatics Protein Data BankPMID:22127860Last checked downnlx_151448
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