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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
Amino Acid-Nucleotide Interaction DatabaseResource, service resource, data or information resource, databaseTHIS RESOURCE IS NO LONGER IN SERVCE, documented September 6, 2016. AANT, the Amino Acid-Nucleotide Interaction Database, contains information derived from all of the protein/nucleic acid complexes with experimentally determined structures in the Protein Data Bank. You can visualize the AANT models using the simple web interface, which relies on the Chime plug-in. You can also download these models for further analysis using publicly available tools for manipulating PDB structures. The software that generates AANT uses HBPLUS to predict hydrogen bond interactions between single bases and single amino acid residues within these complexes. The AANT software uses this information to break down a single PDB structure into scores of individual interactions between either the base, sugar, or phosphate of a nucleotide and the side chain or peptide backbone of a amino acid. The software then superimposes all the interactions between a particular moiety of a nucleotide and a particular moiety of a amino acid residue into a single 3D model, centering on a particular point in the base, sugar, or phosphate. The AANT software then groups geometrically similar interactions into clusters.SCR_004617(Amino Acid-Nucleotide Interaction Database, RRID:SCR_004617)University of Texas at Austin; Texas; USA PMID:14681388Last checked downnlx_61417
UnifracResource, software resource, software application, data analysis software, data processing softwareTHIS RESOURCE IS NO LONGER IN SERVICE, documented Setember 8, 2016. A suite of tools for the comparison of microbial communities using phylogenetic information. It takes as input a single phylogenetic tree that contains sequences derived from at least two different environmental samples and a file describing which sequences came from which sample.microbiome, comparison, microbial community, phylogenetic tree, sequenceSCR_014616(Unifrac, RRID:SCR_014616)listed by: Human Microbiome ProjectLast checked up
CFCResource, software resource, software applicationTHIS RESOURCE IS NO LONGER IN SERVCE, documented September 22, 2016. General-purpose program for monitoring genetic diversity. CFC allows for several pedigree analyses such as: (1) computing inbreeding coefficients and relationships; (2) computing average relationships very quickly within and between specified groups of individuals; (3) computing average relatedness; (4) ancestral decomposition of the average or the individual inbreeding coefficient; (5) ancestral decomposition of the average coancestry; (6) optimizing matings to minimize the average inbreeding coefficients in the next generation; (7) computing founder equivalent, founder genome equivalent and effective number of non-founders; (8) computing numerator relationship matrix, its Cholesky decomposition and its inverse; (9) providing useful information on the structure of pedigrees.gene, genetic, genomic, visual c++, ms-windows, (98/nt/xp)SCR_009146(CFC, RRID:SCR_009146)listed by: Genetic Analysis SoftwareLast checked downnlx_154264
UC Davis Alzheimers Disease Center - ResourcesResource, training service resource, database, biomaterial supply resource, tissue bank, service resource, brain bank, material resource, funding resource, data or information resourceTHIS RESOURCE IS NO LONGER IN SERVICE, documented August 22, 2016. Support research in Alzheimer's disease (AD) offering pilot grants, recruitment of research subjects, access to database, tissue samples, and statistical and research study design consultation for investigators. The scientific effort of the program seeks to: promote research directed at understanding factors that influence the expression and progression of Alzheimer's disease; develop and maintain cohorts of carefully diagnosed and well characterized research subjects available for research studies on Alzheimer's disease and dementia; provide support to investigators in subject recruitment, clinical research, experimental design, and statistical analysis of data; and maintain a variety of samples (brain, DNA, serum) and an extensive electronic database suitable for developing new research and supporting existing programs.brain, dna, serum, brain tissue, tissueSCR_010699(UC Davis Alzheimers Disease Center - Resources, RRID:SCR_010699)UC Davis Alzheimer's Disease Center Alzheimer's disease, AgingMartinez Veterans Health Administration, NIA, State of California's Department of Public Healthlisted by: One Mind Biospecimen Bank ListingLast checked downnlx_82710
LitMinerResource, data or information resource, databaseTHIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. The LitMiner software is a literature data-mining tool that facilitates the identification of major gene regulation key players related to a user-defined field of interest in PubMed abstracts. The prediction of gene-regulatory relationships is based on co-occurrence analysis of key terms within the abstracts. LitMiner predicts relationships between key terms from the biomedical domain in four categories (genes, chemical compounds, diseases and tissues). The usefulness of the LitMiner system has been demonstrated recently in a study that reconstructed disease-related regulatory networks by promoter modeling that was initiated by a LitMiner generated primary gene list. To overcome the limitations and to verify and improve the data, we developed WikiGene, a Wiki-based curation tool that allows revision of the data by expert users over the Internet. It is based on the annotation of key terms in article abstracts followed by statistical co-citation analysis of annotated key terms in order to predict relationships. Key terms belonging to four different categories are used for the annotation process: -Genes: Names of genes and gene products. Gene name recognition is based on Ensembl . Synonyms and aliases are resolved. -Chemical Compounds: Names of chemical compounds and their respective aliases. -Diseases and Phenotypes: Names of diseases and phenotypes -Tissues and Organs: Names of tissues and organs LitMiner uses a database of disease and phenotype terms for literature annotation. Currently, there are 2225 diseases or phenotypes, 801 tissues and organs, and 10477 compounds in the database.gene, biomedical, chemical, compound, disease, identification, literature, medline interfaces, mining, modeling, phenotype, promoter, regulation, regulatory, relationship, tissue, toolSCR_008200(LitMiner, RRID:SCR_008200)Last checked downnif-0000-21241
Connectionist Models of Cognitive, Affective, Brain, and Behavioral DisordersResource, portal, community building portal, data or information resourceTHIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. This site aims to provide a discussion and source list for connectionist and neural network models of disorders associated with mental or brain conditions. Recent connectionist and neural network models of behavior, information processing patterns, and brain activity present in people with cognitive, affective, brain, and behavioral disorders are reviewed on this web site. Ways that assumptions regarding normal and disordered behavior may be represented in connectionist models are discussed for features of various disorders. Similarities and differences between the models and criteria for their evaluation are presented, and suggestions for inclusion of information which may help to make these models more directly comparable in the future are considered. References to Connectionist Models of Cognitive, Affective, Brain, and Behavioral Disorders include: General Neural Network Information Reviews, General Introductions, and Calls for More Connectionist Models of Mental Disorders Models of Psychopathologies and Psychiatric Disorders Models of Cognitive, Affective, Brain, and Behavioral Disorders Not Associated with Psychopathology Additionally, Web Sites for Neural Network Modelers of Disorder are provided.affective, articles, behavior, behavioral disorders, bibliographies, brain, brain activity, cognitive, connectionist, disordered, disorders, human, information processing, keywords: connectionist, mental, models, neural network, normal, psychopathologies, research labsSCR_008088(Connectionist Models of Cognitive, Affective, Brain, and Behavioral Disorders, RRID:SCR_008088)Carnegie Mellon University; Pennsylvania; USA Last checked downnif-0000-10775
Integrated Content EnvironmentResource, software resource, collaboration toolTHIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. The Integrated Content Environment (ICE) is a free Word-processor based system that allows authors to work individually or collaboratively on material for the Web, CD and print. This free web content management system, produced by the University of Southern Queensland, was initially developed by staff at the university to produce course content for online and print delivery. It has also been used for general web site development, and to manage documents in project intranets.integrated content, word processor, collaboration, content managementSCR_001369(Integrated Content Environment, RRID:SCR_001369)University of Southern Queensland; Queensland; Australia Last checked downnif-0000-07757http://ice.usq.edu.au/default.htm https://eprints.usq.edu.au/697/http://www.usq.edu.au/lrds/tech/ice
BayGenomicsResource, biomaterial supply resource, material resource, organism supplier, tissue bankTHIS RESOURCE IS NO LONGER IN SERVICE, documented August 29, 2016. The BayGenomics gene-trap resource provides researchers with access to thousands of mouse embryonic stem (ES) cell lines harboring characterized insertional mutations in both known and novel genes. The major goal of BayGenomics is to identify genes relevant to cardiovascular and pulmonary disease.embryonic, expression, gene, bioinformatic, cardiopulmonary, cell, clone, disease, genomic, germline, insertional, line, mouse, mutant, mutation, pulmonary, stem, cardiovascular, pulmonary diseaseSCR_008168(BayGenomics, RRID:SCR_008168)University of California at San Francisco; California; USA listed by: One Mind Biospecimen Bank ListingLast checked downnif-0000-21042
Eutectic NTSResource, software resource, resourceTHIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. A hardware and software package with which a scientist could trace the structure of neurons and other neuroscientific features directly from tissue sections or from a stack of their images into a computer. Then it also could edit, merge, filter, display in 3D, and make realistic plots of the structures. The NTS also includes a substantial statistical package that provided many, now standardized, mathematical and statistical summaries that described each neuron and compared one population to another. Additionally, NTS also provided an embryonic electrotonic modeler that simulates and displayes the electrical functioning of a cell. The NTS uses a special purpose graphics display processor called the VDP3 whose output is presented on a very high resolution CRT. During tracing, the VDP3 presents a variable-diameter cursor and other information directly in the microscope and enables tracing at a high spatial resolution and with measurement of process diameters limited only by the microscope''s optics. Control of tracing is done with a 3D joystick that allows easy control of five input variables: X,Y,Z position, cursor diameter, and a numeric tag. Finally, superb 3D interactive displays of completed cells are provided on the VDP3.embryonic electronic modeler, cell, hardware, microscope, neuron, optics, software, neuronal tree structure, dendritic tree, segmentation, instrument, equipmentSCR_008062(Eutectic NTS, RRID:SCR_008062)NIDALast checked downnif-0000-10453
OBD-PKB InterfaceResource, ontology, data or information resource, controlled vocabularyTHIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. This interface is for exploring data collected as part of the NIF Neurodegenerative Disease Ontology project. Not generally intended for public consumption yet, but people are welcome to look - large caveat emptor applies. Sponsors: This resource is part of the NIF project.data, disease, neurodegenerative, softwareSCR_002882(OBD-PKB Interface, RRID:SCR_002882)University of California; Berkeley; USA Last checked downnif-0000-25570
UniLibResource, data or information resource, databaseTHIS RESOURCE IS NO LONGER SUPPORTED, documented September 6, 2016. The Unified Library Database, or UniLib, takes a library-level view of the EST and SAGE libraries present in NCBI's dbEST, UniGene and SAGEmap resources. This database was initially developed by NCBI in order to track and annotate libraries being generated by NCI's CGAP project. The query bar of the UniLib Library browser provides the most friendly way to navigate through these libraries. When matches to the Library browser query are returned as summaries, full library records can be retrieved through the linked Record retriever.SCR_004178(UniLib, RRID:SCR_004178)NCBI Last checked downnlx_20445
RNA Virus DatabaseResource, data or information resource, databaseTHIS RESOURCE IS NO LONGER IN SERVICE, documented August 19, 2016. It is a database and web application describing the genome organization and providing analytical tools for the 938 known species of RNA virus. It can identify submitted nucleotide sequences, can place them into multiple whole-genome alignments (in species where more than one isolate has been fully sequenced) and contains translated genome sequences for all species. It has been created for two main purposes: to facilitate the comparative analysis of RNA viruses and to become a hub for other, more specialised virus Web sites.SCR_007899(RNA Virus Database, RRID:SCR_007899)University of Oxford; Oxford; United Kingdom Last checked downnif-0000-03416http://virus.zoo.ox.ac.uk/rnavirusdb/
BiobehavioralResource, blog, narrative resource, data or information resourceTHIS RESOURCE IS NO LONGER IN SERVCE, documented September 6, 2016. Biobehavioral blog on research and medicine as a continuum from biological mechanisms to behavioural phenomena.SCR_008710(Biobehavioral, RRID:SCR_008710)Last checked downnlx_11905
DMAPS - A Database of Multiple Alignments for Protein StructuresResource, data or information resource, databaseTHIS RESOURCE IS NO LONGER IN SERVCE, documented September 6, 2016. DMAPS database contains pre-computed multiple structure alignments for protein chains in the Protein Data Bank (PDB). Automated structure alignments have been generated for classified protein families using CE-MC algorithm. Alignments have been built only for those families with at least three members. Currently, multiple structure alignments are available for 3050 SCOP-, 3087 CATH-, 664 ENZYME- and 1707 CE-based families. Users will be able to retrieve multiple alignments for a given PDB chain classified by one of these criteria.multiple structure alignment, protein, protein family, protein structureSCR_007140(DMAPS - A Database of Multiple Alignments for Protein Structures, RRID:SCR_007140)University at Albany; New York; USA Last checked downnif-0000-02755, SCR_009091, nlx_154108
Microarray Literature-based AnnotationResource, software resource, software application, data analysis software, data processing softwareTHIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. MILANO provides a useful tool for the automatic custom annotation of microarray results which is based on all the available literature. It has two major advances over similar tools: the ability to expand gene names to include all their informative synonyms while removing synonyms that are not informative and access to the GeneRIF database which provides short summaries of curated articles relevant to known genes. MILANO allows annotation of lists of genes derived from microarray results by user defined terms. The annotation strategy is based on counting the number of literature co-occurrences of each gene on the list with a user defined term. This strategy allows the customization of the annotation procedure and thus overcomes one of the major limitations of the functional annotations usually provided with microarray results. MILANO expands the gene names to include all their informative synonyms while filtering out gene symbols that are likely to be less informative as literature searching terms. It supports searching two literature databases: GeneRIF and Medline (through PubMed), allowing retrieval of both quick and comprehensive results. MILANO''s ability can improve microarray analysis by analyzing a list of 150 genes that were affected by p53 overproduction. This analysis reveals that it enables immediate identification of known p53 target genes on this list and assists in sorting the list into genes known to be involved in p53 related pathways, apoptosis and cell cycle arrest. This program performs automatic searches in PubMed or the GeneRIF collection for articles containing co-occurrences of search terms with a list of genes (e.g. from a microarray experiment). The program is used by pasting the list of Gene ID''s or symbols in the Primary Search Term field, and the list of cross-reference search terms in the Secondary Search Term field. The output is a table containing the number of hits for each pair of search terms. Sample input is provided in the fields, so you can just click submit and see what happens. If you want to run data of your own, delete the sample input first.gene, annotation, apoptosis, arrest, cell, cycle, literature, microarray, gene expression, p53, symbolSCR_008206(Microarray Literature-based Annotation, RRID:SCR_008206)Hebrew University of Jerusalem; Jerusalem; Israel Last checked downnif-0000-21264http://milano.md.huji.ac.il/
GOALIEResource, software resourceTHIS RESOURCE IS NO LONGER IN SERVCE, documented September 2, 2016. Generalized Ontological Algorithmic Logical Invariants Extractor (GOALIE) is a tool for the construction of time-course dependent enrichments. Requires an ODBC connection to an instance of the GO database. Platform: Windows compatible, Mac OS X compatible, Linux compatiblegene ontology, statistical analysis, time-courseSCR_000088(GOALIE, RRID:SCR_000088)NYU Bioinformatics Group listed by: Gene Ontology ToolsLast checked downnlx_149255
CoGenT++Resource, data or information resource, databaseTHIS RESOURCE IS NO LONGER IN SERVICE, documented August 26, 2016. A data environment for computational research in comparative and functional genomics, designed to address issues of consistency, reproducibility, scalability and accessibility.computation, genomics, data environment, functional genomicsSCR_000249(CoGenT++, RRID:SCR_000249)European Bioinformatics Institute PMID:16216832Last checked downnif-0000-02674http://cgg.ebi.ac.uk/cgg/cpp_sitemap.html
BioLitResource, software resource, software application, data or information resource, databaseTHIS RESOURCE IS NO LONGER IN SERVICE, documented on May 16, 2016. The establishment of open access literature makes it possible for knowledge to be extracted from scholarly articles and included in other resources. BioLit aims to extract database identifiers and rich meta-data from open access articles in the life sciences and integrate that information with existing biological databases. We have begun prototyping this effort using a clone of the RCSB Protein Data Bank, a database of macromolecular structures. Cyberinfrastructure is integral to all aspects of conducting experimental research and distributing those results. However, it has yet to make a similar impact on the way we communicate that information. Peer-reviewed publications have long been the currency of scientific research as they are the fundamental unit through which scientists communicate with and evaluate each other. However, in striking contrast to the data, publications have yet to benefit from the opportunities offered by cyberinfrastructure. While the means of distributing publications has vastly improved, publishers have done little else to capitalize on the electronic medium. In particular, semantic information describing the content of these publications is sorely lacking, as is the integration of this information with data in public repositories. This is confounding considering that many basic tools for marking-up and integrating publication content in this manner already exist, such as a centralized literature database, relevant ontologies, and machine-readable document standards. We believe that the research community is ripe for a revolution in scientific communication and that the current generation of scientists will be the one to push it forward. These scientists, generally graduate students and new post-docs and have grown up with cyberinfrastructure as a part of their daily lives, not just a specialized aspect of their profession. They have a natural ability to do science in an electronic environment without the need for printed publications or static documents and, in fact, can feel quite limited by the traditional format of a publication. Perhaps most importantly, they appreciate that the sheer amount of data and the number of publications is prohibitive to the traditional methods of keeping current with the literature. Fink, L., Bourne, P. Reinventing Scholarly Communication for the Electronic Age, CTWatch Quarterly, Volume 3, Number 3, August 2007.literature, pubmed, ontologySCR_008270(BioLit, RRID:SCR_008270)University of California at San Diego; California; USA DOI:10.1093/nar/gkn317Last checked downnif-0000-23836
Infectious Disease Biomarker DatabaseResource, data or information resource, databaseTHIS RESOURCE IS NO LONGER IN SERVICE, documented July 22, 2016. A database of biomarkers for diagnosis, detection, protection and characterization of infectious diseases. It provides information on pathogens and biomarkers, such as nucleic acids, proteins, carbohydrates, and immune epitopes. The site links to global news and life science journal search engines as well as provides links to tool functions for gene sequence and protein structure analyses.biomarker, diagnosis, detection, protection, characterization, infectious disease, modeling, simulationSCR_000737(Infectious Disease Biomarker Database, RRID:SCR_000737)Korea University; Seoul; South Korea PMID:17982173Last checked downnif-0000-03007http://biomarker.korea.ac.kr http://biomarker.korea.ac.kr/index_en.jsp
PAMGOResource, ontology, data or information resource, controlled vocabularyTHIS RESOURCE IS NO LONGER IN SERVICE, documented on June 10, 2016. A consortium that created universal descriptors to describe functionally similar gene products and their attributes across all organisms. In 2004, the PAMGO interest group joined the GO consortium to extend the GO to include terms describing various processes related to microbe-host interactions. The organization uses a controlled vocabulary to set a process in place to describe plant associated microbes and their interactions with their plant-hosts. These higher order terms can describe gene products of all types of symbionts (e.g. parasites, commensals, and mutualists), including prokaryotes and eukaryotes that associate with plant or animal hosts. This initiative is a multi-institutional collaborative effort to pool information and research in: the bacteria Dickeya dadantii, Pseudomonas syringae pv tomato and Agrobacterium tumefaciens, the fungus Magnaporthe grisea, the oomycetes Phytophthora sojae and Phytophthora ramorum, and the nematode Meloidogyne hapla.ontology, plant ontology, microbe-host, controlled vocabulary, symbiosis, parasite, mutualist, commensalSCR_000022(PAMGO, RRID:SCR_000022)Virginia Polytechnic Institute and State University; Virginia; USA NSFaffiliated with: Cornell University, New York, USA, North Carolina State University, North Carolina, USA, University of Wisconsin-Madison, Wisconsin, USA, Virginia Bioinformatics InstituteLast checked downnlx_92278
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