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on page 1 showing 20 out of 126 results from 1 sources

Cite this (Adult Blood Lead Epidemiology and Surveillance Interactive Database, RRID:SCR_006915)

URL: http://wwwn.cdc.gov/niosh-survapps/ables/

Resource Type: Resource, data set, data or information resource

Interactive data set on lead exposure (Blood Lead Concentrations greater than or equal to 25 micrograms per deciliter) of adults in the United States. The data comes from laboratory-reported elevated blood lead levels. Recent research has led to increased concerns about the toxicity of lead at low doses. Reflecting this increased concern, the ABLES program updated its case definition for an elevated BLL to a blood lead concentration greater than or equal to 10 micrograms per deciliter in 2009. This new case definition has also been: (1) recommended by the Council of State and Territorial Epidemiologists in 2009; (2) included in CDC''s list of nationally notifiable conditions in 2010; and (3) adopted as the Healthy People 2020 Occupational Safety and Health Objective 7. Given this new case definition, NIOSH will update the ABLES Charts and Interactive Database to include lead exposures to blood lead level greater than or equal to 10 micrograms per deciliter in the near future.

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Cite this (Africa Centre for Health and Population Studies, RRID:SCR_008964)

URL: http://www.africacentre.ac.za/Default.aspx?tabid=69

Resource Type: Resource, data set, data or information resource

Longitudinal datasets of demographic, social, medical and economic information from a rural demographic in northern KwaZulu-Natal, South Africa where HIV prevalence is extremely high. The data may be filtered by demographics, years, or by individuals questionnaires. The datasets may be used by other researchers but the Africa Centre requests notification that anyone contact them when downloading their data. The datasets are provided in three formats: Stata11 .dta; tables in a MS-Access .accdb database; and worksheets in a MS-Excel .xlsx workbook. Datasets are generated approximately every six months containing information spanning the whole period of surveillance from 1/1/2000 to present.

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Cite this (Alaska Satellite Facility, RRID:SCR_003610)

URL: http://www.asf.alaska.edu/

Resource Type: Resource, service resource, data repository, storage service resource

Satellite facility that downlinks, processes, archives, and distributes remote-sensing data to scientific users around the world. Three major components: * Satellite Tracking Ground Station: Part of NASA?s Near Earth Network system of ground stations around the world. * Synthetic Aperture Radar Distributed Active Archive Center (SAR DAAC): ASF maintains the NASA archive of SAR data from a variety of satellites and aircraft, and provides these data and associated specialty support services to U.S. Government-approved researchers in support of NASA?s Earth Science Data and Information System project. * ASF Enterprise Center (ASFE): In support of UAF?s mission to be a student-centered research university, the ASF-E focuses on applications of remote-sensing data, specifically for UAF research. The ASF-E includes the GeoData Center (GDC), which provides data management and archive services for UAF principal investigators and maintains a variety of geophysical data collections in support of scientific research.

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Cite this (Alzheimer's disease ontology, RRID:SCR_010289)

URL: http://purl.bioontology.org/ontology/ADO

Resource Type: Resource, ontology, data or information resource, controlled vocabulary

An open, public ontology representing relevant knowledge on Alzheimer's disease.

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Cite this (AmiGO, RRID:SCR_002143)

URL: http://amigo.geneontology.org/

Resource Type: Resource, data analysis service, database, analysis service resource, software application, production service resource, service resource, software resource, data or information resource

Official Web-based tools for searching and browsing the Gene Ontology database, which consists of a controlled vocabulary of terms covering biological concepts, and a large number of genes or gene products whose attributes have been annotated using GO terms. It can be accessed online at the main installation or deployed locally. The Gene Ontology project is a major bioinformatics initiative with the aim of standardizing the representation of gene and gene product attributes across species and databases. AmiGO can be used to:
* search for a gene or gene product, or a list of gene or gene products, and view the GO term associations
* perform a sequence identity BLAST search and view the GO term associations for the genes or proteins returned
* search for GO terms and view the genes or gene products they are annotated to
* browse the GO ontology and view terms
* the slimmer tool can be used to map the granular annotations of the query set of genes to one or more high-level
* term enrichment tool is used to discover what a set of genes may have in common by examining annotations and finding significant shared GO terms.
* GOOSE is for advanced users who want to run custom SQL queries against the GO database.

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Cite this (Apache Hadoop, RRID:SCR_011879)

URL: http://hadoop.apache.org/

Resource Type: Resource, software resource, software toolkit

Software library providing a framework that allows for the distributed processing of large data sets across clusters of computers using simple programming models. It is designed to scale up from single servers to thousands of machines, each offering local computation and storage. Rather than rely on hardware to deliver high-availability, the library itself is designed to detect and handle failures at the application layer, so delivering a highly-available service on top of a cluster of computers, each of which may be prone to failures. The project includes these modules: * Hadoop Common: The common utilities that support the other Hadoop modules. * Hadoop Distributed File System (HDFS): A distributed file system that provides high-throughput access to application data. * Hadoop YARN: A framework for job scheduling and cluster resource management. * Hadoop MapReduce: A YARN-based system for parallel processing of large data sets.

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Cite this (Argo Genome Browser, RRID:SCR_011763)

URL: http://www.broadinstitute.org/annotation/argo/

Resource Type: Resource, software resource, data set, data or information resource

A tool for visualizing and manually annotating whole genomes that can be run as Applet or Webstart application as well as standalone application.

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Cite this (Arvados, RRID:SCR_002223)

URL: https://arvados.org/

Resource Type: Resource, service resource, data repository, storage service resource

A free and open source bioinformatics platform for storing, organizing, processing, and sharing genomic and other biomedical big data. The platform is designed to make it easier for bioinformaticians to develop analyses, developers to create genomic web applications and IT administers to manage large-scale compute and storage genomic resources. The platform is designed to run on top of cloud operating systems such as Amazon Web Services and OpenStack. Currently, there are implementations that work on AWS and Xen+Debian/Ubuntu. Functionally, Arvados has two major sets of capabilities: (a) data management and (b) compute management.

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Cite this (arXiv, RRID:SCR_006500)

URL: http://arxiv.org/

Resource Type: Resource, data or information resource, database

Electronic archive and distribution server for research articles providing open access to more than 850,000 e-prints in Physics, Mathematics, Computer Science, Quantitative Biology, Quantitative Finance and Statistics. Users can retrieve papers via the web interface. Registered authors may use the web interface to submit their articles to arXiv. Authors can also update their submissions if they choose, though previous versions remain available. Listings of newly submitted articles in areas of interest are available via the web interface, via RSS feeds, and by subscription to automatic email alerts.

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Cite this (ATandT Labs Research - Software Tools, RRID:SCR_002937)

URL: http://www.research.att.com/sw/tools/graphviz/

Resource Type: Resource, software resource, portal, data or information resource

Software tools that have been developed by AT&T Labs researchers. In addition to the software tools available through Open Source and Non-Commercial licenses as listed on this page, AT&T has additional software and technology solutions available for licensing. Please reference the individual project web pages for specific license agreements. If an available license agreement does not meet your needs, please contact attip (at) att.com for assistance with a customized license. Open Source Licenses * AST: Advanced Software Technologies Open Source Collection * Cdt: Container Data Types Library * ECharts: A state machine-based programming language * GGobi: Data visualization for high-dimensional data * GSDjVu/DjVuDigital: Ghostscript driver to convert PS and PDF files to DjVu files * Graphviz: Tools for viewing and interacting with graph diagrams * PADS: Processing Arbitrary Data Streams * Sfio: Portable library for performing I/O * UWIN: Unix on Windows 95 and NT Machines * Vcodex: Software package for data transformation * WSP: Web Scraping Proxy * Yoix: The Yoix Scripting Language and Interpreter * iPlots: Interactive graphics for data analysis in R * vmalloc: Region Memory Allocator Non-Commercial Binary Licenses * BoosTexter: A general purpose machine-learning program * Hancock: A language for processing large-scale data Non-Commercial Source Licenses * ASDT: The AT&T Statistical Dialog Toolkit (ASDT) * Hancock: A language for processing large-scale data

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Cite this (AutoDock Vina, RRID:SCR_011958)

URL: http://vina.scripps.edu/

Resource Type: Resource, software resource

An open-source program for doing molecular docking.

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Cite this (Bambus, RRID:SCR_005068)

URL: http://sourceforge.net/apps/mediawiki/amos/index.php?title=Bambus2

Resource Type: Resource, software resource

Software for scaffolding to address some of the challenges encountered when analyzing metagenomes. Scaffolding represents the task of ordering and orienting contigs by incorporating additional information about their relative placement along the genome. While most other scaffolders are closely tied to a specific assembly program, Bambus accepts the output from most current assemblers and provides the user with great flexibility in choosing the scaffolding parameters. In particular, Bambus is able to accept contig linking data other than specified by mate-pairs. Such sources of information include alignment to a reference genome (Bambus can directly use the output of MUMmer), physical mapping data, or information about gene synteny.

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Cite this (BeeBase, RRID:SCR_008966)

URL: http://hymenopteragenome.org/beebase/

Resource Type: Resource, data analysis service, production service resource, analysis service resource, data set, service resource, data or information resource

Gene sequences and genomes of Bombus terrestris, Bombus impatiens, Apis mellifera and three of its pathogens, that are discoverable and analyzed via genome browsers, blast search, and apollo annotation tool. The genomes of two additional species, Apis dorsata and A. florea are currently under analysis and will soon be incorporated.

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Cite this (BenchWise, RRID:SCR_006364)

URL: http://www.benchwise.org/

Resource Type: Resource, knowledge environment, data or information resource, database

Repository of peer reviews of antibodies to help scientists find the right tools fast. Researchers from schools including Stanford, Harvard, John Hopkins have contributed reviews of over 1500 antibodies. Most of these reviews contain experimental details that are hard to find in publications and yet crucial for the success of antibody usage. In addition, scientists are enabled to connect through knowledge of expertise, as members are required to use their real names and lab affiliations. BenchWise is currently open to a select list of leading research institutes and is completely free. Scientists waste over 100 hours a year on either bad antibodies or finding out the right antibody usage condition, despite the fact that someone, somewhere likely has already done the same. They want to solve this problem by enabling scientists to share their product usage knowledge. Antibody records that are documented in spreadsheets are also accepted and will be parsed into individual reviews and uploaded to save you time.

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Cite this (Binding and Expression Target Analysis, RRID:SCR_005396)

URL: http://cistrome.org/BETA/

Resource Type: Resource, software resource, analysis service resource, data analysis service, service resource, production service resource

A software package that integrates ChIP-seq of transcription factors or chromatin regulators with differential gene expression data to infer direct target genes. BETA has three functions: (1) to predict whether the factor has activating or repressive function; (2) to infer the factor''''s target genes; and (3) to identify the motif of the factor and its collaborators which might modulate the factor''''s activating or repressive function. BETA requires ~2GB RAM and 1h for the whole procedure. BETA may run on the web server at Cistrome or may be downloaded.

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Cite this (BioJS, RRID:SCR_003119)

URL: https://github.com/biojs

Resource Type: Resource, data processing software, software library, software application, data visualization software, software resource, software toolkit

An open source JavaScript library of components for visualisation of biological data on the web.

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Cite this (Bio-Linux, RRID:SCR_005399)

URL: http://nebc.nerc.ac.uk/tools/bio-linux/bio-linux-7-info

Resource Type: Resource, software resource

A free, fully featured, powerful, configurable and easy to maintain bioinformatics workstation that provides more than 500 bioinformatics programs on an Ubuntu Linux 12.04 LTS base. Install it or run it live. There is a graphical menu for bioinformatics programs, as well as easy access to the Bio-Linux bioinformatics documentation system and sample data useful for testing programs. You can run a Bio-Linux system on Amazon EC2 or other cloud computing architectures by using CloudBioLinux.

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Cite this (BioPortal, RRID:SCR_002713)

URL: http://bioportal.bioontology.org/

Resource Type: Resource, data repository, repository, service resource, storage service resource, ontology, controlled vocabulary, data or information resource

Open repository of biomedical ontologies that provides access via Web browsers and Web services to ontologies. It supports ontologies in OBO format, OWL, RDF, Rich Release Format (RRF), Protege frames, and LexGrid XML. Functionality includes the ability to browse, search and visualize ontologies as well as to comment on, and create mappings for ontologies. Any registered user can submit an ontology. The NCBO Annotator and NCBO Resource Index can also be accessed via BioPortal. Additional features: * Add Reviews: rate the ontology according to several criteria and describe your experience using the ontology. * Add Mappings: submit point-to-point mappings or upload bulk mappings created with external tools. Notification of new Mappings is RSS-enabled and Mappings can be browsed via BioPortal and accessed via Web services. * NCBO Annotator: Tool that tags free text with ontology terms. NCBO uses the Annotator to generate ontology annotations, creating an ontology index of these resources accessible via the NCBO Resource Index. The Annotator can be accessed through BioPortal or directly as a Web service. The annotation workflow is based on syntactic concept recognition (using the preferred name and synonyms for terms) and on a set of semantic expansion algorithms that leverage the ontology structure (e.g., is_a relations). * NCBO Resource Index: The NCBO Resource Index is a system for ontology based annotation and indexing of biomedical data; the key functionality of this system is to enable users to locate biomedical data linked via ontology terms. A set of annotations is generated automatically, using the NCBO Annotator, and presented in BioPortal. This service uses a concept recognizer (developed by the National Center for Integrative Biomedical Informatics, University of Michigan) to produce a set of annotations and expand them using ontology is_a relations. * Web services: Documentation on all Web services and example code is available at: BioPortal Web services.

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Cite this (BIRDSUITE, RRID:SCR_001794)

URL: https://www.broadinstitute.org/birdsuite/birdsuite

Resource Type: Resource, software resource, software application

Open-source set of tools to detect and report SNP genotypes, common Copy-Number Polymorphisms (CNPs), and novel, rare, or de novo CNVs in samples processed with the Affymetrix platform. While most of the components of the suite can be run individually (for instance, to only do SNP genotyping), the Birdsuite is especially intended for integrated analysis of SNPs and CNVs.

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Cite this (Bisulfighter, RRID:SCR_005440)

URL: https://code.google.com/p/bisulfighter/

Resource Type: Resource, software resource

A software package for detecting methylated cytosines (mCs) and differentially methylated regions (DMRs) from bisulfite sequencing data.

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