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on page 1 showing 20 out of 925 results

Cite this (1000 Genomes: A Deep Catalog of Human Genetic Variation, RRID:SCR_006828)

URL: http://www.1000genomes.org/

Resource Type: Resource, organization portal, database, consortium, data set, portal, data or information resource

International collaboration producing an extensive public catalog of human genetic variation, including SNPs and structural variants, and their haplotype contexts, in an effort to provide a foundation for investigating the relationship between genotype and phenotype. The genomes of about 2500 unidentified people from about 25 populations around the world were sequenced using next-generation sequencing technologies. Redundant sequencing on various platforms and by different groups of scientists of the same samples can be compared. The results of the study are freely and publicly accessible to researchers worldwide. The consortium identified the following populations whose DNA will be sequenced: Yoruba in Ibadan, Nigeria; Japanese in Tokyo; Chinese in Beijing; Utah residents with ancestry from northern and western Europe; Luhya in Webuye, Kenya; Maasai in Kinyawa, Kenya; Toscani in Italy; Gujarati Indians in Houston; Chinese in metropolitan Denver; people of Mexican ancestry in Los Angeles; and people of African ancestry in the southwestern United States. The goal Project is to find most genetic variants that have frequencies of at least 1% in the populations studied. Sequencing is still too expensive to deeply sequence the many samples being studied for this project. However, any particular region of the genome generally contains a limited number of haplotypes. Data can be combined across many samples to allow efficient detection of most of the variants in a region. The Project currently plans to sequence each sample to about 4X coverage; at this depth sequencing cannot provide the complete genotype of each sample, but should allow the detection of most variants with frequencies as low as 1%. Combining the data from 2500 samples should allow highly accurate estimation (imputation) of the variants and genotypes for each sample that were not seen directly by the light sequencing. All samples from the 1000 genomes are available as lymphoblastoid cell lines (LCLs) and LCL derived DNA from the Coriell Cell Repository as part of the NHGRI Catalog. The sequence and alignment data generated by the 1000genomes project is made available as quickly as possible via their mirrored ftp sites. ftp://ftp.1000genomes.ebi.ac.uk ftp://ftp-trace.ncbi.nlm.nih.gov/1000genomes

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Cite this (1DegreeBio, RRID:SCR_011994)

URL: http://1degreebio.org/

Resource Type: Resource, software resource

A registry which provides links and reviews for material resources such as reagents, equipment, digital tools, and providers, as well as the companies that sell them. Users can search for specific materials or search by vendor, product, or service type.

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Cite this (2100 Expert Software, RRID:SCR_014466)

URL: http://www.genomics.agilent.com/en/product.jsp?cid=AG-PT-106&tabId=AG-PR-1002&_requestid=815672

Resource Type: Resource, data analytics software, software application, software resource

A software for analyzing digital assay data. The software performs RNA quality control, comparison between multiple chips, smear analysis, and data export in multiple formats.

  • From Current Category

    3dsvm

Cite this (3dsvm, RRID:SCR_014083)

URL: http://www.nitrc.org/projects/afni_3dsvm/

Resource Type: Resource, software resource, image analysis software, data processing software, software application

A command-line program and plugin for AFNI built around SVM-Light. It performs support vector machine (SVM) analysis on fMRI data and runs on Unix+X11+Motif systems, including SGI, Solaris, Linux, and Mac OS X.

  • From Current Category

Cite this (60-Second Mind, RRID:SCR_000925)

URL: http://www.scientificamerican.com/podcast/60-second-mind/

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

A podcast of neuroscience news in minute-intervals from the Scientific American. New episodes become available every Saturday.

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Cite this (ABCDE Format, RRID:SCR_002428)

URL: http://www.w3.org/wiki/images/5/51/HCLSIG$$SWANSIOC$$Actions$$RhetoricalStructure$$models$$abcde$abcde_example.htm

Resource Type: Resource, software resource, software application, text-mining software

Proposed format for papers to be machine-readable for computers and wikis. The goal is to make mining, integration, and consumption of published information by semantic browsers and wikis easier.

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    AbMiner

Cite this (AbMiner, RRID:SCR_014544)

URL: https://discover.nci.nih.gov/abminer/

Resource Type: Resource, data or information resource, database

A tool that allows users to search for appropriate, commercially available antibodies for research purposes, and to match each antibody to its respective genomic identifiers. The antibodies are screened by Western blot and the results are listed on AbMiner. AbMiner also includes the diluitons used and vendor information for all antibodies. Users can conduct general or advanced searches and browse antibodies by gene.

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Cite this (AbsCN-seq, RRID:SCR_006409)

URL: http://bioinformatics.oxfordjournals.org/content/early/2014/01/02/bioinformatics.btt759.abstract?sid=e62f3c2b-26dc-428b-ba24-99e92a277d77

Resource Type: Resource, software resource

Statistical software to estimate tumor purity, ploidy and absolute copy numbers from next generation sequencing data.

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Cite this (ABSORB: Atlas Building by Self-Organized Registration and Bundling, RRID:SCR_007018)

URL: http://bric.unc.edu/ideagroup/free-softwares/ABSORB/

Resource Type: Resource, image analysis software, data processing software, source code, software application, software resource, registration software

This software package implements an algorithm for effective groupwise registration. The required input is a set of 3D MR intensity images (in Analyze format with paired .hdr and .img files) with a text file (.txt) listing all header file (.hdr) names. The output is the set of registered images together with the corresponding dense deformation fields. This software has been tested on Windows XP (32-bit) and Linux (64-bit, kernel version 2.6.18-194.el5). The images should be pre-processed before applying ABSORB: * All brain MR images used as inputs to ABSORB should be in the same situation (e.g., skull-stripped or not, cerebellum removed or not, etc.). * The input images should be in Analyze format with paired header and image files. This software was developed in IDEA group in UNC-Chapel Hill.

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Cite this (AbundanceBin, RRID:SCR_004648)

URL: http://omics.informatics.indiana.edu/AbundanceBin/

Resource Type: Resource, software resource

An abundance-based software tool for binning metagenomic sequences, such that the reads classified in a bin belong to species of identical or very similar abundances. AbundanceBin also gives estimations of species abundances and their genome sizes -two important characteristic parameters for a microbial community.

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Cite this (Academic Joy, RRID:SCR_013820)

URL: http://www.academicjoy.net/index.html

Resource Type: Resource, software resource, collaboration tool, data or information resource

A collaboration tool that aims to spread the stories and advice of researchers in the sciences, engineering, and the humanities. Researchers can share and collaborate on ideas, find resources and tools, and read the stories of other researchers.

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Cite this (Academic Seismic Portal at UTIG, RRID:SCR_000403)

URL: http://www.ig.utexas.edu/sdc/

Resource Type: Resource, service resource, data or information resource, data repository, storage service resource, database

Database of processed seismic reflection / refraction data providing access to metadata, SEG-Y files, navigation files, seismic profile images, processing histories and more. The main features of the web site include a geographic search engine using Google Plugins, a metadata search engine, and metadata pages for the various seismic programs. Metadata are uploaded into mySQL, a public-domain SQL server, and then PHP scripts query the metadata and directories, creating web pages, displaying images, and providing ftp links. The minimum requirements for data submission are: * unrestricted access to the navigation and small raster image (about 300 x 600 pixels) * file format is SEG-Y (they can help with this) * information relating geographic location to the traces in the file (this is often a big part of what they create) They also need basic descriptive information (metadata) about acquisition, navigation geometry, processing sequence and provenance (and pass some of our consistency tests). The submitted metadata is naturally highly variable but could include cruise reports, processing reports, important citations, etc.

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    AcroMine

Cite this (AcroMine, RRID:SCR_013196)

URL: http://www.nactem.ac.uk/software/acromine/

Resource Type: Resource, web service, software resource, service resource, data access protocol

An acronym dictionary which can be used to find distinct expanded forms of acronyms from MEDLINE. This freely available service can be used through your browser or by integrating it with your applications using the ReSTful service. Acromine identifies abbreviation definitions by assuming a word sequence co-occurring frequently with a parenthetical expression to be a potential expanded form. Applied to the whole MEDLINE (9,635,599 abstracts), the implemented system extracted 68,007 abbreviation candidates and recognized 467,402 expanded forms. The current Acromine achieves 99% precision and 82-95% recall on our evaluation corpus that roughly emulates the whole MEDLINE.

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Cite this (ACS ChemWorx, RRID:SCR_013785)

URL: https://hp.acschemworx.acs.org

Resource Type: Resource, software resource

A web application which provides tools to share references and generate bibliographies with colleagues, organize and access references, and track metrics for ACS articles. Articles are automatically synced to user libraries and are accessible from multiple devices.

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Cite this (ADA GENNID Study, RRID:SCR_000527)

URL: http://ccr.coriell.org/Sections/Collections/ADA/?SsId=12

Resource Type: Resource, data set, biomaterial supply resource, data or information resource, material resource, cell repository

The purpose of the American Diabetes Association (ADA), GENNID Study (Genetics of non-insulin dependent diabetes mellitus, NIDDM) is to establish a national database and cell repository consisting of information and genetic material from families with well-documented NIDDM. The GENNID Study will provide investigators with the information and samples necessary to conduct genetic linkage studies and locate the genes for NIDDM. Non-Hispanic white, Hispanic, African-American, and Japanese-American multiplex NIDDM families, with a minimum of one affected sib-pair, are being collected by the eight Harold Rifkin Family Acquisition Centers. Detailed family and medical histories are obtained from all participants. Family members with diabetes have fasting blood samples drawn, while nondiabetic family members have an oral glucose tolerance test and, when possible, insulin sensitivity and insulin secretion measurements by frequently sampled intravenous glucose tolerance testing or euglycemic insulin clamp. Lymphoblastoid cell lines are established for all participants. DNA samples and extensive phenotypic data are available from the American Diabetes Association's GENNID study (Genetics of NIDDM). GENNID has collected detailed family histories and a broad array of data on 170 large pedigrees, all of which contain at least one affected sib pair, with a total of 650 affected individuals and approximately 1,200 total subjects. Included are approximately 65 Caucasian, 60 Hispanic, 25 African American, and 20 Japanese American pedigrees. In addition, GENNID also contains DNA and data on 1,000 additional affected sib pairs in each of three groups, African American, Caucasian, and Hispanic. DNA and phenotypic data, including race, gender and age, are available for all members of the pedigrees. The data set includes multiple metabolic factors, including carbohydrate metabolism, lipid metabolism, and body size measures, as well as lifestyle variables obtained by questionnaire (e.g., employment, exercise, etc.). The GENNID resource is ideally suited for genetic linkage and association studies as well as SNP discovery and typing. Investigators interested in obtaining the DNA samples and/or data will need to submit a proposal to the Association that addresses the genetics of type 2 diabetes.

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Cite this (AD Clinical Trials Database, RRID:SCR_005863)

URL: http://www.alzheimers.org/clinicaltrials/

Resource Type: Resource, data or information resource, clinical database, database

A database of Alzheimer's disease and dementia clinical trials currently in progress at centers throughout the U.S.

  • From Current Category

Cite this (ADHD-200 Preprocessed Data, RRID:SCR_000576)

URL: http://neurobureau.projects.nitrc.org/ADHD200/Introduction.html

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

Preprocessed versions of the ADHD-200 Global Competition data including both preprocessed versions of structural and functional datasets previously made available by the ADHD-200 consortium, as well as initial standard subject-level analyses. The ADHD-200 Sample is pleased to announce the unrestricted public release of 776 resting-state fMRI and anatomical datasets aggregated across 8 independent imaging sites, 491 of which were obtained from typically developing individuals and 285 in children and adolescents with ADHD (ages: 7-21 years old). Accompanying phenotypic information includes: diagnostic status, dimensional ADHD symptom measures, age, sex, intelligence quotient (IQ) and lifetime medication status. Preliminary quality control assessments (usable vs. questionable) based upon visual timeseries inspection are included for all resting state fMRI scans. In accordance with HIPAA guidelines and 1000 Functional Connectomes Project protocols, all datasets are anonymous, with no protected health information included. They hope this release will open collaborative possibilities and contributions from researchers not traditionally addressing brain data so for those whose specialties lay outside of MRI and fMRI data processing, the competition is now one step easier to join. The preprocessed data is being made freely available through efforts of The Neuro Bureau as well as the ADHD-200 consortium. They ask that you acknowledge both of these organizations in any publications (conference, journal, etc.) that make use of this data. None of the preprocessing would be possible without the freely available imaging analysis packages, so please also acknowledge the relevant packages and resources as well as any other specific release related acknowledgements. You must be logged into NITRC to download the ADHD-200 datasets, http://www.nitrc.org/projects/neurobureau

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Cite this (Advanced Image Data Analyzer, RRID:SCR_014440)

URL: https://www.raytest.com/bio-imaging/evaluation-software/aida-biopackage.html

Resource Type: Resource, software resource, image analysis software, data processing software, software application

Bioimaging analysis software used to acquire quantitative and qualitative data from various types of biological samples. The software provides a variety of image modification features, including contrast optimizing, image printing, 1-dimensional densitometry, fragment length and molecular weight determination, and 2-D densitometry.

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Cite this (Advanced Neuroscience Imaging Research Laboratory Software Packages, RRID:SCR_002926)

URL: http://www.fmri.wfubmc.edu/cms/software

Resource Type: Resource, software resource, software toolkit

Research group based in the Department of Radiology of Wake Forest University School of Medicine devoted to the application of novel image analysis methods to research studies. The ANSIR lab also maintains a fully-automated functional and structural image processing pipeline supporting the image storage and analysis needs of a variety of scientists and imaging studies at Wake Forest. Software packages and toolkits are currently available for download from the ANSIR Laboratory, including: WFU Biological Parametric Mapping Toolbox, WFU_PickAtlas, and Adaptive Staircase Procedure for E-Prime.

  • From Current Category

    AffinDB

Cite this (AffinDB, RRID:SCR_001690)

URL: http://pc1664.pharmazie.uni-marburg.de/affinity/

Resource Type: Resource, data or information resource, database

Database of affinity data for protein-ligand complexes of the Protein Data Bank (PDB) providing direct and free access to the experimental affinity of a given complex structure. Affinity data are exclusively obtained from the scientific literature. As of Thursday, May 01st, 2014, AffinDB contains 748 affinity values covering 474 different PDB complexes. More than one affinity value may be associated with a single PDB complex, which is most frequently due to multiple references reporting affinity data for the same complex. AffinDB provides access to data in three different forms:
# Summary information for PDB entry
# Affinity information window
# Tabular reports

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