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Cite this ((at)Note, RRID:SCR_005342)

URL: http://darwin.di.uminho.pt/anote2/wiki/index.php/Main_Page

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

THIS RESOURCE IS NO LONGER AVAILABLE. Documented September 18, 2017

Text Mining platform that copes with major Information Retrieval and Information Extraction tasks and promotes multi-disciplinary research. It aims to provide support to three different usage roles: biologists, text miners and application developers. The workbench supports the retrieval, processing and annotation of documents as well as their analysis at different levels.

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Cite this (100, 000 Genomes Project, RRID:SCR_010502)

URL: http://www.genomicsengland.co.uk/the-100000-genomes-project/

Resource Type: Resource, data or information resource, database

The project will focus on patients with a rare disease and their families and patients with cancer. The first samples for sequencing are being taken from patients living in England with discussions taking place with Scotland, Wales and Northern Ireland about potential future involvement. Genomics England, a company wholly owned and funded by the Department of Health, was set up to deliver this flagship project which will sequence 100,000 whole genomes from NHS patients by 2017. Its four main aims are; to create an ethical and transparent programme based on consent; to bring benefit to patients and set up a genomic medicine service for the NHS; to enable new scientific discovery and medical insights; and to kick start the development of a UK genomics industry.

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Cite this (1000 Functional Connectomes Project, RRID:SCR_005361)

URL: http://fcon_1000.projects.nitrc.org/

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

Database of resting state fMRI (R-fMRI) datasets collected from sites around the world. It demonstrates open sharing of R-fMRI data and aims to emphasize the aggregation and sharing of well-phenotyped datasets.

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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 (1000 Genomes Project and AWS, RRID:SCR_008801)

URL: http://aws.amazon.com/1000genomes/

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

A dataset containing the full genomic sequence of 1,700 individuals, freely available for research use. The 1000 Genomes Project is an international research effort coordinated by a consortium of 75 companies and organizations to establish the most detailed catalogue of human genetic variation. The project has grown to 200 terabytes of genomic data including DNA sequenced from more than 1,700 individuals that researchers can now access on AWS for use in disease research free of charge. The dataset containing the full genomic sequence of 1,700 individuals is now available to all via Amazon S3. The data can be found at: http://s3.amazonaws.com/1000genomes The 1000 Genomes Project aims to include the genomes of more than 2,662 individuals from 26 populations around the world, and the NIH will continue to add the remaining genome samples to the data collection this year. Public Data Sets on AWS provide a centralized repository of public data hosted on Amazon Simple Storage Service (Amazon S3). The data can be seamlessly accessed from AWS services such Amazon Elastic Compute Cloud (Amazon EC2) and Amazon Elastic MapReduce (Amazon EMR), which provide organizations with the highly scalable compute resources needed to take advantage of these large data collections. AWS is storing the public data sets at no charge to the community. Researchers pay only for the additional AWS resources they need for further processing or analysis of the data. All 200 TB of the latest 1000 Genomes Project data is available in a publicly available Amazon S3 bucket. You can access the data via simple HTTP requests, or take advantage of the AWS SDKs in languages such as Ruby, Java, Python, .NET and PHP. Researchers can use the Amazon EC2 utility computing service to dive into this data without the usual capital investment required to work with data at this scale. AWS also provides a number of orchestration and automation services to help teams make their research available to others to remix and reuse. Making the data available via a bucket in Amazon S3 also means that customers can crunch the information using Hadoop via Amazon Elastic MapReduce, and take advantage of the growing collection of tools for running bioinformatics job flows, such as CloudBurst and Crossbow.

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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 (2009 Grantees Meeting, RRID:SCR_014081)

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

Resource Type: Resource, meeting resource, training resource

This project is meant for planning the NITRC Grantee meetings. The meetings introduce NITRC participants to one another, promote discussion of common interests, and identify opportunities for collaboration and interoperability. The 2009 meeting for NITRC enhancement grant awardees was held on June 18, 2009 (8:00 AM - 5:00 PM) in San Francisco at the San Francisco Marriott.

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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.

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Cite this (2200 TapeStation Instrument, RRID:SCR_014994)

URL: http://www.genomics.agilent.com/en/TapeStation-System/2200-TapeStation-Instrument/?cid=AG-PT-181&tabId=AG-PR-1004

Resource Type: Resource

Hardware system which automates RNA, DNA, and protein sample QC, including sample loading, separation, and imaging.

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Cite this (2DMAP, RRID:SCR_009036)

URL: http://www.genlink.wustl.edu/software

Resource Type: Resource, software resource, software application

THIS RESOURCE IS NO LONGER IN SERVCE, documented September 22, 2016. Software application for constructing 2-d crossover-based map.

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Cite this (2LD, RRID:SCR_000826)

URL: https://github.com/gaow/genetic-analysis-software/blob/master/pages/2LD.md

Resource Type: Resource, software resource, software application

THIS RESOURCE IS NO LONGER IN SERVCE, documented September 22, 2016. Software program for calculating linkage disequilibrium (LD) measures between two polymorphic markers.

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Cite this (2SNP, RRID:SCR_009038)

URL: https://github.com/gaow/genetic-analysis-software/blob/master/pages/2SNP.md

Resource Type: Resource, software resource, software application

THIS RESOURCE IS NO LONGER IN SERVCE, documented September 22, 2016. An algorithm resource for scalable phasing method for trios and unrelated individuals.

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Cite this (3DBar, RRID:SCR_008896)

URL: http://www.3dbar.org

Resource Type: Resource, production service resource, analysis service resource, reference atlas, software resource, service resource, atlas, data or information resource

Software package for reconstructing three-dimensional models of brain structures from 2-D delineations using a customizable and reproducible workflow. 3dBAR also works as an on-line service (http://service.3dbar.org) offering a variety of functions for the hosted datasets: * downloading reconstructions of desired brain structures in predefined quality levels in various supported formats as well as created using customizable settings, * previewing models as bitmap thumbnails and (for webGL enabled browsers) interactive manipulation (zooming, rotating, etc.) of the structures, * downloading slides from available datasets as SVG drawings. 3dBAR service can also be used by other websites or applications to enhance their functionality. * Operating System: Linux * Programming Language: Python * Supported Data Format: NIfTI-1, Other Format, VRML

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    3D Brain

Cite this (3D Brain, RRID:SCR_013138)

URL: https://itunes.apple.com/be/app/3d-brain/id331399332?mt=8

Resource Type: Resource, software application, narrative resource, training material, software resource, mobile app, data or information resource

iPhone and iPad app that provides a good overview of the brain and its structures allowing you to rotate and zoom around 29 interactive structures with your touch screen. Discover how each brain region functions, what happens when it is injured, and how it is involved in mental illness. Each detailed structure comes with information on functions, disorders, brain damage, case studies, and links to modern research. Compatible with iPhone, iPod touch and iPad. Requires iOS 3.0 or later.

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Cite this (3D DTI Atlas of the Rat Brain In Postnatal Day 5 14 and Adulthood, RRID:SCR_009437)

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

Resource Type: Resource, atlas, reference atlas, data or information resource

3D DTI anatomical rat brain atlases have been created by the UNC- Chapel Hill Department of Psychiatry and the CAMID research collaboration. There are three age groups, postnatal day 5, postnatal day 14, and postnatal day 72. The subjects were Sprague-Dawley rats that were controls in a study on cocaine abuse and development. The P5 and P14 templates were made from scans of twenty rats each (ten female, ten male); the P72, from six females. The individual cases have been resampled to isotropic resolution, manually skull-stripped, and deformably registered via an unbiased atlas building method to create a template for each age group. Each template was then manually segmented using itk-SNAP software. Each atlas is made up of 3 files, a template image, a segmentation, and a label file.

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Cite this (3D Facial Norms Database, RRID:SCR_005991)

URL: https://www.facebase.org/facial_norms/

Resource Type: Resource, data or information resource, database

Database of high-quality craniofacial anthropometric normative data for the research and clinical community based on digital stereophotogrammetry. Unlike traditional craniofacial normative datasets that are limited to measures obtained with handheld calipers and tape measurers, the anthropometric data provided here are based on digital stereophotogrammetry, a method of 3D surface imaging ideally suited for capturing human facial surface morphology. Also unlike more traditional normative craniofacial resources, the 3D Facial Norms Database allows users to interact with data via an intuitive graphical interface and - given proper credentials - gain access to individual-level data, allowing users to perform their own analyses.

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Cite this (3D-footprint, RRID:SCR_015713)

URL: http://floresta.eead.csic.es/3dfootprint

Resource Type: Resource, data or information resource, database

Database of DNA-binding protein structures that is updated with Protein Data Bank complexes. It provides structure-based binding specificities and sequence logos, classification and clusters of protein-DNA interfaces, and downloads/stats.

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Cite this (3D-Genomics Database, RRID:SCR_007430)

URL: http://www.sbg.bio.ic.ac.uk/3dgenomics/searchpage1.cgi

Resource Type: Resource, data or information resource, database

THIS RESOURCE IS NO LONGER IN SERVICE, documented August 29, 2016. Database containing structural annotations for the proteomes of just under 100 organisms. Using data derived from public databases of translated genomic sequences, representatives from the major branches of Life are included: Prokaryota, Eukaryota and Archaea. The annotations stored in the database may be accessed in a number of ways. The help page provides information on how to access the database. 3D-GENOMICS is now part of a larger project, called e-Protein. The project brings together similar databases at three sites: Imperial College London , University College London and the European Bioinformatics Institute . e-Protein''s mission statement is To provide a fully automated distributed pipeline for large-scale structural and functional annotation of all major proteomes via the use of cutting-edge computer GRID technologies. The following databases are incorporated: NRprot, SCOP, ASTRAL, PFAM, Prosite, taxonomy, COG The following eukaryotic genomes are incorporated: Anopheles gambiae, protein sequences from the mosquito genome; Arabidopsis thaliana, protein sequences from the Arabidopsis genome; Caenorhabditis briggsae, protein sequences from the C.briggsae genome; Caenorhabditis elegans protein sequences from the worm genome; Ciona intestinalis protein sequences from the sea squirt genome; Danio rerio protein sequences from the zebrafish genome; Drosophila melanogaster protein sequences from the fruitfly genome; Encephalitozoon cuniculi protein sequences from the E.cuniculi genome; Fugu rubripes protein sequences from the pufferfish genome; Guillardia theta protein sequences from the G.theta genome; Homo sapiens protein sequences from the human genome; Mus musculus protein sequences from the mouse genome; Neurospora crassa protein sequences from the N.crassa genome; Oryza sativa protein sequences from the rice genome; Plasmodium falciparum protein sequences from the P.falciparum genome; Rattus norvegicus protein sequences from the rat genome; Saccharomyces cerevisiae protein sequences from the yeast genome; Schizosaccharomyces pombe protein sequences from the yeast genome

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Cite this (3DID: 3D Interacting Domains, RRID:SCR_007425)

URL: http://3did.irbbarcelona.org

Resource Type: Resource, data or information resource, database

A database of domain-domain and peptide-mediated interactions of known 3D structures. The database of 3D Interaction Domains (3did) is a collection of domain-domain and domain-peptide interactions for which high-resolution three-dimensional structures are known. 3did exploits structural information to provide critical molecular details necessary for understanding how these interactions occur. It also offers an overview of how similar in structure are interactions between different members of the same protein family. The database also contains GO-based functional annotations and interactions between yeast proteins from large-scale interaction discovery studies. Sponsors: This resource is partially supported by the Spanish Ministerio de Educacin y Ciencia (PSE-010000-2007-1 and BIO2007-62426) and the 3D-Repertoire from the European Commission under FP6 contract LSHG-CT-2005-512028. Keywords: Database, Domain, Peptide, Protein, 3D structure, Interaction, Dimentional, Structure, Molecular, Functional, Annotation, Interaction, Yeast, Study, Research,

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Cite this (3D Interactive Chemical Shift Imaging, RRID:SCR_002581)

URL: https://www.nitrc.org/projects/threedicsi/

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

A user-friendly and comprehensive software program for multi-dimensional CSI data visualization, spectral processing, localization, quantification and multi-variate analysis.

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