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on page 1 showing 20 out of 1,261 results

Cite this (1000 Fungal Genome Project, RRID:SCR_016463)

URL: https://genome.jgi.doe.gov/programs/fungi/1000fungalgenomes.jsf

Resource Type: Resource, topical portal, data access protocol, database, web service, organism-related portal, portal, software resource, project portal, data or information resource

Web application to provide genomic information for fungi. Includes sequenced fungal genomes, those in progress, and selected nominations. You can log in and nominate new species for genome sequencing in the families or only one reference genome if you can provide DNA/RNA samples for their sequencing. Used to explore the diversity of fungi important for energy and the environment.

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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 (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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    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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    4Peaks

Cite this (4Peaks, RRID:SCR_000015)

URL: http://nucleobytes.com/index.php/4peaks

Resource Type: Resource, software resource, software application

Software application for viewing and editing sequence trace files.

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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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    AAL

Cite this (AAL, RRID:SCR_003550)

URL: http://www.gin.cnrs.fr/spip.php?article216

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

Software for automated anatomical labeling of activations in SPM (Statistical Parametric Mapping) using a macroscopic anatomical parcellation of the MNI MRI single-subject brain. The software was used for an automated anatomical parcellation of the spatially normalized single-subject high-resolution T1 volume provided by the Montreal Neurological Institute (MNI) (D. L. Collins et al., 1998, Trans. Med. Imag. 17, 463468, PubMed). Using this parcellation method, three procedures to perform the automated anatomical labeling of functional studies were proposed: (1) labeling of an extremum defined by a set of coordinates, (2) percentage of voxels belonging to each of the anatomical volumes of interest (AVOI) intersected by a sphere centered by a set of coordinates, and (3) percentage of voxels belonging to each of the AVOI intersected by an activated cluster. An interface with the Statistical Parametric Mapping package is provided as a freeware to researchers of the neuroimaging community.

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    ABACAS

Cite this (ABACAS, RRID:SCR_015852)

URL: http://abacas.sourceforge.net

Resource Type: Resource, software resource, software application

Software that contiguates (align, order, orientate), visualizes and designs primers to close gaps on shotgun assembled contigs based on a reference sequence. ABACAS finds alignment positions and identifies syntenies of assembled contigs against the reference, then generates a pseudomolecule taking overlapping contigs and gaps into account.

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Cite this (ABCDreport, RRID:SCR_016030)

URL: https://github.com/ABCD-STUDY/ABCDreport

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

Software application as a simple system to review study progress. Used in ABCD study.

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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 Karma, RRID:SCR_014017)

URL: http://academickarma.org

Resource Type: Resource, service resource, production service resource

A peer review management system which encourages timely and high quality peer review by using a credit system. Reviewers complete reviews using a general webform on academickarma.org, and if that review is submited to an editor within ten days, the reviewer is awarded a certain amount of points (karma credits). The author and editor both receive the review. Editors can use Academic Karma to identify specialized reviewers for future reference. A reviewer's personal profile, which includes the amount of karma credits they've received, is connected to their ORCID account and publication record for an overview of the reviewer's work.

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    ACQ4

Cite this (ACQ4, RRID:SCR_016444)

URL: http://www.acq4.org/

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

Python-based software for experimental neurophysiology. It includes support for patch-clamp electrophysiology, multiphoton imaging, scanning laser photostimulation, and many other experimental techniques.

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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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    ADaCGH

Cite this (ADaCGH, RRID:SCR_010916)

URL: http://adacgh.bioinfo.cnio.es/

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

A web tool for the analysis of aCGH data sets. They focus on calling gains and losses and estimating the number of copy changes. Note: ADaCGH will continue being maintained, but is deprecated. Their new tool for CGH and CNV is WaviCGH, http://wavi.bioinfo.cnio.es/

  • 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 (Adult ADHD Self-Report Scale, RRID:SCR_003663)

URL: http://www.help4adhd.org/documents/adultadhdselfreportscale-asrs-v1-1.pdf

Resource Type: Resource, material resource, assessment test provider

A self reporting scale to assess if adult patients are suffering from symptoms of attention deficit-hyperactivity disorder (ADHD). The Symptom Checklist is an instrument consisting of the eighteen DSM-IV-TR criteria. Six of the eighteen questions were found to be the most predictive of symptoms consistent with ADHD. These six questions are the basis for the ASRS v1.1 Screener and are also Part A of the Symptom Checklist. Part B of the Symptom Checklist contains the remaining twelve questions.

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