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on page 1 showing 20 out of 455 results

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 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 (3D Ribosomal Modification Maps Database, RRID:SCR_003097)

URL: http://people.biochem.umass.edu/fournierlab/3dmodmap/

Resource Type: Resource, data or information resource, database

Database of maps showing the sites of modified rRNA nucleotides. Access to the rRNA sequences, secondary structures both with modification sites indicated, 3D modification maps and the supporting tables of equivalent nucleotides for rRNA from model organisms including yeast, arabidopsis, e. coli and human is provided. This database complements the Yeast snoRNA Database at UMass-Amherst and relies on linking to some content from that database, as well as to others by colleagues in related fields. Therefore, please be very cognizant as to the source when citing information obtained herein. Locations of modified rRNA nucleotides within the 3D structure of the ribosome.

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    Abgent

Cite this (Abgent, RRID:SCR_008393)

URL: http://abgent.com

Resource Type: Resource, antibody supplier, core facility, service resource, access service resource, reagent supplier, material resource

An antibody supplier and core facility.

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    AceView

Cite this (AceView, RRID:SCR_002277)

URL: http://www.ncbi.nlm.nih.gov/ieb/research/acembly/

Resource Type: Resource, data or information resource, database

THIS RESOURCE IS NO LONGER SUPPORTED, documented August 29, 2016. AceView offers an integrated view of the human, nematode and Arabidopsis genes reconstructed by co-alignment of all publicly available mRNAs and ESTs on the genome sequence. Our goals are to offer a reliable up-to-date resource on the genes and their functions and to stimulate further validating experiments at the bench. AceView provides a curated, comprehensive and non-redundant sequence representation of all public mRNA sequences (mRNAs from GenBank or RefSeq, and single pass cDNA sequences from dbEST and Trace). These experimental cDNA sequences are first co-aligned on the genome then clustered into a minimal number of alternative transcript variants and grouped into genes. Using exhaustively and with high quality standards the available cDNA sequences evidences the beauty and complexity of mammals' transcriptome, and the relative simplicity of the nematode and plant transcriptomes. Genes are classified according to their inferred coding potential; many presumably non-coding genes are discovered. Genes are named by Entrez Gene names when available, else by AceView gene names, stable from release to release. Alternative features (promoters, introns and exons, polyadenylation signals) and coding potential, including motifs, domains, and homologies are annotated in depth; tissues where expression has been observed are listed in order of representation; diseases, phenotypes, pathways, functions, localization or interactions are annotated by mining selected sources, in particular PubMed, GAD and Entrez Gene, and also by performing manual annotation, especially in the worm. In this way, both the anatomy and physiology of the experimentally cDNA supported human, mouse and nematode genes are thoroughly annotated. Our goals are to offer an up-to-date resource on the genes, in the hope to stimulate further experiments at the bench, or to help medical research. AceView can be queried by meaningful words or groups of words as well as by most standard identifiers, such as gene names, Entrez Gene ID, UniGene ID, GenBank accessions.

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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 (ADHD-200 Sample, RRID:SCR_005358)

URL: http://fcon_1000.projects.nitrc.org/indi/adhd200/index.html#

Resource Type: Resource, disease-related portal, data set, topical portal, portal, data or information resource

A grassroots initiative dedicated to accelerating the scientific community''''s understanding of the neural basis of ADHD through the implementation of open data-sharing and discovery-based science. They believe that a community-wide effort focused on advancing functional and structural imaging examinations of the developing brain will accelerate the rate at which neuroscience can inform clinical practice. The ADHD-200 Global Competition invited participants to develop diagnostic classification tools for ADHD diagnosis based on functional and structural magnetic resonance imaging (MRI) of the brain. Applying their tools, participants provided diagnostic labels for previously unlabeled datasets. The competition assessed diagnostic accuracy of each submission and invited research papers describing novel, neuroscientific ideas related to ADHD diagnosis. Twenty-one international teams, from a mix of disciplines, including statistics, mathematics, and computer science, submitted diagnostic labels, with some trying their hand at imaging analysis and psychiatric diagnosis for the first time. The data for the competition was provided by the ADHD-200 Consortium. Consortium members from institutions around the world provided de-identified, HIPAA compliant imaging datasets from almost 800 children with and without ADHD. A phenotypic file including all of the test set subjects and their diagnostic codes can be downloaded. Winner is presented. The ADHD-200 consortium included: * Brown University, Providence, RI, USA (Brown) * The Kennedy Krieger Institute, Baltimore, MD, USA (KKI) * The Donders Institute, Nijmegen, The Netherlands (NeuroImage) * New York University Medical Center, New York, NY, USA (NYU) * Oregon Health and Science University, Portland, OR, USA (OHSU) * Peking University, Beijing, P.R.China (Peking 1-3) * The University of Pittsburgh, Pittsburgh, PA, USA (Pittsburgh) * Washington University in St. Louis, St. Louis, MO, USA (WashU)

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Cite this (ADMET Predictor, RRID:SCR_014903)

URL: http://www.simulations-plus.com/Products.aspx?pID=13

Resource Type: Resource, software resource, software application

Software program for advanced predictive modeling of Absorption, Distribution, Metabolism, Elimination, and Toxicity (ADMET) properties of chemical substances in the human body. ADMET Predictor can estimate a number of vital ADMET properties (listed below) from molecular structures and build predictive models of new properties from user's data.

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    AFIDs

Cite this (AFIDs, RRID:SCR_016623)

URL: https://github.com/jclauneuro/afids

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

Software tool as an open framework for evaluating correspondence between magnetic resonance images of the human brain using fiducial placement.

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Cite this (Aging Dementia and Traumatic Brain Injury Study, RRID:SCR_014554)

URL: http://aging.brain-map.org/

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

The Aging, Dementia and Traumatic Brain Injury Study is a detailed neuropathologic, molecular and transcriptomic characterization of brains of control and TBI exposure cases from a unique aged population-based cohort from the Adult Changes in Thought (ACT) study. The study contains six data sets: histology and immunohistochemistry, in situ hybridization, rna-seq, protein quantification by luminex, isoprostane quantification, and specimen metadata.

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    AGRICOLA

Cite this (AGRICOLA, RRID:SCR_008158)

URL: http://agricola.nal.usda.gov/

Resource Type: Resource, data or information resource, database

A database, catalog and index to the collections of the National Agricultural Library, as well as a primary public source for world-wide access to agricultural information. This database resource covers materials in all formats and periods, including printed works from as far back as the 15th century. AGRICOLA is a bibliographic database of citations to the agricultural literature created by the National Agricultural Library and its cooperators. The records describe publications and resources encompassing all aspects of agriculture and allied disciplines, including animal and veterinary sciences, entomology, plant sciences, forestry, aquaculture and fisheries, farming and farming systems, agricultural economics, extension and education, food and human nutrition, and earth and environmental sciences. Although the NAL Catalog (AGRICOLA) does not contain the text of the materials it cites, thousands of its records are linked to full-text documents online, with new links added daily. The NAL Catalog (AGRICOLA) is organized into two bibliographic data sets: *The NAL Online Public Access Catalog (AGRICOLA NAL) contains citations to books, audiovisuals, serials, and other materials, most of which are in the Library''s collection. (The Catalog does contain some records for items not held at NAL.) *The Article Citation Database (AGRICOLA IND) includes citations, many with abstracts, to journal articles (see Journals Indexed in AGRICOLA), book chapters, reports, and reprints, selected primarily from the materials found in the NAL Catalog.

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Cite this (AIDS.gov Blog, RRID:SCR_007156)

URL: http://blog.aids.gov/

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

The AIDS.gov blog serves as a forum to foster public discussion on using new media effectively in response to HIV/AIDS, as well as HIV/AIDS research and policies. Along with weekly new media posts, the blog features other AIDS.gov-authored posts, guest posts, cross-posts from the White House Office of National AIDS Policy blog and the CDC Health Protection Perspectives blog, PEPFAR blog, and posts from the National Institute of Allergies and Infectious Diseases'' (NIAID) Division of AIDS. A large number of Federal agencies and programs are engaged in HIV/AIDS prevention, testing, treatment, policy, and research efforts in the United States. AIDS.gov serves as a gateway for information about these Federal efforts, with a focus on domestic programs. Since the launch of AIDS.gov on December 1, 2006 (World AIDS Day), there has been a growing interest in using new media tools to disseminate information about HIV/AIDS and improve prevention, testing, treatment, and research outcomes. AIDS.gov created this blog to address that interest, and has since expanded content areas to include key US Government HIV/AIDS-related research and policy posts, among other topics.

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Cite this (AIDS.gov Podcast, RRID:SCR_006750)

URL: http://www.aids.gov/podcast/podcast-gallery/

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

Podcasts from AIDS.gov, featuring information from the Federal government about HIV/AIDS prevention, testing, research, treatment, and using new media in response to HIV/AIDS. Categories include: Basic HIV information, New Media, Federal Programs and Policies, HIV/AIDS Awareness Days, and Real Stories.

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    AIDS.gov

Cite this (AIDS.gov, RRID:SCR_005356)

URL: http://www.aids.gov/

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

AIDS.gov works to increase HIV testing and care among people most at-risk for, or living with, HIV, by using emerging communication strategies to provide access to Federal HIV information, policies (e.g. the National HIV/AIDS Strategy), programs, and resources. Objectives # Expand visibility of timely and relevant Federal HIV policies, programs, and resources to the American public. # Increase use of new media tools by government, minority, and other community partners to extend the reach of HIV programs to communities at greatest risk. # Increase knowledge about HIV and access to HIV services for people most at-risk for, or living with, HIV. Unless otherwise noted, material presented on the AIDS.gov Web site is considered Federal government information and is in the public domain. That means this information may be freely copied and distributed. We request that you use appropriate attribution to AIDS.gov. AIDS.gov receives planning guidance from a cross agency planning group and uses a logic model (70 KB) and Communications Plan (702 KB) to guide AIDS.gov activities.

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Cite this (AIDSinfo Drug Database, RRID:SCR_012899)

URL: http://aidsinfo.nih.gov/DrugsNew/Default.aspx?MenuItem=Drugs

Resource Type: Resource, narrative resource, data or information resource, training material, database

The AIDSinfo Drug Database provides fact sheets on HIV/AIDS related drugs. The fact sheets describe the drug''s use, pharmacology, side effects, and other information. The database includes: -Approved and investigational HIV/AIDS related drugs -Three versions of each fact sheet: patient, health professional, and Spanish. AIDSinfo is a 100% federally funded U.S. Department of Health and Human Services (DHHS) project that offers the latest federally approved information on HIV/AIDS clinical research, treatment and prevention, and medical practice guidelines for people living with HIV/AIDS, their families and friends, health care providers, scientists, and researchers. Sponsors: -National Institutes of Health (NIH) Office of AIDS Research National Institute of Allergy and Infectious Diseases (NIAID) National Library of Medicine (NLM) -Health Resources and Services Administration (HRSA) -Centers for Disease Control and Prevention (CDC) -Centers for Medicare and Medicaid Services (CMS)

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Cite this (Alabama Head Injury Foundation, RRID:SCR_004580)

URL: http://www.ahif.org/

Resource Type: Resource, disease-related portal, topical portal, patient-support portal, portal, data or information resource

The Alabama Head Injury Foundation (AHIF) was founded in 1983 to increase public awareness of Traumatic Brain Injury (TBI) and to stimulate the development of supportive services. Today, AHIF is among the largest state brain injury associations in the nation with model programs and statewide services. Its mission is to improve the quality of life for people who have survived traumatic brain injuries and for their families. Whether the injury is mild or severe the life of the injured person and their family is changed forever. The impact can be both emotionally and financially devastating. AHIF provides the information to help clients and families understand the results of injury. AHIF helps access available resources and provides services and programs which meet the unique needs of individuals with traumatic brain injury (TBI) as well as spinal cord injury (SCI) in certain programs.

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Cite this (Alizadehlab: MeeboChip and HeeboChip Open Source Project, RRID:SCR_008384)

URL: http://alizadehlab.stanford.edu/

Resource Type: Resource, data or information resource, database

This is an open-source Mouse Exonic Evidence-Based Oligonucleotide Chip (MEEBOChip), and are in the process of building the human counterpart, HEEBOChip. The set of 70mers for MEEBOChip is already available from Illumina, Inc., with synthesis of HEEBOChip 70mers in progress. Both arrays are based on a novel selection of exonic long-oligonucleotides (70-mers) from a genomic annotation of the corresponding complete genome sequences, using a transcriptome-based annotation of exon structure for each genomic locus. Using a combination of existing and custom-tailored tools and datasets (including millions of mRNA and EST sequences), we built and performed a systematic examination of transcript-supported exon structure for each genomic locus at the base-pair level (i.e., exonic evidence). This strategy allowed them to select both constitutive and in many cases alternative exons for nearly every gene in the corresponding genome (e.g., protocadherin locus), allowing an unprecedented exploration of human and mouse biology. Furthermore, they used experimentally derived data to hone the selection of these 70mers, helping maximize their performance under typical fluorescent labeling and hybridization conditions. Specifically, they applied and refined the ArrayOligoSelector algorithm from Joe DeRisis laboratory to select 70mers, considering not only their uniqueness (i.e., hybridization specificity) within the content of the entire genome, but also to overcome the known biases of labeling and hybridization methods (e.g., 3-biased reverse transcription and in vitro transcription reactions).

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Cite this (Allen Human Brain Atlas, RRID:SCR_007416)

URL: http://human.brain-map.org/

Resource Type: Resource, data processing software, database, software application, data visualization software, software resource, atlas, data or information resource

A multi-modal atlas of the human brain that integrates anatomic and genomic information, coupled with a suite of visualization and mining tools to create an open public resource for brain researchers and other scientists across a wide range of specialties. Data modalities incorporated into this resource include magnetic resonance imaging (MRI), diffusion tensor imaging (DTI), histology and gene expression data derived from both microarray and in situ hybridization (ISH) approaches. Brain Explorer 2 is a desktop software application for viewing the human brain anatomy and gene expression data in 3D. It is available for download. After installing Brain Explorer 2, you can view gene expression data by performing a gene search from the Microarray page or from within Brain Explorer 2''s main window.

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Cite this (Allen Institute for Brain Science, RRID:SCR_006491)

URL: http://www.brain-map.org

Resource Type: Resource, atlas, topical portal, portal, data or information resource

Independent 501(c)(3) nonprofit medical research organization dedicated to accelerating the understanding of how the human brain works. Utilizing the mouse model system, a multidisciplinary group of neuroscientists, molecular biologists, informaticists, engineers, mathematicians, statisticians, and computational biologists have joined together to investigate expression of 20,000 genes in the adult mouse brain and to map gene expression to a cellular level beyond neuroanatomic boundaries. The data generated from this joint effort is contained in the publicly available Allen Brain Atlas application. Molecular approaches to understanding the functional organization of the brain promise new insights into the relationships between genes, brain, behavior and disease. To facilitate such insights, the Allen Institute produces large-scale projects and makes the resulting data and tools freely available online to scientists worldwide. These open resources, all available at www.brain-map.org, are intended to foster scientific discovery and collaboration. Atlases: Allen Developing Mouse Brain Atlas: A map of gene expression in the developing mouse brain. Building on the Allen Mouse Brain Atlas, this atlas reveals gene expression patterns from embryonic through postnatal stages to provide information about both spatial and temporal regulation of gene expression. Allen Spinal Cord Atlas: A genome-wide map of gene expression throughout the adult and juvenile mouse spinal cord. The Atlas was made possible through the generous support of a diverse consortium of funders, representing disease organizations, foundations, and corporate and private donors. Allen Mouse Brain Atlas (formerly Allen Brain Atlas): A genome-wide, three-dimensional map of gene expression in the adult mouse brain. Similar in scale to the Human Genome Project, the Atlas reveals the expression patterns of approximately 20,000 genes throughout the entire adult mouse brain down to the cellular level. The Allen Institutes inaugural project, the Atlas was completed in 2006. Studies: Mouse Diversity Study: Characterization of gene expression in the brain across genetic backgrounds and sex. Expanding on the Allen Mouse Brain Atlas, this resource includes data for 49 pharmaceutical drug target genes and a selected set of additional genes across seven mouse strains and in female mice. Transgenic Mouse Study: Comprehensive characterization of the expression patterns of genetically-controlled markers or tool genes in the brains of transgenic mice. Providing standardized, detailed, anatomical profiling of transgene expression throughout the brain, this dataset is intended to reveal the potential of each transgenic mouse line and help researchers choose the appropriate tools for their studies. Human Cortex Study: A collection of gene expression data in the adult human neocortex. Providing data for several categories of genes across different cortical regions and human individuals, including control and schizophrenic cases, the dataset has the potential to enable exploration of variability in cortical gene expression across different ages, between genders across different regions of the cortex and in schizophrenia. Sleep Study: A comprehensive collection of gene expression data in the mouse brain for five different conditions of sleep and wakefulness. Generated in collaboration with SRI International, this unique dataset is intended to help sleep researchers advance understanding of sleep deprivation and the dynamic changes underlying sleep/wake cycles. The sleep study was funded by an award from the U.S. Department of Defense.

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Cite this (AllenInstitute - YouTube, RRID:SCR_005435)

URL: http://www.youtube.com/user/AllenInstitute

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

Videos uploaded to YouTube by Allen Institute. The Allen Institute for Brain Science is an independent nonprofit medical research organization dedicated to accelerating the understanding of how the human brain works. Through a product-focused approach, we generate innovative public resources used by researchers and organizations around the globe. Additionally, we drive technological and analytical advances, creating new knowledge and providing new ways to address questions about the brain in health and disease. Our work and efforts are intended to fuel discovery for the broader scientific community worldwide. The Allen Institute was launched in 2003 with generous seed funding from founder and philanthropist Paul G. Allen and is supported by a diversity of public and private funds.

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