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Showing 1 to 25 of 25 items tagged as data analysis


Structural Biology Knowledgebase

database

Provider: Nature.com and PSI (Protein Structure Initiative)
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Descriptions: The Structural Biology Knowledgebase (SBKB) is the product of a collaboration between the Protein Structure Initiative (PSI) and Nature Publishing Group (NPG.) The site offers an easy way of keeping up to date on the latest developments from the PSI, and more generally, in the fields of structural genomics and structural biology. Some areas of this site require a free registration involving affirmation of a statement declaring that one's purpose is strictly non-commercial and that one is an academic.
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Protein Data Bank: An Information Portal to Biological Macromolecular Structures

database

Provider: RCSB (Research Collaboratory for Structural Bioinformatics)
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Descriptions:  "The RCSB (Research Collaboratory for Structural Bioinformatics) is dedicated to improving our understanding of the function of biological systems through the study of the 3-D structure of biological macromolecules. RCSB members work cooperatively and equally through joint grants and subsequently provide free public resources and publications to assist others and further the fields of bioinformatics and biology."  Protein Data Bank (PDB) curates and annotates data according to agreed-upon standards and is a member of the ww (world wide) PDB. Use this database to perform simple and advanced searches based on sequence, structure and function annotations, and to visualize, download, and analyze molecules. The database is primarily for researchers, but the site also includes an entire section (PDB101) of information quite accessible enough for educational purposes. Check out the "Molecule of the Month" feature. The extensive archive contains information about experimentally-determined structures of proteins, nucleic acids, and complex assemblies.  As with many scientific databases, a personal log-in affords access to more features. The database is managed by Rutgers and University of California San Diego.
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HealthMap – Global Disease Alert Map

website

Provider: Harvard Medical School, MIT, and others
Descriptions: HealthMap brings together disparate data sources for a unified and comprehensive view of the current global state of infectious diseases and their effect on human and animal health. Integrates outbreak data of varying reliability, ranging from news sources (such as Google News) to curated personal accounts (such as ProMED) to validated official alerts (such as World Health Organization). Data is aggregated by disease and displayed by location for user-friendly access to the original alert. HealthMap provides real-time information on emerging infectious diseases. A site of particular interest to public health officials and international travelers.
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Effective Health Care Program – AHRQ

database

Provider: Agency for Healthcare Research and Quality (AHRQ)
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Descriptions: First funded by Congress in 2005, the Effective Health Care Program funds and synthesizes the findings of teams of researchers and clinicians across North America, to identify ways to improve the quality of health care through evidence-based decision-making. Research summaries are available for consumers (many with Spanish translations), clinicians and policy-makers. Also for patients, short videos on treatment options, helpful comparative charts on the effectiveness of different treatments for various conditions. Many resources in various formats are provided. The Program invites comments and topic research/review suggestions, and data deposit by medical professionals. Links are provided to plug-ins for viewing video content.
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Health Informatics Worldwide

website

Provider: Institute of Medical Biometry and Medical Informatics Freiburg, Germany
Descriptions: A regularly updated index of links to websites devoted to health informatics, medical and nursing informatics. Institutions and organizations are listed by country and also can be browsed by topic category. On the main page is a listing of upcoming international informatics conferences and events.
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U.S. Global Health Policy: an Online Gateway for the Latest Data and Information on the U.S. Role in Global Health

website

Provider: Kaiser Family Foundation
Descriptions: This interactive site provides news, facts, and statistical data on significant health topics and indicators across the globe. Data may be retrieved and organized by health topic or country and a data sheet may also be created which compares up to five countries on an unlimited number of indicators.
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F1000Research

database

Provider: F1000
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Descriptions: F1000Research is an open online journal based on an alternative model of scientific publishing and peer review. Peer review is open, attributed, and done post-publication, once a work has been submitted to internal review and posted. F1000 strongly encourages publication of accompanying datasets under liberal Creative Commons licensing terms. Citations contain information on the stage of refereeing and approval of references. Many Texas Medical Center faculty members are also on the distinguished international editorial staff at F1000.
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WolframAlpha: Computational Knowledge Engine

database

Provider: Wolfram Alpha, LLC
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Descriptions: WolframAlpha is a computational database/search engine that interprets natural language queries, returning dynamic answers. Although still in development, it currently "...contains 10+ trillion pieces of data, 50,000+ types of algorithms and models, and linguistic capabilities for 1000+ domains." Enter a food item, and the engine generates a page of its nutritional, caloric, vitamin, mineral and physical properties. Input any integer for information about its forms, qualities and expressions. Explore a surname or given name-- view, among other data, its trend in popularity from the 1890's to the present. Input a disease name, and generate a series of graphs illustrating prevalence, average age of onset, sex distribution, medical coverage and more. Use the disease name as a cause of death, and mortality statistics are presented. Apps are now available to download for use with iPhone, iPad and Android.
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DataCite

website

Provider: DataCite
Descriptions: DataCite is an international organization established in December, 2009 to promote and facilitate the expansion of the DOI (Digital Object Identifier) system to include scientific datasets. Membership includes publishers, libraries and data centers. Researchers will benefit from access to scientific data supporting findings explicated in full-text articles, and will be able to link to that underlying data in the same way DOI enables links to text. DataCite provides standards and workflows for the publication of this data, and enables researchers to reliably locate and cite submitted data.
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Better Data, Better Health

website

Provider: Robert Wood Johnson Foundation
Descriptions: This website contains data sets, reports and rankings that include information on the quality of care delivery, patient outcomes, and patient feedback on physicians, hospitals, and cost. A "data hub" provides interactive graphics of state populations broken out by ethnicity, educational attainment, and age group for a number of healthcare measures, such as rates of the uninsured, portion of state budgets spent on healthcare, healthcare quality, and more. The focus of this website is discussion and demonstration of how "big data" can serve to improve health care in the United States.
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NextBio Basic

database

Provider: NextBio
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Descriptions: NextBio Basic is a free web application for searching biomedical and genetic information. It provides access to a 'curated, correlated database' of public data into which NextBio integrates Medline literature, clinical trial information, and news. Its semantic framework is based on gene, tissue, disease and compound ontologies. Registered users (registration for this basic version is free) can personalize their experience, communicate, collaborate and share data with the rest of the NextBio community. For the registered user, a single search for a gene yields quick results arranged by category: an overview of the gene; a list of tissues in which the gene is expressed; diseases and compounds relating to the gene; a list of the top associated researchers and authors; literature, associated clinical trials, and more.
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NDB: Nucleic Acid Database

database

Provider: The Nucleic Acids Database Research Project/Rutgers University
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Descriptions: A portal for 3-D structural information about nucleic acids, the NDB contains information about experimentally-determined nucleic acids and complex assemblies. Search by annotations relating to sequence, structure and function; download, analyze, and learn about nucleic acids.
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NCMIR – National Center for Microscopy and Imaging Research

database

Provider: National Center for Microscopy and Imaging Research/University of California San Diego
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Descriptions: NCMIR develops technologies to facilitate understanding of biological systems from the gross anatomical to the molecular scale and makes those technologies available to biomedical researchers. NCMIR provides expertise, infrastructure, technological development, and an environment in which new information about the 3D ultrastructure of tissues, cells, and macromolecular complexes can be easily obtained and analyzed.
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NCBI (National Center for Biotechnology Information)

database

Provider: National Center for Biotechnology Information/National Library of Medicine
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Descriptions: The National Center for Biotechnology Information advances science and health by providing access to biomedical and genomic information. NCBI provides a large number of resources for scientific research, including software and many databases.
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KEGG (Kyoto Encyclopedia of Genes and Genomics)

database

Provider: Kanehisa Laboratories, Japan
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Descriptions: KEGG is a resource purposed to facilitate understanding of the functions and utilities of the biological system--  cells, organisms and ultimately the ecosystem--  based on genomic and molecular-level information. It is a computer representation of the biological system, consisting of the molecular building blocks-- genes, proteins and chemical substances, integrated with molecular wiring diagrams of interaction, reaction and relational networks. Extensive data is available to view; ftp downloading requires a subscription. KEGG was developed in collaboration with the Bioinformatics Center, Institute for Chemical Research, Kyoto University and the Human Genome Center, Institute of Medical Science, University of Tokyo.
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NITRC: The Source for Neuroimaging Tools and Resources

website

Provider: Neuroimaging Informatics Tools and Resources Clearinghouse
Descriptions: Neuroimaging Informatics Tools and Resources Clearinghouse (NITRC) is sponsored by the NIH Blueprint for Neuroscience Research. It offers the neuroscience community free databases and applications for imaging, a forum and a news feed. Researchers can look for applications based on their attributes and popularity, and can also compare similar utilities, check on software development stages, and submit their own databases and applications for sharing. Many links to related resources are also provided here.
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New England Complex Systems Institute

website

Provider: New England Complex Systems Institute
Descriptions: The science of complex systems builds upon the traditional focus on individual systems or parts of systems, concentrating instead on integration of interdependency within and between systems that form networks of cause and effect. With humanity as its scale, complex systems research applies scientific method to further the understanding and predictability of behavior, social interaction, and the consequences of societal policies and decisions. The New England Complex Systems Institute develops and applies new mathematical approaches and multiscale analysis to diverse scientific and social systems like cell science, biodiversity, altruism, ethnic violence, economic crisis, climate change, and the healthcare system. Free full-text access to many papers on complex systems is available here.
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NBIC (Netherlands BioInformatics Centre)

website

Provider: Netherlands BioInformatics Centre
Descriptions: NBIC is engaged in bioinformatics research and education. Its website includes free software downloads, information on databases and projects, a journal and newsletter, and secondary-level education materials.
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Global Health Data Exchange (GHDx) – Institute for Health Metrics and Evaluation (IHME)

database

Provider: Institute for Health Metrics and Evaluation (IHME)
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Descriptions: GHDx is a catalog of the world's health and demographic data. Use the GHDx to research population census data, surveys, registries, indicators and estimates, administrative health data, and financial data related to health. The provider, the IHME, is an educational and research public health organization, and provides fellowships at the bachelor's and graduate levels. IHME publishes the BioMed Central journal, Population Health Metrics, and various open-access reports. There are many interesting resources here. Users should visit the Data Visualizations page and see other items listed under the "Tools" tab.
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FlyBase: A Database of Drosophila Genes and Genomes

database

Provider: National Institutes of Health
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Descriptions: A visually beautiful, rich and well-organized home for Drosophila researchers, with forums, tools, links to other important sites (including Interactive Fly), high-quality images, a genome browser, and many more helpful tools and features. New FlyBase users can check under the News and link out to the explanatory article, FlyBase 101: the Basics of Navigating FlyBase. The FlyBase project is carried out by a consortium of Drosophila researchers and computer scientists from Harvard University, University of Cambridge, Indiana University and the University of New Mexico, and is funded by grants from NIH, British Medical Research Council, National Science Foundation, and Indiana University
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FedStats

database

Provider: FedStats.gov
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Descriptions: FedStats is a portal to virtually all the statistics gathered by U.S. Government agencies and bureaus. For some of these, compiling statistics is their main mission; for others, the activity supports their other work. Searches can be done by state or by topic under general subject categories-- agriculture, crime, demographics, education, energy and environment, health, labor, commerce and economics. A full list of agencies is provided, with information on the kinds of statistics they produce. International data of various kinds is also accessible here, some of it comparative.
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DBGET search

database

Provider: Kyoto University Bioinformatics Center
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Descriptions: DBGET is an integrated database retrieval system for accessing a web of molecular biology databases within GenomeNet and KEGG (Kyoto Encyclopedia of Genes and Genomes.)
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Center for Biological Sequence Analysis

database

Provider: Technical University of Denmark
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Descriptions: The Center does basic research in the fields of bioinformatics and systems biology. A multidisciplinary group of scientists works in ten specialist research areas (see the CBS Map) and is one of the largest such groups in European academia. Datasets, software, a publications list, and hundreds of links to other related data repositories are included here. Also includes a set of links to courses and lectures.
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SJR- SCImago Journal and Country Rank

database

Provider: SCImago
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Descriptions: Based on data indexed in SCOPUS, SJR graphs a number of metrics on scientific publications and publishing. Some unique aspects of the journal analysis include: proportion of cited to uncited/citable to uncitable articles; percentage of a journal's articles that are indicative of research resulting from international collaboration; ranking of countries and regions of the world according to publication output and citation; and an interactive map feature that generates graphic co-citation networks among disciplines, by country and time period. The opening page of SCImago sums it up: "Rank - Analyze - Compare - Visualize."
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1000 Genomes

database

Provider: 1000 Genomes
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Descriptions: 1000 Genomes: a deep catalog of human genetic variation "...is the first project to sequence the genomes of a large number of people, to provide a comprehensive resource on human genetic variation... The goal of the 1000 Genomes Project is to find most genetic variants that have frequencies of at least 1% in the populations studied." 1000 Genomes is an international endeavor, with participants from institutes, governments and universities world-wide. "DNA from the samples will be available for researchers to follow up with more detailed studies of variation in particular regions. The cell lines will allow researches to study cellular phenotypes such as gene expression, epigenetic patterns, and drug response. The extensive genotype data available on the samples, and the trio samples for some of the populations, will allow researchers to map regions of the genome computationally that affect the cellular phenotypes, and to study the heritability of these phenotypes."
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