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Showing 1 to 27 of 27 items tagged as genomics


SpringerProtocols

database

Provider: Springer Science & Business Media LLC
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Descriptions: SpringerProtocols is said to be the most comprehensive and trustworthy online database of reproducible laboratory protocols in the biomedical and life sciences. From the book series Methods in Molecular Biology and numerous other sources, this collection offers researchers access to decades of step-by-step protocols for use in the lab. With an emphasis on clarity, each protocol is organized in an easily-reproduced, recipe style. All protocols have been written by experts in the field, and are reviewed first by editors distinguished in the relevant specific subject areas, and then by Springer's own editorial staff. Contains some open-access protocols. Mobile version of website available.
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Structural Biology Knowledgebase

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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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GenomeNet

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Provider: Kyoto University Bioinformatics Center
Descriptions: GenomeNet is a network of database and computational services for genome research and related research areas in biomedical sciences, operated by the Kyoto University Bioinformatics Center. The service was first developed at Kyoto University as part of a group of research projects begun in 1991 under the Japanese human genome program. It includes bioinformatics tools in sequence, chemical and genome analysis; community databases dealing with cyanobacteria, bacillus subtilis, and gene expression profiles; ontologies; and more. The KEGG database, which has its own entry in this list, is a part of GenomeNet.
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DBGET

website

Provider: Kyoto University Bioinformatics Center
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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OMIM – Online Mendelian Inheritance in Man

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Provider: Johns Hopkins University School of Medicine
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Descriptions: OMIM is a comprehensive, authoritative compendium of human genes and genetic phenotypes that is freely available and updated daily. The full-text, referenced overviews in OMIM contain information on all known mendelian disorders and over 12,000 genes. OMIM focuses on the relationship between phenotype and genotype. It is updated daily, and the entries contain copious links to other genetics resources. Registration required for ftp downloading on the part of nonprofit entities; commercial use/use by a commercial entity requires a license.
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NIH Data Sharing Repositories

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Provider: National Institutes of Health/National Library of Medicine
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Descriptions: This is a portal with a sortable list of 45 NIH and outside entities' data repositories and data-sharing facilitation sites that offer open-source software. Links to submission and download policies and instructions are provided for each. Research areas include: genomics of the nematode, drosophila, zebrafish and rat; sequencing data; peptides and proteins; pathogens and vectors; the NCI cancer imaging repository; neuroscience, rare diseases, Parkinson's, autism, and more.
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Proteopedia: Life in 3-D

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Provider: Weizmann Institute of Science
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Descriptions: Proteopedia is a free, collaborative (wiki) 3-D encyclopedia of proteins and other molecules. The images can be reduced and restored by component with a toggle, or caused to rotate from any starting angle. Contains an introduction to structural biology and features sections on biomolecules, enzymes, metabolism, gene expression/replication, diseases, immune system, and methods of determining and analyzing structure and sequence. Contains a table of contents and a detailed structure index
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NextBio Basic

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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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Neuroscience Information Framework

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Provider: National Institutes of Health
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Descriptions: The Neuroscience Information Framework is a dynamic inventory of web-based neuroscience resources: data, materials, and tools. An initiative of the NIH Blueprint for Neuroscience Research, NIF advances neuroscience research by enabling discovery and access to public research data and tools worldwide through an open source, networked environment. The NIF project is designed to serve the biomedical research community. The more participation from the community, the better the NIF... Collaborating institutions working on the current version of NIF include University of California, San Diego, California Institute of Technology, George Mason University, Yale University Medical College, and Washington University.
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NCBI Bookshelf

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Provider: National Center for Biotechnology Information
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Descriptions: Collaborating with authors and publishers, the National Center for Biotechnology Information (NCBI) adapts biomedical books for the web. They may either be accessed via direct search or via "Books" links in PubMed abstracts. There are more than 1,400 open-access titles in the Bookshelf. Browse by date, title, subject, publisher and document type. Among the titles are guides to using NCBI databases and sites, Surgeon General reports, and information from various agencies.
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NCBI (National Center for Biotechnology Information)

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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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Scitable

website

Provider: Nature Education
Descriptions: Scitable is a free website with international participation; its current focus is on all aspects of genetics. Created for educators and students working at the graduate and undergraduate levels, it may well be accessible enough for some high school students. Includes many free articles within "topic rooms," and offers blogging, the ability to post questions, opportunities to contribute as writer or mentor, and formation of groups for discussion or curriculum. Free registration required for full participation.
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Public Health Genomics

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Provider: Centers for Disease Control and Prevention
Descriptions: The CDC presents links and resources for consumers and health professionals here. Topics include genetic counseling and testing, newborn screening, population research, genomics and more.
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PharmGKB: Pharmacogenomics Knowledge Base

website

Provider: U.S. Department of Health and Human Services/Stanford University
Descriptions: PharmGKB's mission is "to collect, encode, and disseminate knowledge about the impact of human genetic variations on drug response. We curate primary genotype and phenotype data, annotate gene variants and gene-drug-disease relationships via literature review, and summarize important PGx genes and drug pathways."
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KEGG (Kyoto Encyclopedia of Genes and Genomics)

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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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IntegromeDB

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Provider: Researchers at University of California, San Diego
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Descriptions: Created by four university colleagues, IntegromeDB brings together literally hundreds of resources to provide an integrated database of genomic, proteomic, transcriptive, genetic and functional data. Featured in the database are gene function, orthology, gene expression, pathways, protein interactions, mutations and SNPs, disease relationships, and related drugs and compounds. Those not yet familiar with IntegromeDB may want to read the group's open-access article, IntegromeDB: an integrated system and biological search engine.
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Neuroscience Information Framework 3.1

website

Provider: National Institutes of Health
Descriptions: The Neuroscience Information Framework (NIF) is a semantically-enhanced portal to a dynamic inventory of Web-based neuroscience resources. An initiative of the NIH Blueprint for Neuroscience Research, NIF enhances discovery and access to often unindexed but publicly available research data, datasets, software and tools in the deep web, as well as linking to PubMed records and open-access literature. The NIF Project provides the NIF Registry, Antibody Registry, Drug Related Gene Database, neuroscience ontology and a way to contribute to it (via the NeuroLex wiki) and semantic tagging services. NIF Navigator, a customizable, stand-alone search tool for incorporation into websites or wikis, draws query results from all the NIF's own components and from other sites and accessible databases. The valuable resources at NIF are too numerous to be described adequately 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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National Institute of General Medical Sciences (NIGMS)

website

Provider: NIGMS - National Institute of General Medical Sciences
Descriptions: "The mission of [NIGMS] is to support research that increases understanding of life processes and lays the foundation for advances in disease diagnosis, treatment, and prevention." NIGMS provides training and career grants, including a grants and opportunities program for minorities. This website is a gold mine for educators, providing scientist interviews, short films on special topics, an image database, posters, fact sheets, even interactive games. One can access or sign up for Biomedical Beat, the free NIGMS online newsletter, as well as order many other free publications. For researchers there is a blog, NIGMS Feedback Loop, that keeps one up to date on funding opportunities and future plans.
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Gene Ontology

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Provider: Gene Ontology Project
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Descriptions: "The Gene Ontology project is a major bioinformatics initiative with the aim of standardizing the representation of gene and gene product attributes across species and databases. The project provides a controlled vocabulary of terms for describing gene product characteristics and gene product annotation data from GO Consortium members, as well as tools to access and process this data."  The Ontologies describe three aspects of molecular biology- biological processes, cellular components, and molecular functions. Gene Ontology's collected tools list includes hundreds from all over the world: specialized browsers, search engines, statistical analysis and visualization tools, and many other kinds. This project began as a collaboration between three model organism databases, FlyBase (Drosophila), the Saccharomyces Genome Database  and the Mouse Genome Database  in 1998. Since then, the GO Consortium has grown to include many other databases, including several of the world's major repositories for plant, animal and microbial genomes. See the GO Consortium page for a full list of member organizations.
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FlyBase: A Database of Drosophila Genes and Genomes

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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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DBGET search

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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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dbGaP- Database of Genotypes and Phenotypes

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Provider: National Center for Biotechnology Information
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Descriptions: In dbGaP, NCBI archives and distributes the results of studies investigating the interaction of genotype and phenotype. Genome-wide association studies, medical sequencing, molecular diagnostic assays, and associations between genotype and non-clinical traits are covered. dbGaP contains both open- and controlled-access data. Non-sensitive data are released on a broad scale, but sensitive data sets involving personal health information are not publicly accessible. Search by study or disease, or use Advanced Search.
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BLAST (NCBI)

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Provider: National Center for Biotechnology Information
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Descriptions: The Basic Local Alignment Search Tool (BLAST) finds regions of local similarity between sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches. BLAST can be used to infer functional and evolutionary relationships between sequences as well as help identify members of gene families.
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BioMart Bio Portal

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Provider: BioMart
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Descriptions: The BioMart project provides free software and data services to the international scientific community in order to foster scientific collaboration and facilitate the scientific discovery process. The project adheres to the open source philosophy of promoting collaboration and code reuse. The majority of the contributed databases are of plant or human genomics-oriented data. Under Community, view the linked database list with descriptions and contributor names. Databases originate from the UK, USA, France, Spain, China and other countries. There are three separate portal websites-- the central "Bio" portal, a cancer portal, and one for mouse data.  Unfortunately, no link back to BioMart is provided once the user accesses one of the other portals.
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EBook Collection – EBSCOHost (EBooks on EBSCOHost)

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Provider: EBSCO
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Descriptions: An expanding collection with more than 100,000 titles in trade, reference, science, technology, medicine and literature. Some content is out of copyright, free with subscription; some is licensed by the Texas State Library for TexShare; and some is provided by the University of Texas at Austin.
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1000 Genomes

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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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