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Showing 1 to 21 of 21 items tagged as bioinformatics


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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SpringerOpen

database

Provider: Springer
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Descriptions: Springer hosts a collection of more than 120 peer-reviewed, open access journals and more than 20 open access ebooks, covering the science, technology and medicine (STM) fields.  OA journals and ebooks provide authors the opportunity to retain copyright, while making their research available to the worldwide scientific community.
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Structure (NCBI)

database

Provider: National Center for Biotechnology Information (NCBI)
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Descriptions: The NCBI Structure Group, a part of the Computational Biology Branch of NCBI, developed this suite of four free molecular and protein databases, each of which is itself made up of several others, and all of which can be searched individually. Macromolecular Structures, Conserved Domains, Small Molecules, and Biological Systems are the four main resources here- tools designed to facilitate discovery of sequence, function and structure associations. The tab labeled "Discover" does a good job of explaining how to use the Structure databases and how to access various facets of information on a molecule or protein from any point in NCBI's many resources.
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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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UniProt

database

Provider: UniProt Consortium
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Descriptions: "The mission of UniProt is to provide the scientific community with a comprehensive, high-quality and freely accessible resource of protein sequence and functional information."  Available material consists of: UniProtKB, a two-section protein knowledge-base consisting of SwissProt and TrEMBL; UniRef (sequence clusters;) UniParc (a sequence archive for tracking sequences and identifiers) and the supporting data (literature citations, taxonomy, keywords, nomenclature, guidelines and indexes.) A user manual and primer on annotation are provided as well. UniProt is distributed free under a Creative Commons attribution license. Updates are frequent and updated releases must be downloaded from the website. Much of UniProt's funding is provided by the NIH.
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NIH Data Sharing Repositories

database

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

database

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

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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Neuroimaging Informatics Tools and Resources Clearinghouse (NITRC)

database

Provider: NITRC,
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Descriptions: Originally funded by the NIH Blueprint for Neuroscience Research, NITRC facilitates finding and comparing neuroimaging resources for functional and structural neuroimaging analyses—tools that were once hidden in a researcher's laboratory and well-known resources. NITRC collects and points to standardized information about tools, making the task of finding and comparing them easier. This site can help researchers find the right functional or structural neuroimaging tool or resource and serve as an aid in deciding whether it will be helpful to them. 
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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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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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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

database

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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GoPubMed

database

Provider: Transinsight
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Descriptions: GoPubMed is an innovative, powerful search tool that combines the MeSH (Medical Subject Headings) and GO (Gene Ontology) terminologies to optimize the effectiveness of queries to PubMed- for everyone, but for molecular biologists in particular. Searching elicits results presented very quickly (maximum display: the most recent 1,000 citations), along with a sidebar presenting the full results in categorized, hierarchical groups of terms that help the user to focus in further- the producers of this search engine refer to it as a "knowledge-based semantic search." There are many more features to this search tool than can be described here.
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GigaDB

database

Provider: GigaScience and BGI
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Descriptions: GigaDB is an open repository of datasets that support the research published in the open access BioMed Central bioinformatics journal, GigaScience. GigaDB provides a place from which to download supporting data and tools associated with papers published in GigaScience, thus facilitating the reproducibility of research. DataCite DOIs are assigned to these accompanying datasets, an identification device which serves to facilitate tracking and discoverability, and to provide additional credit to the authors who make their data publicly available.
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Gene Ontology

database

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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GQuery: Global Cross-database NCBI Search

database

Provider: National Center for Bioinformatics Information (NCBI)
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Descriptions: Integrated, text-based search and retrieval system used at the National Center for Biotechnology Information for its major databases: PubMed, Nucleotide and Protein Sequences, Protein Structures, Complete Genomes, Taxonomy, and others. GQuery integrates the scientific literature, DNA and protein sequence databases, 3D protein structure and protein domain data, population study datasets, expression data, assemblies of complete genomes, and taxonomic information into a tightly interlinked system.
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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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DrugBank: Open Data Drug & Drug Target Database

database

Provider: David Wishart/University of Alberta, CA
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Descriptions: A bio- and chemical informatics resource that combines detailed drug (chemical, pharmacological and pharmaceutical) data with comprehensive drug targeting (sequence, structure, and pathway) information. The database contains nearly 4300 drug entries, including FDA-approved small molecule drugs, FDA-approved biotech (protein/peptide) drugs, "nutraceuticals" and experimental drugs. Contains more than 6,800 drug entries with almost 4,300 non-redundant protein sequences linked. Each entry, or  DrugCard, contains more than 80 data fields, half of which are devoted to drug/chemical data and the other half to drug target/protein data. Downloads and information on rights, acknowledgement and usage are available here.
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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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