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Found 15 result(s)

INTREPID bioinformatics

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!!! >>> intrepidbio.com expired <<< !!!! Intrepid Bioinformatics serves as a community for genetic researchers and scientific programmers who need to achieve meaningful use of their genetic research data – but can’t spend tremendous amounts of time or money in the process. The Intrepid Bioinformatics system automates time consuming manual processes, shortens workflow, and eliminates the threat of lost data in a faster, cheaper, and better environment than existing solutions. The system also provides the functionality and community features needed to analyze the large volumes of Next Generation Sequencing and Single Nucleotide Polymorphism data, which is generated for a wide range of purposes from disease tracking and animal breeding to medical diagnosis and treatment.

Database of Interacting Proteins

DIP

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The DIP database catalogs experimentally determined interactions between proteins. It combines information from a variety of sources to create a single, consistent set of protein-protein interactions. The data stored within the DIP database were curated, both, manually by expert curators and also automatically using computational approaches that utilize the the knowledge about the protein-protein interaction networks extracted from the most reliable, core subset of the DIP data. Please, check the reference page to find articles describing the DIP database in greater detail. The Database of Ligand-Receptor Partners (DLRP) is a subset of DIP (Database of Interacting Proteins). The DLRP is a database of protein ligand and protein receptor pairs that are known to interact with each other. By interact we mean that the ligand and receptor are members of a ligand-receptor complex and, unless otherwise noted, transduce a signal. In some instances the ligand and/or receptor may form a heterocomplex with other ligands/receptors in order to be functional. We have entered the majority of interactions in DLRP as full DIP entries, with links to references and additional information

GeneCorner Plasmid Collection

BCCM/GeneCorner Plasmid Collection

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The BCCM/GeneCorner Plasmid Collection accepts plasmids from and distributes plasmids to researchers worldwide. Funding by the Belgian Science Policy (Belspo) allowed BCCM/GeneCorner to evolve into a unique plasmid repository in Europe.

BIGG Database

Biochemically, Genetically and Genomically structured genome-scale metabolic network reconstructions

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BiGG is a knowledgebase of Biochemically, Genetically and Genomically structured genome-scale metabolic network reconstructions. BiGG integrates several published genome-scale metabolic networks into one resource with standard nomenclature which allows components to be compared across different organisms. BiGG can be used to browse model content, visualize metabolic pathway maps, and export SBML files of the models for further analysis by external software packages. Users may follow links from BiGG to several external databases to obtain additional information on genes, proteins, reactions, metabolites and citations of interest.

GeneCards

The Human Gene Database

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GeneCards is a searchable, integrative database that provides comprehensive, user-friendly information on all annotated and predicted human genes. It automatically integrates gene-centric data from ~125 web sources, including genomic, transcriptomic, proteomic, genetic, clinical and functional information.

Yeast Resource Center Public Image Repository

YRC Public Image Repository

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The Yeast Resource Center Public Image Repository is a database of fluorescent microscopy images and their associated metadata/experimental parameters. The images depict the localization, co-localization and FRET (fluorescence energy transfer) of proteins in cells, particularly in the budding yeast Saccharomyces cerevisiae as a model organism. Users may download the entire datasets to improve their research.

J. Craig Venter Institute

JCVI

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JCVI is a world leader in genomic research. The Institute studies the societal implications of genomics in addition to genomics itself. The Institute's research involves genomic medicine; environmental genomic analysis; clean energy; synthetic biology; and ethics, law, and economics.

GenBank

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GenBank® is a comprehensive database that contains publicly available nucleotide sequences for almost 260 000 formally described species. These sequences are obtained primarily through submissions from individual laboratories and batch submissions from large-scale sequencing projects, including whole-genome shotgun (WGS) and environmental sampling projects. Most submissions are made using the web-based BankIt or standalone Sequin programs, and GenBank staff assigns accession numbers upon data receipt. Daily data exchange with the European Nucleotide Archive (ENA) and the DNA Data Bank of Japan (DDBJ) ensures worldwide coverage. GenBank is accessible through the NCBI Entrez retrieval system, which integrates data from the major DNA and protein sequence databases along with taxonomy, genome, mapping, protein structure and domain information, and the biomedical journal literature via PubMed. BLAST provides sequence similarity searches of GenBank and other sequence databases. Complete bimonthly releases and daily updates of the GenBank database are available by FTP.

Cancer Cell Line Encyclopedia

CCLE

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The Cancer Cell Line Encyclopedia project is a collaboration between the Broad Institute, and the Novartis Institutes for Biomedical Research and its Genomics Institute of the Novartis Research Foundation to conduct a detailed genetic and pharmacologic characterization of a large panel of human cancer models, to develop integrated computational analyses that link distinct pharmacologic vulnerabilities to genomic patterns and to translate cell line integrative genomics into cancer patient stratification. The CCLE provides public access to genomic data, analysis and visualization for about 1000 cell lines.

EcoGene

Escherichia coli strain K12 genome database

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<<<!!!<<< The repository is no longer available. 2019-12-02: no more access to EcoGene >>>!!!<<<

CanGEM

Cancer GEnome Mine

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>>>!!!<<<As stated 2017-05-23 Cancer GEnome Mine is no longer available >>>!!!<<< Cancer GEnome Mine is a public database for storing clinical information about tumor samples and microarray data, with emphasis on array comparative genomic hybridization (aCGH) and data mining of gene copy number changes.

caArray

Array Data Management System

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>>>!!!<<< caArray Retirement Announcement >>>!!!<<< The National Cancer Institute (NCI) Center for Biomedical Informatics and Information Technology (CBIIT) instance of the caArray database was retired on March 31st, 2015. All publicly-accessible caArray data and annotations will be archived and will remain available via FTP download https://wiki.nci.nih.gov/x/UYHeDQ and is also available at GEO http://www.ncbi.nlm.nih.gov/geo/ . >>>!!!<<< While NCI will not be able to provide technical support for the caArray software after the retirement, the source code is available on GitHub https://github.com/NCIP/caarray , and we encourage continued community development. Molecular Analysis of Brain Neoplasia (Rembrandt fine-00037) gene expression data has been loaded into ArrayExpress: http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-3073 >>>!!!<<< caArray is an open-source, web and programmatically accessible microarray data management system that supports the annotation of microarray data using MAGE-TAB and web-based forms. Data and annotations may be kept private to the owner, shared with user-defined collaboration groups, or made public. The NCI instance of caArray hosts many cancer-related public datasets available for download.

ALEXA

ALEXA-A

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ALEXA is a microarray design platform for 'alternative expression analysis'. This platform facilitates the design of expression arrays for analysis of mRNA isoforms generated from a single locus by the use of alternative transcription initiation, splicing and polyadenylation sites. We use the term 'ALEXA' to describe a collection of novel genomic methods for 'alternative expression' analysis. 'Alternative expression' refers to the identification and quantification of alternative mRNA transcripts produced by alternative transcript initiation, alternative splicing and alternative polyadenylation. This website provides supplementary materials, source code and other downloads for recent publications describing our studies of alternative expression (AE). Most recently we have developed a method, 'ALEXA-Seq' and associated resources for alternative expression analysis by massively parallel RNA sequencing.

NCBI

National Center for Biotechnology Information

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The National Center for Biotechnology Information advances science and health by providing access to biomedical and genomic information

UCSC Genome Browser

University of California Santa Cruz Genome Bioinformatics

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It is an interactive website offering access to genome sequence data from a variety of vertebrate and invertebrate species and major model organisms, integrated with a large collection of aligned annotations. The Browser is a graphical viewer optimized to support fast interactive performance and is an open-source, web-based tool suite built on top of a MySQL database for rapid visualization, examination, and querying of the data at many levels.