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Found 28 result(s)

Open Tree of Life

Tree of Life - Evolution

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The tree of life links all biodiversity through a shared evolutionary history. This project will produce the first online, comprehensive first-draft tree of all 1.8 million named species, accessible to both the public and scientific communities. Assembly of the tree will incorporate previously-published results, with strong collaborations between computational and empirical biologists to develop, test and improve methods of data synthesis. This initial tree of life will not be static; instead, we will develop tools for scientists to update and revise the tree as new data come in. Early release of the tree and tools will motivate data sharing and facilitate ongoing synthesis of knowledge.

Canada's Michael Smith Genome Sciences Centre

GSC

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We are a leading international centre for genomics and bioinformatics research. Our mandate is to advance knowledge about cancer and other diseases, to improve human health through disease prevention, diagnosis and therapeutic approaches, and to realize the social and economic benefits of genomics research.

IMEx

The International Molecular Exchange Consortium

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The IMEx consortium is an international collaboration between a group of major public interaction data providers who have agreed to share curation effort and develop and work to a single set of curation rules when capturing data from both directly deposited interaction data or from publications in peer-reviewed journals, capture full details of an interaction in a “deep” curation model, perform a complete curation of all protein-protein interactions experimentally demonstrated within a publication, make these interaction available in a single search interface on a common website, provide the data in standards compliant download formats, make all IMEx records freely accessible under the Creative Commons Attribution License

Expression Atlas

Gene Expression Atlas

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The Expression Atlas provides information on gene expression patterns under different biological conditions such as a gene knock out, a plant treated with a compound, or in a particular organism part or cell. It includes both microarray and RNA-seq data. The data is re-analysed in-house to detect interesting expression patterns under the conditions of the original experiment. There are two components to the Expression Atlas, the Baseline Atlas and the Differential Atlas. The Baseline Atlas displays information about which gene products are present (and at what abundance) in "normal" conditions (e.g. tissue, cell type). It aims to answer questions such as "which genes are specifically expressed in human kidney?". This component of the Expression Atlas consists of highly-curated and quality-checked RNA-seq experiments from ArrayExpress. It has data for many different animal and plant species. New experiments are added as they become available. The Differential Atlas allows users to identify genes that are up- or down-regulated in a wide variety of different experimental conditions such as yeast mutants, cadmium treated plants, cystic fibrosis or the effect on gene expression of mind-body practice. Both microarray and RNA-seq experiments are included in the Differential Atlas. Experiments are selected from ArrayExpress and groups of samples are manually identified for comparison e.g. those with wild type genotype compared to those with a gene knock out. Each experiment is processed through our in-house differential expression statistical analysis pipeline to identify genes with a high probability of differential expression.

Portal de Datos Genómicos del SNDG

Sistema Nacional de Datos Genómicos - Portal de datos

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<<<!!!<<< This repository is no longer available. >>>!!!>>>

Greengenes

The Greengenes Database

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Greengenes is an Earth Sciences website that assists clinical and environmental microbiologists from around the globe in classifying microorganisms from their local environments. A 16S rRNA gene database addresses limitations of public repositories by providing chimera screening, standard alignment, and taxonomic classification using multiple published taxonomies.

ChIP-Seq Transcription Factor Data

ChIP-Seq

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We developed a method, ChIP-sequencing (ChIP-seq), combining chromatin immunoprecipitation (ChIP) and massively parallel sequencing to identify mammalian DNA sequences bound by transcription factors in vivo. We used ChIP-seq to map STAT1 targets in interferon-gamma (IFN-gamma)-stimulated and unstimulated human HeLa S3 cells, and compared the method's performance to ChIP-PCR and to ChIP-chip for four chromosomes.For both Chromatin- immunoprecipation Transcription Factors and Histone modifications. Sequence files and the associated probability files are also provided.

IMGT/LIGM-DBI

International ImMunoGeneTics information system / Laboratoire d'ImmunoGénétique Moléculaire-Database

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IMGT/LIGM-DB is a comprehensive database of Immunoglobulins (IG) and T cell Receptors (TR) from human and other vertebrates, with translation for fully annotated sequences.

Wellcome Trust Sanger Institute, Scientific resources

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The Wellcome Trust Sanger Institute is a charitably funded genomic research centre located in Hinxton, nine miles south of Cambridge in the UK. We study diseases that have an impact on health globally by investigating genomes. Building on our past achievements and based on priorities that exploit the unique expertise of our Faculty of researchers, we will lead global efforts to understand the biology of genomes. We are convinced of the importance of making this research available and accessible for all audiences. reduce global health burdens.

GENCODE

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GENCODE is a scientific project in genome research and part of the ENCODE (ENCyclopedia Of DNA Elements) scale-up project. The GENCODE consortium was initially formed as part of the pilot phase of the ENCODE project to identify and map all protein-coding genes within the ENCODE regions (approx. 1% of Human genome). Given the initial success of the project, GENCODE now aims to build an “Encyclopedia of genes and genes variants” by identifying all gene features in the human and mouse genome using a combination of computational analysis, manual annotation, and experimental validation, and annotating all evidence-based gene features in the entire human genome at a high accuracy.

enviPath

The enironmental contaminant biotransormation pathway resource

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enviPath is a database and prediction system for the microbial biotransformation of organic environmental contaminants. The database provides the possibility to store and view experimentally observed biotransformation pathways. The pathway prediction system provides different relative reasoning models to predict likely biotransformation pathways and products.

RCSB Protein Data Bank

RCSB PDB

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The Protein Data Bank (PDB) archive is the single worldwide repository of information about the 3D structures of large biological molecules, including proteins and nucleic acids. These are the molecules of life that are found in all organisms including bacteria, yeast, plants, flies, other animals, and humans. Understanding the shape of a molecule helps to understand how it works. This knowledge can be used to help deduce a structure's role in human health and disease, and in drug development. The structures in the archive range from tiny proteins and bits of DNA to complex molecular machines like the ribosome.

SWISS-MODEL Repository

SMR

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The SWISS-MODEL Repository is a database of annotated three-dimensional comparative protein structure models generated by the fully automated homology-modelling pipeline SWISS-MODEL.

IODP Bremen Core Repository

BCR

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The Bremen Core Repository - BCR, for International Ocean Discovery Program (IODP), Integrated Ocean Discovery Program (IODP), Ocean Drilling Program (ODP), and Deep Sea Drilling Project (DSDP) cores from the Atlantic Ocean, Mediterranean and Black Seas and Arctic Ocean is operated at University of Bremen within the framework of the German participation in IODP. It is one of three IODP repositories (beside Gulf Coast Repository (GCR) in College Station, TX, and Kochi Core Center (KCC), Japan). One of the scientific goals of IODP is to research the deep biosphere and the subseafloor ocean. IODP has deep-frozen microbiological samples from the subseafloor available for interested researchers and will continue to collect and preserve geomicrobiology samples for future research.

CyberCell Database

CCDB

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The CyberCell database (CCDB) is a comprehensive collection of detailed enzymatic, biological, chemical, genetic, and molecular biological data about E. coli (strain K12, MG1655). It is intended to provide sufficient information and querying capacity for biologists and computer scientists to use computers or detailed mathematical models to simulate all or part of a bacterial cell at a nanoscopic (10-9 m), mesoscopic (10-8 m).The CyberCell database CCDB actually consists of 4 browsable databases: 1) the main CyberCell database (CCDB - containing gene and protein information), 2) the 3D structure database (CC3D – containing information for structural proteomics), 3) the RNA database (CCRD – containing tRNA and rRNA information), and 4) the metabolite database (CCMD – containing metabolite information). Each of these databases is accessible through hyperlinked buttons located at the top of the CCDB homepage. All CCDB sub-databases are fully web enabled, permitting a wide variety of interactive browsing, search and display operations. and microscopic (10-6 m) level.

The Cancer Immunome Atlas

TCIA

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The Cancer Immunome Database (TCIA) provides results of comprehensive immunogenomic analyses of next generation sequencing data (NGS) data for 20 solid cancers from The Cancer Genome Atlas (TCGA) and other datasource. The Cancer Immunome Atlas (TCIA) was developed and is maintained at the Division of Bioinformatics (ICBI). The database can be queried for the gene expression of specific immune-related gene sets, cellular composition of immune infiltrates (characterized using gene set enrichment analyses and deconvolution), neoantigens and cancer-germline antigens, HLA types, and tumor heterogeneity (estimated from cancer cell fractions). Moreover it provides survival analyses for different types immunological parameters. TCIA will be constantly updated with new data and results.

Malaria Atlas Project

MAP

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The Malaria Atlas Project (MAP) brings together researchers based around the world with expertise in a wide range of disciplines from public health to mathematics, geography and epidemiology. We work together to generate new and innovative methods of mapping malaria risk. Ultimately our goal is to produce a comprehensive range of maps and estimates that will support effective planning of malaria control at national and international scales.

KBase

KBase: The U.S. Department of Energy Systems Biology Knowledgebase

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The Department of Energy Systems Biology Knowledgebase (KBase) is a software and data platform designed to meet the grand challenge of systems biology: predicting and designing biological function. KBase integrates data and tools in a unified graphical interface so users do not need to access them from numerous sources or learn multiple systems in order to create and run sophisticated systems biology workflows. Users can perform large-scale analyses and combine multiple lines of evidence to model plant and microbial physiology and community dynamics. KBase is the first large-scale bioinformatics system that enables users to upload their own data, analyze it (along with collaborator and public data), build increasingly realistic models, and share and publish their workflows and conclusions. KBase aims to provide a knowledgebase: an integrated environment where knowledge and insights are created and multiplied.

Follicular Lymphoma Genome Data at Canada's Michael Smith Genome Sciences Centre (BCGSC)

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<<<!!!<<< Genome data generated by BC Genome Sciences Centre is no longer available through this site as it is regularly deposited into controlled data repositories such as the European Genome Phenome Archive (EGA); ICGC (International Cancer Genome Consortium) and the Genome Data Commons (GDC) >>>!!!>>> Mapping, copy number analysis, sequence and gene expression data generated by the High Resolution Analysis of Follicular Lymphoma Genomes project. The data will be available for 24 patients with follicular lymphoma. All data will be made as widely and freely available as possible while safeguarding the privacy of participants, and protecting confidential and proprietary data.The data from this project will be submitted to public genomic data sources. These sources will be listed on this web site as the data becomes available in these external data sources.

Mouse Atlas of Gene Expression

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<<<!!!<<< This repository is no longer available >>>!!!>>>

Human Metabolome Database

HMDB

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The Human Metabolome Database (HMDB) is a freely available electronic database containing detailed information about small molecule metabolites found in the human body. It is intended to be used for applications in metabolomics, clinical chemistry, biomarker discovery and general education.

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.

UCLanData

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Repository of research data sets created under the auspices of the University of Central Lancashire

Australian Drosophila Ecology and Evolution Resource

ADEER

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The Australian Drosophila Ecology and Evolution Resource (ADEER) from the Hoffmann lab and other contributors is a nationally significant life science collection. The Drosophila Clinal Data Collection contains data on populations along the eastern coast of Australia. It remains an excellent resource for understanding past and future evolutionary responses to climate change. The Drosophila Genomic Data Collection hosts Drosophila genomes sequenced as part of the Genomic Basis for Adaptation to Climate Change Project. 23 genomes have been sequenced as part of this project. Currently assemblies and annotations are available for Drosophila birchii, D. bunnanda, D. hydei, and D. repleta. The Drosophila Species Distribution Data Collection contains distribution data of nine drosophilid species that have been collected in Australia by the Hoffmann lab and other research groups between 1924 and 2005. More than 300 drosophilid species have been identified in the tropical and temperate forests located on the east coast of Australia. Many species are restricted to the tropics, a few are temperate specialists, and some have broad distributions across climatic regions. Their varied distribution along the tropical - temperate cline provide a powerful tool for studying climate adaptation and species distribution limits.

The Antibody Registry

ABR

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The Antibody Registry supports the RRID Initiative and exists to give researchers a way to universally identify antibodies used in publications. The registry lists many commercial antibodies from over 200 vendors, which have been assigned a unique identifier and over 2000 individual laboratories. If the antibody that you are using does not appear in the list, an entry can be made by filling in as little as 2 pieces of information: the catalog number and the url of the vendor where our curators can find information and material data sheets.