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Found 65 result(s)

GISAID

GISAID EpiFlu database

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The GISAID Initiative promotes the international sharing of all influenza virus sequences, related clinical and epidemiological data associated with human viruses, and geographical as well as species-specific data associated with avian and other animal viruses, to help researchers understand how the viruses evolve, spread and potentially become pandemics. *** GISAID does so by overcoming disincentives/hurdles or restrictions, which discourage or prevented sharing of influenza data prior to formal publication. *** The Initiative ensures that open access to data in GISAID is provided free-of-charge and to everyone, provided individuals identify themselves and agree to uphold the GISAID sharing mechanism governed through its Database Access Agreement. GISAID calls on all users to agree to the basic premise of upholding scientific etiquette, by acknowledging the originating laboratories providing the specimen and the submitting laboratories who generate the sequence data, ensuring fair exploitation of results derived from the data, and that all users agree that no restrictions shall be attached to data submitted to GISAID, to promote collaboration among researchers on the basis of open sharing of data and respect for all rights and interests.

hPSCreg

human Pluripotent Stem Cell registry

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The human pluripotent stem cell registry (hPSCreg) is a public registry and data portal for human embryonic and induced pluripotent stem cell lines (hESC and hiPSC). The Registry provides comprehensive and standardized biological and legal information as well as tools to search and compare information from multiple hPSC sources and hence addresses a translational research need. To facilitate unambiguous identification over different resources, hPSCreg automatically creates a unique standardized name (identifier) for each cell line registered. In addition to biological information, hPSCreg stores extensive data about ethical standards regarding cell sourcing and conditions for application and privacy protection. hPSCreg is the first global registry that holds both, manually validated scientific and ethical information on hPSC lines, and provides access by means of a user-friendly, mobile-ready web application.

COVID-19 Data Portal

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The COVID-19 Data Portal was launched in April 2020 to bring together relevant datasets for sharing and analysis in an effort to accelerate coronavirus research. It enables researchers to upload, access and analyse COVID-19 related reference data and specialist datasets as part of the wider European COVID-19 Data Platform.

Cancer Genomics Hub

CGHub

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>>>>!!!!<<<< The Cancer Genomics Hub mission is now completed. The Cancer Genomics Hub was established in August 2011 to provide a repository to The Cancer Genome Atlas, the childhood cancer initiative Therapeutically Applicable Research to Generate Effective Treatments and the Cancer Genome Characterization Initiative. CGHub rapidly grew to be the largest database of cancer genomes in the world, storing more than 2.5 petabytes of data and serving downloads of nearly 3 petabytes per month. As the central repository for the foundational genome files, CGHub streamlined team science efforts as data became as easy to obtain as downloading from a hard drive. The convenient access to Big Data, and the collaborations that CGHub made possible, are now essential to cancer research. That work continues at the NCI's Genomic Data Commons. All files previously stored at CGHub can be found there. The Website for the Genomic Data Commons is here: https://gdc.nci.nih.gov/ >>>>!!!!<<<< The Cancer Genomics Hub (CGHub) is a secure repository for storing, cataloging, and accessing cancer genome sequences, alignments, and mutation information from the Cancer Genome Atlas (TCGA) consortium and related projects. Access to CGHub Data: All researchers using CGHub must meet the access and use criteria established by the National Institutes of Health (NIH) to ensure the privacy, security, and integrity of participant data. CGHub also hosts some publicly available data, in particular data from the Cancer Cell Line Encyclopedia. All metadata is publicly available and the catalog of metadata and associated BAMs can be explored using the CGHub Data Browser.

NIDDK Information Network

National Institute of Diabetes and Digestive and Kidney Disease Information Network

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The NIDDK Information Network (dkNET) serves the needs of basic and clinical investigators by providing seamless access to large pools of data and research resources relevant to the mission of The National Institute of Diabetes Digestive and Kidney Diseases (NIDDK).

bio.tools

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bio.tools is a software registry for bioinformatics and the life sciences.

MorpheusML model repository

Morpheus model repository

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The public MorpheusML model repository collects, curates, documents and tests computational models for multi-scale and multicellular biological systems. Model must be encoded in the model description language MorpheusML. Subsections of the repository distinguish published models from contributed non-published and example models. New models are simulated in Morpheus or Artistoo independently from the authors and results are compared to published results. Successful reproduction is documented on the model's webpage. Models in this repository are included into the CI and test pipelines for each release of the model simulator Morpheus to check and guarantee reproducibility of results across future simulator updates. The model’s webpage provides a History-link to all past model versions and edits that are automatically tracked via Git. Each model is registered with a unique and persistent ID of the format M..... The model description page (incl. the biological context and key results of that model), the model’s XML file, the associated paper, and all further files (often simulation result videos) connected with that model can be retrieved via a persistent URL of the format https://identifiers.org/morpheus/M..... - for technical details on the citable ModelID please see https://registry.identifiers.org/registry/morpheus - for the model definition standard MorpheusML please see https://doi.org/10.25504/FAIRsharing.78b6a6 - for the model simulator Morpheus please see https://morpheus.gitlab.io - for the model simulator Artistoo please see https://artistoo.net/converter.html

National Parasite Resource Center

国家寄生虫资源库

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From 2005 to 2008, with the support of the Ministry of Science and Technology (MOST), the construction of parasite germplasm repositories has spread to 20 conservation institutions in 15 provinces (cities) nationwide, with 3 physical exhibition halls; 3 live parasite conservation centers. A total of 1115 species/117814 pieces of parasitic germplasm resources of 23 orders in 11 phyla have been integrated into the physical library and database, including human parasites and vectors, animal parasites, plant nematodes, medical insects, trematodes, and parasitic snails, and the resources are combined with moderate distribution, medium- and long-term support, and off-site duplicates. The number of resources accounts for 39.27% of the national total. Through 10 years of accumulation, we have built the largest and only parasite species resource database in the field of parasites in China, and created a sharing platform of parasite germplasm resource center.

IMGT/PRIMER-DB

International ImMunoGeneTics information system/PRIMER-Database

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The IMGT/PRIMER-DB database provides standardized information on oligonucleotides or primers of the immunoglobulins (IG) and T cell receptors (TR).

BRENDA

BRENDA Enzyme Database

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BRENDA is the main collection of enzyme functional data available to the scientific community worldwide. The enzymes are classified according to the Enzyme Commission list of enzymes. It is available free of charge for via the internet (http://www.brenda-enzymes.org/) and as an in-house database for commercial users (requests to our distributor Biobase). The enzymes are classified according to the Enzyme Commission list of enzymes. Some 5000 "different" enzymes are covered. Frequently enzymes with very different properties are included under the same EC number. BRENDA includes biochemical and molecular information on classification, nomenclature, reaction, specificity, functional parameters, occurrence, enzyme structure, application, engineering, stability, disease, isolation, and preparation. The database also provides additional information on ligands, which function as natural or in vitro substrates/products, inhibitors, activating compounds, cofactors, bound metals, and other attributes.

Array Express

functional genomics data

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ArrayExpress is one of the major international repositories for high-throughput functional genomics data from both microarray and high-throughput sequencing studies, many of which are supported by peer-reviewed publications. Data sets are submitted directly to ArrayExpress and curated by a team of specialist biological curators. In the past (until 2018) datasets from the NCBI Gene Expression Omnibus database were imported on a weekly basis. Data is collected to MIAME and MINSEQE standards.

The Zebrafish Information Network

ZFIN

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ZFIN serves as the zebrafish model organism database. The long term goals for ZFIN are a) to be the community database resource for the laboratory use of zebrafish, b) to develop and support integrated zebrafish genetic, genomic and developmental information, c) to maintain the definitive reference data sets of zebrafish research information, d) to link this information extensively to corresponding data in other model organism and human databases, e) to facilitate the use of zebrafish as a model for human biology and f) to serve the needs of the research community. ZIRC is the Zebrafish International Resource Center, an independent NIH-funded facility providing a wide range of zebrafish lines, probes and health services. ZFIN works closely with ZIRC to connect our genetic data with available probes and fish lines.

National Center for Ecological Analysis and Synthesis Data Repository

NCEAS Data Repository

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The NCEAS Data Repository contains information about the research data sets collected and collated as part of NCEAS' funded activities. Information in the NCEAS Data Repository is concurrently available through the Knowledge Network for Biocomplexity (KNB), an international data repository. A number of the data sets were synthesized from multiple data sources that originated from the efforts of many contributors, while others originated from a single. Datasets can be found at KNB repository https://knb.ecoinformatics.org/data , creator=NCEAS

DNA Data Bank of Japan

DDBJ

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DDBJ; DNA Data Bank of Japan is the sole nucleotide sequence data bank in Asia, which is officially certified to collect nucleotide sequences from researchers and to issue the internationally recognized accession number to data submitters.Since we exchange the collected data with EMBL-Bank/EBI; European Bioinformatics Institute and GenBank/NCBI; National Center for Biotechnology Information on a daily basis, the three data banks share virtually the same data at any given time. The virtually unified database is called "INSD; International Nucleotide Sequence Database DDBJ collects sequence data mainly from Japanese researchers, but of course accepts data and issue the accession number to researchers in any other countries.

Mutant Mouse Resource & Research Centers

MMRRC

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The MMRRC is the nation’s premier national public repository system for mutant mice. Funded by the NIH continuously since 1999, the MMRRC archives and distributes scientifically valuable spontaneous and induced mutant mouse strains and ES cell lines for use by the biomedical research community. The MMRRC consists of a national network of breeding and distribution repositories and an Informatics Coordination and Service Center located at 4 major academic centers across the nation. The MMRRC is committed to upholding the highest standards of experimental design and quality control to optimize the reproducibility of research studies using mutant mice.

The Chemical Probes Portal

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The Chemical Probes Portal is an online open access catalog of annotated small molecule inhibitors, agonists and other chemical tools for biological research and preclinical drug discovery. Annotations for are extensive and distinguish between activity in cells and model organisms.

University of Waterloo Dataverse

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The University of Waterloo Dataverse is a data repository for research outputs of our faculty, students, and staff. Files are held in a secure environment on Canadian servers. Researchers can choose to make content available to the public, to specific individuals, or to keep it private.

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.

LINCS Data Portal

Library of Integrated Network-based Signatures Data Portal

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LINCS Data Portal provides access to LINCS data from various sources. The program has six Data and Signature Generation Centers: Drug Toxicity Signature Generation Center, HMS LINCS Center, LINCS Center for Transcriptomics, LINCS Proteomic Characterization Center for Signaling and Epigenetics, MEP LINCS Center, and NeuroLINCS Center.

World Register of Marine Species

WoRMS

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The World Register of Marine Species (WoRMS) integrates approximately 100 marine datbases to provide an authoritative and comprehensive list of marine organisms. WoRMS has an editorial system where taxonomic groups are managed by experts responsible for the quality of the information. WorMS register of marine species emerged from the European Register of Marine Species (ERMS) and the Flanders Marine Institute (VLIZ). WoRMS is a contribution to Lifewatch, Catalogue of Life, Encyclopedia of Life, Global Biodiversity Information Facility and the Census of Marine Life.

GermOnline

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GermOnline 4.0 is a cross-species database gateway focusing on high-throughput expression data relevant for germline development, the meiotic cell cycle and mitosis in healthy versus malignant cells. The portal provides access to the Saccharomyces Genomics Viewer (SGV) which facilitates online interpretation of complex data from experiments with high-density oligonucleotide tiling microarrays that cover the entire yeast genome.

database of Sequence Tagged Sites

dbSTS

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<<<!!!<<< The page is no longer available. This database was already retired, and on this page users could find information on how to search and use these sequences. dbSTS was an NCBI resource that contained sequence data for short genomic landmark sequences or Sequence Tagged Sites. STS sequences are incorporated into the STS Division of GenBank. >>>!!!>>>

Tierstimmenarchiv - Museum für Naturkunde Berlin

Animal Sound Archive - Museum für Naturkunde Berlin

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The Animal Sound Archive at the Museum für Naturkunde in Berlin is one of the oldest and largest collections of animal sounds. Presently, the collection consists of about 120,000 bioacoustical recordings comprising almost all groups of animals: 1.800 bird species 580 mammalian species more then150 species of invertebrates; some fishes, amphibians and reptiles

OMICtools

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>>>!!!<<< OMICtools is no longer online >>>!!!<<< We founded OMICtools in 2012 with the vision to drive progress in life science. We wanted to empower life science practitioners all over the world to achieve breakthroughs by getting data to talk. While we made tremendous progress over the past three years, developing a bioinformatics database of software and dynamic protocols, attracting more than 1.5M visitors a year, we lacked the financial support we needed to continue. We certainly gave it our all. We'd like to thank everyone who believed in us and supported us on this journey: all our users, our community, our friends, families and employees (who we consider as our extended family!). omicX will probably shut down its operations within the next few weeks. The team and I remain firmly committed to our vision, particularly at this very difficult time. It is now, more than ever before, that researchers need access to a resource that pools collective scientific intelligence. We have accumulated an awful lot of experience which we are keen to share. If your institution would be interested in taking over our website and database, to provide researchers with continued access to the platform, or you simply want to stay in touch with the omicX team, contact us at contact@omictools.com or at carine.toutain@fhbx.eu.

Ag Data Commons

USDA’s Open Research Data

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Ag Data Commons provides access to a wide variety of open data relevant to agricultural research. We are a centralized repository for data already on the web, as well as for new data being published for the first time. While compliance with the U.S. Federal public access and open data directives is important, we aim to surpass them. Our goal is to foster innovative data re-use, integration, and visualization to support bigger, better science and policy.