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Found 38 result(s)
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The European Xenopus Resource Centre (EXRC) is situated in Portsmouth, United Kingdom and provides tools and services to support researchers using Xenopus models. The EXRC depends on researchers to obtain and deposit Xenopus transgenic and mutant lines, Xenopus in-situ hybridization clones, Xenopus specific antibodies and other resources with the centre. EXRC staff perform quality assurance testing on these reagents and then makes them available to the community at cost. EXRC also supplies wild type Xenopus, embryos, oocytes, egg extracts, X.tropicalis Fosmids, X.laevis BACs and ORFeomes.
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AlphaFold DB provides open access to protein structure predictions for the human proteome and 20 other key organisms to accelerate scientific research.
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A bioinformatic database of antimicrobial resistance genes, their products and associated phenotypes.
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The LJMU Research Data Repository is the University's institutional repository where researchers can safely deposit and store research data on an Open Access basis.
Data stored in the LJMU Research Data Repository can be made freely available to anyone online and located by users of web search engines.
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The Intermediate Filament Database will function as a continuously updated review of the intermediate filament field and it is hoped that users will contribute to the development and expansion of the database on a regular basis. Contributions may include novel variants, new patients with previously discovered sequence and allelic variants. Suggestions on ways to improve the database are also welcome.
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!!! >>> the repository is offline >>> !!! GOBASE is a taxonomically broad organelle genome database that organizes and integrates diverse data related to mitochondria and chloroplasts. GOBASE is currently expanding to include information on representative bacteria that are thought to be specifically related to the bacterial ancestors of mitochondria and chloroplasts
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<<<!!!<<< The repository is no longer available. You can find the data using https://www.re3data.org/repository/r3d100010199 and searching for WATCH. Further information see: https://catalogue.ceh.ac.uk/documents/ba6e8ddd-22a9-457d-acf4-d63cd34f2dda >>>!!!>>>
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<<<!!!<<< As of 2023, support to maintain the www.modencode.org and intermine.modencode.org sites have been retired following the end of funding. To access data from the modENCODE project, or for questions regarding the data they make available, please visit these databases:
Fly data:
FlyBase: ModENCODE data at FlyBase: https://wiki.flybase.org/wiki/FlyBase:ModENCODE_data_at_FlyBase
FlyBase: https://www.re3data.org/repository/r3d100010591
Worm data: WormBase https://www.re3data.org/repository/r3d100010424
Data, including modENCODE and modERN project data, is also available at the ENCODE Portal: https://www.re3data.org/repository/r3d100013051 (search metadata and view datasets for Drosophila and Caenorhabditis https://www.encodeproject.org/matrix/?type=Experiment&control_type!=*&status=released&replicates.library.biosample.donor.organism.scientific_name=Drosophila+melanogaster&replicates.library.biosample.donor.organism.scientific_name=Caenorhabditis+elegans&replicates.library.biosample.donor.organism.scientific_name=Drosophila+pseudoobscura&replicates.library.biosample.donor.organism.scientific_name=Drosophila+mojavensis).
>>>!!!>>>
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INDEPTH is a global network of research centres that conduct longitudinal health and demographic evaluation of populations in low- and middle-income countries (LMICs). INDEPTH aims to strengthen global capacity for Health and Demographic Surveillance Systems (HDSSs), and to mount multi-site research to guide health priorities and policies in LMICs, based on up-to-date scientific evidence. The data collected by the INDEPTH Network members constitute a valuable resource of population and health data for LMIC countries. This repository aims to make well documented anonymised longitudinal microdata from these Centres available to data users.
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<<<!!!<<< See UniProt entry https://www.re3data.org/repository/r3d100011521 >>>!!!>>>
UniProtKB/Swiss-Prot is the manually annotated and reviewed section of the UniProt Knowledgebase (UniProtKB).
It is a high quality annotated and non-redundant protein sequence database, which brings together experimental results, computed features and scientific conclusions.
Since 2002, it is maintained by the UniProt consortium and is accessible via the UniProt website.
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>>>!!!<<< as stated 2017-06-09 MPIDB is no longer available under URL http://www.jcvi.org/mpidb/about.php >>>!!!<<< The microbial protein interaction database (MPIDB) aims to collect and provide all known physical microbial interactions. Currently, 24,295 experimentally determined interactions among proteins of 250 bacterial species/strains can be browsed and downloaded. These microbial interactions have been manually curated from the literature or imported from other databases (IntAct, DIP, BIND, MINT) and are linked to 26,578 experimental evidences (PubMed ID, PSI-MI methods). In contrast to these databases, interactions in MPIDB are further supported by 68,346 additional evidences based on interaction conservation, protein complex membership, and 3D domain contacts (iPfam, 3did). We do not include (spoke/matrix) binary interactions infered from pull-down experiments.
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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
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When published in 2005, the Millennium Run was the largest ever simulation of the formation of structure within the ΛCDM cosmology. It uses 10(10) particles to follow the dark matter distribution in a cubic region 500h(−1)Mpc on a side, and has a spatial resolution of 5h−1kpc. Application of simplified modelling techniques to the stored output of this calculation allows the formation and evolution of the ~10(7) galaxies more luminous than the Small Magellanic Cloud to be simulated for a variety of assumptions about the detailed physics involved. As part of the activities of the German Astrophysical Virtual Observatory we have created relational databases to store the detailed assembly histories both of all the haloes and subhaloes resolved by the simulation, and of all the galaxies that form within these structures for two independent models of the galaxy formation physics. We have implemented a Structured Query Language (SQL) server on these databases. This allows easy access to many properties of the galaxies and halos, as well as to the spatial and temporal relations between them. Information is output in table format compatible with standard Virtual Observatory tools. With this announcement (from 1/8/2006) we are making these structures fully accessible to all users. Interested scientists can learn SQL and test queries on a small, openly accessible version of the Millennium Run (with volume 1/512 that of the full simulation). They can then request accounts to run similar queries on the databases for the full simulations. In 2008 and 2012 the simulations were repeated.
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>>>!!!<<< GeneDB will be taken offline 1st of August 2021, as none of the genomes are curated at Sanger anymore. All genomes on GeneDB can now be found on PlasmoDB, FungiDB, TriTrypDB and Wormbase Parasite. >>>!!!<<<
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The WDC Geomagnetism, Edinburgh has a comprehensive set of digital geomagnetic data as well as indices of geomagnetic activity supplied from a worldwide network of magnetic observatories. The data and services at the WDC are available for scientific use without restrictions.
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The miRBase database is a searchable database of published miRNA sequences and annotation. Each entry in the miRBase Sequence database represents a predicted hairpin portion of a miRNA transcript (termed mir in the database), with information on the location and sequence of the mature miRNA sequence (termed miR). Both hairpin and mature sequences are available for searching and browsing, and entries can also be retrieved by name, keyword, references and annotation. All sequence and annotation data are also available for download. The miRBase Registry provides miRNA gene hunters with unique names for novel miRNA genes prior to publication of results.
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PDBe is the European resource for the collection, organisation and dissemination of data on biological macromolecular structures. In collaboration with the other worldwide Protein Data Bank (wwPDB) partners - the Research Collaboratory for Structural Bioinformatics (RCSB) and BioMagResBank (BMRB) in the USA and the Protein Data Bank of Japan (PDBj) - we work to collate, maintain and provide access to the global repository of macromolecular structure data. We develop tools, services and resources to make structure-related data more accessible to the biomedical community.
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The ADAS Project is a self-funding (i.e. funded by participants) project consisting of most major fusion laboratories along with other astrophysical and university groups. As an implementation, it is an interconnected set of computer codes and data collections for modelling the radiating properties of ions and atoms in plasmas. It can address plasmas ranging from the interstellar medium through the solar atmosphere and laboratory thermonuclear fusion devices to technological plasmas. ADAS assists in the analysis and interpretation of spectral emission and supports detailed plasma models.
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Chempound is a new generation repository architecture based on RDF, semantic dictionaries and linked data. It has been developed to hold any type of chemical object expressible in CML and is exemplified by crystallographic experiments and computational chemistry calculations. In both examples, the repository can hold >50k entries which can be searched by SPARQL endpoints and pre-indexing of key fields. The Chempound architecture is general and adaptable to other fields of data-rich science.
The Chempound software is hosted at http://bitbucket.org/chempound and is available under the Apache License, Version 2.0
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<<<!!!<<< This repository is no longer available.
SPECTRa (Submission, Preservation and Exposure of Chemistry Teaching and Research Data) was a collaboration between Cambridge University and Imperial College to research issues in the deposition of chemistry data in Open Access digital repositories. Funded by the JISC (Joint Information Systems Committee) under its Digital Repositories programme, it ran from October 2005 to March 2007. Requirements for and attitudes towards data archiving and open access publication were discovered by interview and survey. This led to the development of a set of Open Source software tools for packaging and submitting X-ray crystallography, NMR spectra and computational chemistry data to DSpace digital repositories.
This collection will hold reports, presentations and papers published from the project: https://www.repository.cam.ac.uk/handle/1810/183858 >>>!!!>>>
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The European Nucleotide Archive (ENA) captures and presents information relating to experimental workflows that are based around nucleotide sequencing. A typical workflow includes the isolation and preparation of material for sequencing, a run of a sequencing machine in which sequencing data are produced and a subsequent bioinformatic analysis pipeline. ENA records this information in a data model that covers input information (sample, experimental setup, machine configuration), output machine data (sequence traces, reads and quality scores) and interpreted information (assembly, mapping, functional annotation).
Data arrive at ENA from a variety of sources. These include submissions of raw data, assembled sequences and annotation from small-scale sequencing efforts, data provision from the major European sequencing centres and routine and comprehensive exchange with our partners in the International Nucleotide Sequence Database Collaboration (INSDC).
Provision of nucleotide sequence data to ENA or its INSDC partners has become a central and mandatory step in the dissemination of research findings to the scientific community. ENA works with publishers of scientific literature and funding bodies to ensure compliance with these principles and to provide optimal submission systems and data access tools that work seamlessly with the published literature.
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<<<!!!<<< CRAWDAD has moved to IEEE-Dataport https://www.re3data.org/repository/r3d100012569
The datasets in the Community Resource for Archiving Wireless Data at Dartmouth (CRAWDAD) repository are now hosted as the CRAWDAD Collection on IEEE Dataport. After nearly two decades as a stand-alone archive at crawdad.org, the migration of the collection to IEEE DataPort provides permanence and new visibility. >>>!!!>>>
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-----<<<<< The repository is no longer available. This record is out-dated. The Matter lab provides the archived database version of 2012 and 2013 at https://www.matter.toronto.edu/basic-content-page/data-download. Data linked from the World Community Grid - The Clean Energy Project see at https://www.worldcommunitygrid.org/research/cep1/overview.do and on fighshare https://figshare.com/articles/dataset/moldata_csv/9640427 >>>>>----- The Clean Energy Project Database (CEPDB) is a massive reference database for organic semiconductors with a particular emphasis on photovoltaic applications. It was created to store and provide access to data from computational as well as experimental studies, on both known and virtual compounds. It is a free and open resource designed to support researchers in the field of organic electronics in their scientific pursuits.
The CEPDB was established as part of the Harvard Clean Energy Project (CEP), a virtual high-throughput screening initiative to identify promising new candidates for the next generation of carbon-based solar cell materials.
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The NBN Atlas is a collaborative project that aggregates biodiversity data from multiple sources and makes it available and usable online. It is the UK’s largest collection of freely available biodiversity data.
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The PRIDE PRoteomics IDEntifications database is a centralized, standards compliant, public data repository for proteomics data, including protein and peptide identifications, post-translational modifications and supporting spectral evidence. PRIDE encourages and welcomes direct user submissions of mass spectrometry data to be published in peer-reviewed publications.
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- re3data COREF
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- Cite this service: re3data.org - Registry of Research Data Repositories. https://doi.org/10.17616/R3D last accessed: 2024-04-27
