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Found 72 result(s)

Project Data Sphere

PDS

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Project Data Sphere, LLC, operates a free digital library-laboratory where the research community can broadly share, integrate and analyze historical, de-identified, patient-level data from academic and industry cancer Phase II-III clinical trials. These patient-level datasets are available through the Project Data Sphere platform to researchers affiliated with life science companies, hospitals and institutions, as well as independent researchers, at no cost and without requiring a research proposal.

Stanford Network Analysis Project

SNAP

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Stanford Network Analysis Platform (SNAP) is a general purpose network analysis and graph mining library. It is written in C++ and easily scales to massive networks with hundreds of millions of nodes, and billions of edges. It efficiently manipulates large graphs, calculates structural properties, generates regular and random graphs, and supports attributes on nodes and edges. SNAP is also available through the NodeXL which is a graphical front-end that integrates network analysis into Microsoft Office and Excel. The SNAP library is being actively developed since 2004 and is organically growing as a result of our research pursuits in analysis of large social and information networks. Largest network we analyzed so far using the library was the Microsoft Instant Messenger network from 2006 with 240 million nodes and 1.3 billion edges. The datasets available on the website were mostly collected (scraped) for the purposes of our research. The website was launched in July 2009.

HUGO Gene Nomenclature Committee

HGNC

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The HUGO Gene Nomenclature Committee (HGNC) assigned unique gene symbols and names to over 35,000 human loci, of which around 19,000 are protein coding. This curated online repository of HGNC-approved gene nomenclature and associated resources includes links to genomic, proteomic and phenotypic information, as well as dedicated gene family pages.

WorldWide Antimalarial Resistance Network

WWARN

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The WorldWide Antimalarial Resistance Network (WWARN) is a collaborative platform generating innovative resources and reliable evidence to inform the malaria community on the factors affecting the efficacy of antimalarial medicines. Access to data is provided through diverse Tools and Resources: WWARN Explorer, Molecular Surveyor K13 Methodology, Molecular Surveyor pfmdr1 & pfcrt, Molecular Surveyor dhfr & dhps.

Pombase

The scientific resource for fission yeast

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PomBase is a comprehensive database for the fission yeast Schizosaccharomyces pombe, providing structural and functional annotation, literature curation and access to large-scale data sets.

NMRshiftDB

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nmrshiftdb is a NMR database (web database) for organic structures and their nuclear magnetic resonance (nmr) spectra. It allows for spectrum prediction (13C, 1H and other nuclei) as well as for searching spectra, structures and other properties. Last not least, it features peer-reviewed submission of datasets by its users. The nmrshiftdb2 software is open source, the data is published under an open content license. Please consult the documentation for more detailed information. nmrshiftdb2 is the continuation of the NMRShiftDB project with additional data and bugfixes and changes in the software.

RDP

Ribosomal Database Project

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<<<!!!<<< The RDP website is no longer available. A stand-alone version of the RDP Classifier is available on Sorceforge https://sourceforge.net/projects/rdp-classifier/. Instructions for installing a command-line version of RDP Tools can be found at Dr. J.Quensen's Website https://john-quensen.com/tutorials/tutorial-1/ and https://jfq3.gitbook.io/rdptools-docker/rdptools-docker/readme. >>>!!!>>>

VegBank

The Vegetation Plot Archive Project

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VegBank is the vegetation plot database of the Ecological Society of America's Panel on Vegetation Classification. VegBank consists of three linked databases that contain the actual plot records, vegetation types recognized in the U.S. National Vegetation Classification and other vegetation types submitted by users, and all plant taxa recognized by ITIS/USDA as well as all other plant taxa recorded in plot records. Vegetation records, community types and plant taxa may be submitted to VegBank and may be subsequently searched, viewed, annotated, revised, interpreted, downloaded, and cited. VegBank receives its data from the VegBank community of users.

ModelDB

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ModelDB is a curated database of published models in the broad domain of computational neuroscience. It addresses the need for access to such models in order to evaluate their validity and extend their use. It can handle computational models expressed in any textual form, including procedural or declarative languages (e.g. C++, XML dialects) and source code written for any simulation environment. The model source code doesn't even have to reside inside ModelDB; it just has to be available from some publicly accessible online repository or WWW site.

Canadian Astronomy Data Centre

Centre canadien de données astronomiques

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The Canadian Astronomy Data Centre (CADC) was established in 1986 by the National Research Council of Canada (NRC), through a grant provided by the Canadian Space Agency (CSA). Over the past 30 years the CADC has evolved from an archiving centre---hosting data from Hubble Space Telescope, Canada-France-Hawaii Telescope, the Gemini observatories, and the James Clerk Maxwell Telescope---into a Science Platform for data-intensive astronomy. The CADC, in partnership with Shared Services Canada, Compute Canada, CANARIE and the university community (funded through the Canadian Foundation for Innovation), offers cloud computing, user-managed storage, group management, and data publication services, in addition to its ongoing mission to provide permanent storage for major data collections. Located at NRC Herzberg Astronomy and Astrophysics Research Centre in Victoria, BC, the CADC staff consists of professional astronomers, software developers, and operations staff who work with the community to develop and deliver leading-edge services to advance Canadian research. The CADC plays a leading role in international efforts to improve the scientific/technical landscape that supports data intensive science. This includes leadership roles in the International Virtual Observatory Alliance and participation in organizations like the Research Data Alliance, CODATA, and the World Data Systems. CADC also contributes significantly to future Canadian projects like the Square Kilometre Array and TMT. In 2019, the Canadian Astronomy Data Centre (CADC) delivered over 2 Petabytes of data (over 200 million individual files) to thousands of astronomers in Canada and in over 80 other countries. The cloud processing system completed over 6 million jobs (over 1100 core years) in 2019.

IntAct

IntAct Molecular Interaction Database

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IntAct provides a freely available, open source database system and analysis tools for molecular interaction data. All interactions are derived from literature curation or direct user submissions and are freely available.

US Virtual Astronomical Observatory

VAO

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The US Virtual Astronomical Observatory (VAO) is the VO effort based in the US, and it is one of many VO projects currently underway worldwide. The primary emphasis of the VAO is to provide new scientific research capabilities to the astronomy community. Thus an essential component of the VAO activity is obtaining input from US astronomers about the research tools that are most urgently needed in their work, and this information will guide the development efforts of the VAO. >>>!!!<<< Funding discontinued in 2014 and all software, documentation, and other digital assets developed under the VAO are stored in the VAO Project Repository https://sites.google.com/site/usvirtualobservatory/ . Code is archived on Github https://github.com/TomMcGlynn/usvirtualobservatory . >>>!!!<<<

Virus Pathogen Resource

ViPR

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<<<!!!<<< This repository is no longer available. >>>!!!>>> Migration of the data, tools, and services from IRD and ViPR to BV-BRC is complete! We are now in the sunsetting phase of the transition. Starting on October 31, 2022, launching the IRD or ViPR home pages will redirect you to the new BV-BRC home page. The current plan is to completely shut down IRD and ViPR by the end of this calendar year. Although it will still be possible to use those sites until shutdown, we strongly encourage you to start using BV-BRC now.

U.S. Energy Information Administration

EIA

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The U.S. Energy Information Administration (EIA) collects, analyzes, and disseminates independent and impartial energy information to promote sound policymaking, efficient markets, and public understanding of energy and its interaction with the economy and the environment.

LinkedEarth Wiki

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LinkedEarth is an EarthCube-funded project aiming to better organize and share Earth Science data, especially paleoclimate data. LinkedEarth facilitates the work of scientists by empowering them to curate their own data and to build new tools centered around those.

TriTrypDB

kinetoplastid genomics resource

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TriTrypDB is an integrated genomic and functional genomic database for pathogens of the family Trypanosomatidae, including organisms in both Leishmania and Trypanosoma genera. TriTrypDB and its continued development are possible through the collaborative efforts between EuPathDB, GeneDB and colleagues at the Seattle Biomedical Research Institute (SBRI).

PSLC DataShop

Pittsburgh Science of Learning Center DataShop

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PSLC DataShop houses datasets in the areas of learning science and educational software. The site also provides online tools for analyzing and reporting the data.

NITRC

Neuroimaging Informatics Tools and Resources Clearinghouse

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Neuroimaging Tools and Resources Collaboratory (NITRC) is currently a free one-stop-shop environment for science researchers that need resources such as neuroimaging analysis software, publicly available data sets, and computing power. Since its debut in 2007, NITRC has helped the neuroscience community to use software and data produced from research that, before NITRC, was routinely lost or disregarded, to make further discoveries. NITRC provides free access to data and enables pay-per-use cloud-based access to unlimited computing power, enabling worldwide scientific collaboration with minimal startup and cost. With NITRC and its components—the Resources Registry (NITRC-R), Image Repository (NITRC-IR), and Computational Environment (NITRC-CE)—a researcher can obtain pilot or proof-of-concept data to validate a hypothesis for a few dollars.

Berkeley Drosophila Genome Project

BDGP

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The goals of the Drosophila Genome Center are to finish the sequence of the euchromatic genome of Drosophila melanogaster to high quality and to generate and maintain biological annotations of this sequence. In addition to genomic sequencing, the BDGP is 1) producing gene disruptions using P element-mediated mutagenesis on a scale unprecedented in metazoans; 2) characterizing the sequence and expression of cDNAs; and 3) developing informatics tools that support the experimental process, identify features of DNA sequence, and allow us to present up-to-date information about the annotated sequence to the research community.

Kinsources.net

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Kinsources is an open and interactive platform to archive, share, analyze and compare kinship data used in scientific research. Kinsources is not just another genealogy website, but a peer-reviewed repository designed for comparative and collaborative research. The aim of Kinsources is to provide kinship studies with a large and solid empirical base. Kinsources combines the functionality of communal data repository with a toolbox providing researchers with advanced software for analyzing kinship data. The software Puck (Program for the Use and Computation of Kinship data) is integrated in the statistical package and the search engine of the Kinsources website. Kinsources is part of a research perspective that seeks to understand the interaction between genealogy, terminology and space in the emergence of kinship structures. Hosted by the TGIR HumaNum, the platform ensures both security and free access to the scientific data is validated by the research community.

VectorBase

Bioinformatics Resource for Invertebrate Vectors of Human Pathogens

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VectorBase provides data on arthropod vectors of human pathogens. Sequence data, gene expression data, images, population data, and insecticide resistance data for arthropod vectors are available for download. VectorBase also offers genome browser, gene expression and microarray repository, and BLAST searches for all VectorBase genomes. VectorBase Genomes include Aedes aegypti, Anopheles gambiae, Culex quinquefasciatus, Ixodes scapularis, Pediculus humanus, Rhodnius prolixus. VectorBase is one the Bioinformatics Resource Centers (BRC) projects which is funded by National Institute of Allergy and Infectious Diseases (NAID).

NCBI Genome

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<<<!!!<<< Effective May 2024, NCBI's Genome resource will no longer be available. NCBI Genome data can now be found on the NCBI Datasets taxonomy pages. https://www.re3data.org/repository/r3d100014298 >>>!!!>>> The Genome database contains annotations and analysis of eukaryotic and prokaryotic genomes, as well as tools that allow users to compare genomes and gene sequences from humans, microbes, plants, viruses and organelles. Users can browse by organism, and view genome maps and protein clusters.

Xenbase

Xenopus Genomics Database

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Xenbase's mission is to provide the international research community with a comprehensive, integrated and easy to use web based resource that gives access the diverse and rich genomic, expression and functional data available from Xenopus research. Xenbase also provides a critical data sharing infrastructure for many other NIH-funded projects, and is a focal point for the Xenopus community. In addition to our primary goal of supporting Xenopus researchers, Xenbase enhances the availability and visibility of Xenopus data to the broader biomedical research community.

ORegAnno

Open regulatory annotation database

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<<<!!!<<< 2017-06-02: We recently suffered a server failure and are working to bring the full ORegAnno website back online. In the meantime, you may download the complete database here: http://www.oreganno.org/dump/ ; Data are also available through UCSC Genome Browser (e.g., hg38 -> Regulation -> ORegAnno) https://genome.ucsc.edu/cgi-bin/hgTrackUi?hgsid=686342163_2it3aVMQVoXWn0wuCjkNOVX39wxy&c=chr1&g=oreganno >>>!!!>>> The Open REGulatory ANNOtation database (ORegAnno) is an open database for the curation of known regulatory elements from scientific literature. Annotation is collected from users worldwide for various biological assays and is automatically cross-referenced against PubMED, Entrez Gene, EnsEMBL, dbSNP, the eVOC: Cell type ontology, and the Taxonomy database, where appropriate, with information regarding the original experimentation performed (evidence). ORegAnno further provides an open validation process for all regulatory annotation in the public domain. Assigned validators receive notification of new records in the database and are able to cross-reference the citation to ensure record integrity. Validators have the ability to modify any record (deprecating the old record and creating a new one) if an error is found. Further, any contributor to the database can comment on any annotation by marking errors, or adding special reports into function as they see fit. These features of ORegAnno ensure that the collection is of the highest quality and uniquely provides a dynamic view of our changing understanding of gene regulation in the various genomes.

Prognostics Center of Excellence Data Set Repository

PCoE Datasets

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NASA's Prognostics Center of Excellence hosts the Prognostics Data Repository to provide data used in the development of prognostic algorithms, and time series of nominal to failed states. Data are donated from universities, agencies, or companies on an ongoing process.