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Found 604 result(s)

OrthoMCL

Ortholog Groups of Protein Sequences

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OrthoMCL is a genome-scale algorithm for grouping orthologous protein sequences. It provides not only groups shared by two or more species/genomes, but also groups representing species-specific gene expansion families. So it serves as an important utility for automated eukaryotic genome annotation. OrthoMCL starts with reciprocal best hits within each genome as potential in-paralog/recent paralog pairs and reciprocal best hits across any two genomes as potential ortholog pairs. Related proteins are interlinked in a similarity graph. Then MCL (Markov Clustering algorithm,Van Dongen 2000; www.micans.org/mcl) is invoked to split mega-clusters. This process is analogous to the manual review in COG construction. MCL clustering is based on weights between each pair of proteins, so to correct for differences in evolutionary distance the weights are normalized before running MCL.

AmoebaDB

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AmoebaDB belongs to the EuPathDB family of databases and is an integrated genomic and functional genomic database for Entamoeba and Acanthamoeba parasites. In its first iteration (released in early 2010), AmoebaDB contains the genomes of three Entamoeba species (see below). AmoebaDB integrates whole genome sequence and annotation and will rapidly expand to include experimental data and environmental isolate sequences provided by community researchers . The database includes supplemental bioinformatics analyses and a web interface for data-mining.

ToxoDB

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ToxoDB is a genome database for the genus Toxoplasma, a set of single-celled eukaryotic pathogens that cause human and animal diseases, including toxoplasmosis.

DOE Data Explorer

DDE

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The DOE Data Explorer (DDE) is an information tool to help you locate DOE's collections of data and non-text information and, at the same time, retrieve individual datasets within some of those collections. It includes collection citations prepared by the Office of Scientific and Technical Information, as well as citations for individual datasets submitted from DOE Data Centers and other organizations.

LiDA

Lietuvos humanitarinių ir socialinių mokslų duomenų archyvas

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Lithuanian Data Archive for Social Sciences and Humanities (LiDA) is a virtual digital infrastructure for SSH data and research resources acquisition, long-term preservation and dissemination. All the data and research resources are documented in both English and Lithuanian according to international standards. Access to the resources is provided via Dataverse repository. LiDA curates different types of resources and they are published into catalogues according to the type: Survey Data, Aggregated Data (including Historical Statistics), Encoded Data (including News Media Studies), and Textual Data. Also, LiDA holds collections of social sciences and humanities data deposited by Lithuanian science and higher education institutions and Lithuanian state institutions (Data of Other Institutions). LiDA is hosted by the Centre for Data Analysis and Archiving of Kaunas University of Technology (data.ktu.edu).

IDOC-DATA

Integrated Data and Operation Center repository

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IDOC-DATA is a department of IDOC IDOC (Integrated Data & Operation Center) has existed since 2003 as a satellite operations center and data center for the Institute of Space Astrophysics (IAS) in Orsay, France. Since then, it has operated within the OSUPS (Observatoire des Sciences de l'Univers de l'Université Paris-Saclay - first french university in shanghai ranking), which includes three institutes: IAS, AIM (Astrophysique, Interprétation, Modélisation - IRFU, CEA) and GEOPS (Geosciences Paris-Saclay) . IDOC participates in the space missions of OSUPS and its partners, from mission design to long-term scientific data archiving. For each phase of the missions, IDOC offers three kinds of services in the scientific themes of OSUPS and therefore IDOC's activities are divided into three departments: IDOC-INSTR: instrument design and testing, IDOC-OPE: instrument operations, IDOC-DATA: data management and data value chain: to produce the different levels of data constructed from observations of these instruments and make them available to users for ergonomic and efficient scientific interpretation (IDOC-DATA). It includes the responsibility: - To build access to these datasets. - To offer the corresponding services such as catalogue management, visualization tools, software pipeline automation, etc. - To preserve the availability and reliability of this hardware and software infrastructure, its confidentiality where applicable and its security.

The Netlib

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The Netlib repository contains freely available software, documents, and databases of interest to the numerical, scientific computing, and other communities.

FungiDB

The Fungal and Oomycete Genomics Resource

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FungiDB belongs to the EuPathDB family of databases and is an integrated genomic and functional genomic database for the kingdom Fungi. FungiDB was first released in early 2011 as a collaborative project between EuPathDB and the group of Jason Stajich (University of California, Riverside). At the end of 2015, FungiDB was integrated into the EuPathDB bioinformatic resource center. FungiDB integrates whole genome sequence and annotation and also includes experimental and environmental isolate sequence data. The database includes comparative genomics, analysis of gene expression, and supplemental bioinformatics analyses and a web interface for data-mining.

PAIN repository

Pain and Interoception Imaging Network Repository

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The PAIN Repository is a recently funded NIH initiative, which has two components: an archive for already collected imaging data (Archived Repository), and a repository for structural and functional brain images and metadata acquired prospectively using standardized acquisition parameters (Standardized Repository) in healthy control subjects and patients with different types of chronic pain. The PAIN Repository provides the infrastructure for storage of standardized resting state functional, diffusion tensor imaging and structural brain imaging data and associated biological, physiological and behavioral metadata from multiple scanning sites, and provides tools to facilitate analysis of the resulting comprehensive data sets.

RAVE database

Radial Velocity Experiment Database

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RAVE (RAdial Velocity Experiment) is a multi-fiber spectroscopic astronomical survey of stars in the Milky Way using the 1.2-m UK Schmidt Telescope of the Anglo-Australian Observatory (AAO). The RAVE collaboration consists of researchers from over 20 institutions around the world and is coordinated by the Leibniz-Institut für Astrophysik Potsdam. As a southern hemisphere survey covering 20,000 square degrees of the sky, RAVE's primary aim is to derive the radial velocity of stars from the observed spectra. Additional information is also derived such as effective temperature, surface gravity, metallicity, photometric parallax and elemental abundance data for the stars. The survey represents a giant leap forward in our understanding of our own Milky Way galaxy; with RAVE's vast stellar kinematic database the structure, formation and evolution of our Galaxy can be studied.

HALO database

High Altitude and LOng Range database

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HALO-DB is the web platform of a data retrieval and long-term archive system. The system was established to hold and to manage a wide range of data based on observations of the HALO research aircraft and data which are related to HALO observations. HALO (High-Altitude and LOng-range aircraft) is the new German research aircraft (German Science Community (DFG)). The aircraft, a Gulfstream GV-550 Business-Jet, is strongly modified for the application as a research platform. HALO offers several advantages for scientific campaigns, such as its high range of more than 10000 km, a high maximum altitude of more than 15 km, as well as a relatively high payload.

FlyReactome

a curated knowledgebase of drosophila melanogaster pathways

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<<<!!!<<< This repository is no longer available. This record is out dated >>>!!!>>>- eir fields, maintained by the FlyReactome staff.

NOAA Institutional Repository

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The NOAA Repository is a digital library of scientific literature and research produced by the National Oceanic and Atmospheric Administration. The repository contains NOAA publications, as defined in the NOAA Publications Policy, dating from NOAA’s formation in 1970 to present and NOAA-authored and -funded journal articles from 2015 forward.

Metlin

The original and most comprehensive MS/MS metabolite database

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METLIN represents the largest MS/MS collection of data with the database generated at multiple collision energies and in positive and negative ionization modes. The data is generated on multiple instrument types including SCIEX, Agilent, Bruker and Waters QTOF mass spectrometers.

TCCON Data Archive

Total Carbon Column Observing Network Data Archive

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TCCON is a network of ground-based Fourier Transform Spectrometers recording direct solar spectra in the near-infrared spectral region. From these spectra, accurate and precise column-averaged abundance of CO2, CH4, N2O, HF, CO, H2O, and HDO are retrieved.

Avibase

the world bird database

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Avibase is an extensive database information system about all birds of the world, containing over 60 million records about 10,000 species and 22,000 subspecies of birds, including distribution information, taxonomy, synonyms in several languages and more. This site is managed by Denis Lepage and hosted by Bird Studies Canada, the Canadian copartner of Birdlife International. Avibase has been a work in progress since 1992 and I am now pleased to offer it as a service to the bird-watching and scientific community.

The USGS Land Cover Institute

LCI

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The USGS currently houses the institute at the Center for Earth Resources Observation and Science (EROS) in Sioux Falls, South Dakota. The LCI will address land cover topics from local to global scales, and in both domestic and international settings. The USGS through the Land Cover Institute serves as a facilitator for land cover and land use science, applications, and production functions. The institute assists in the availability and technical support of land cover data sets through increasing public and scientific awareness of the importance of land cover science. LCI continues, after the reorganization of the World Data Centers in 2009, serving as the World Data Center (WDC) for land cover data for access to, or information about, land cover data of the world

Endangered Languages Archive

ELAR

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The Endangered Languages Archive (ELAR) is a digital repository for preserving multimedia collections of endangered languages from all over the world, making them available for future generations. In ELAR’s collections you can find recordings of every-day conversations, instructions on how to build fish traps or boats, explanations of kinship systems and the use of medicinal plants, and learn about art forms like string figures and sand drawings. ELAR’s collections are unique records of local knowledge systems encoded in their languages, described by the holders of the knowledge themselves.

New Mexico Bureau of Geology & Mineral Resources Data Repository

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Archiving data and housing geological collections is an important role the Bureau of Geology plays in improving our understanding of the geology of New Mexico. Aside from our numerous publications, several datasets are available to the public. Data in this repository supplements published papers in our publications. Please refer to both the published material and the repository documentation before using this data. Please cite repository data as shown in each repository listing.

National Science Digital Library

NSDL

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The National Science Digital Library provides high quality online educational resources for teaching and learning, with current emphasis on the sciences, technology, engineering, and mathematics (STEM) disciplines—both formal and informal, institutional and individual, in local, state, national, and international educational settings. The NSDL collection contains structured descriptive information (metadata) about web-based educational resources held on other sites by their providers. These providers have contribute this metadata to NSDL for organized search and open access to educational resources via this website and its services.

JASPAR

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JASPAR is the leading open-access database of matrix profiles describing the DNA-binding patterns of transcription factors and other proteins interacting with DNA in a sequence-specific manner.

Cellosaurus

Cellosaurus - a knowledge resource on cell lines

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The Cellosaurus is a knowledge resource on cell lines. It attempts to describe all cell lines used in biomedical research. Its scope includes: Immortalized cell lines, Naturally immortal cell lines (example: stem cell lines), Finite life cell lines when those are distributed and used widely, Vertebrate cell line with an emphasis on human, mouse and rat cell lines, Invertebrate (insects and ticks) cell lines. Its scope does not include: Primary cell lines (with the exception of the finite life cell lines described above), Plant cell lines. Cellosaurus was initiated to be used as a cell line controlled vocabulary in the context of the neXtProt knowledgebase, but it quickly become apparent that there was a need for a cell line knowledge resource that would serve the needs of individual researchers, cell line distributors and bioinformatic resources. This leads to an increase of the scope and depth of the content of the Cellosaurus. The Cellosaurus is a participant of the Resource Identification Initiative and contributes actively to the work of the International Cell Line Authentication Committee (ICLAC). It is a Global Core Biodata Resource, an ELIXIR Core Data Resource and an IRDiRC Recognized Resource.

GeoReM

Geological and Environmental Reference Materials

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GeoReM is a Max Planck Institute database for reference materials of geological and environmental interest, such as rock powders, synthetic and natural glasses as well as mineral, isotopic, biological, river water and seawater reference materials. GeoReM contains published analytical data and compilation values (major and trace element concentrations and mass fractions, radiogenic and stable isotope ratios). GeoReM contains all important metadata about the analytical values such as uncertainty, analytical method and laboratory. Sample information and references are also included. GeoReM complements the three earthchem databases: GEOROC, NAVDAT and PETDB.

PermaSense High-Alpine Permafrost Data

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Data from high-alpine mountain permafrost research sites.

ForestPlots.net

FP

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ForestPlots.net is a web-accessible secure repository for forest plot inventories in South America, Africa and Asia. The database includes plot geographical information; location, taxonomic information and diameter measurements of trees inside each plot; and participants in plot establishment and re-measurement, including principal investigators, field assistants, students.