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Found 23 result(s)

Electron Microscopy Public Image Archive

EMPIAR

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EMPIAR, the Electron Microscopy Public Image Archive, is a public resource for raw, 2D electron microscopy images. Here, you can browse, upload, download and reprocess the thousands of raw, 2D images used to build a 3D structure. The purpose of EMPIAR is to provide an easy access to the state-of-the-art raw data to facilitate methods development and validation, which will lead to better 3D structures. It complements the Electron Microscopy Data Bank (EMDB), where 3D images are stored, and uses the fault-tolerant Aspera platform for data transfers

Electron Microscopy Data Bank

EMDB

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The Electron Microscopy Data Bank (EMDB) is a public repository for electron microscopy density maps of macromolecular complexes and subcellular structures. It covers a variety of techniques, including single-particle analysis, electron tomography, and electron (2D) crystallography.

Image Data Resource

IDR

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The IDR makes datasets that have never previously been accessible publicly available, allowing the community to search, view, mine and even process and analyze large, complex, multidimensional life sciences image data. Sharing data promotes the validation of experimental methods and scientific conclusions, the comparison with new data obtained by the global scientific community, and enables data reuse by developers of new analysis and processing tools.

Brain Image Library

BIL

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Brain Image Library (BIL) is an NIH-funded public resource serving the neuroscience community by providing a persistent centralized repository for brain microscopy data. Data scope of the BIL archive includes whole brain microscopy image datasets and their accompanying secondary data such as neuron morphologies, targeted microscope-enabled experiments including connectivity between cells and spatial transcriptomics, and other historical collections of value to the community. The BIL Analysis Ecosystem provides an integrated computational and visualization system to explore, visualize, and access BIL data without having to download it.

Cellular Phenotype database

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The Cellular Phenotype database stores data derived from high-throughput phenotypic studies and it is being developed as part of the Systems Microscopy Network of Excellence project. The aim of the Cellular Phenotype database is to provide easy access to phenotypic data and facilitate the integration of independent phenotypic studies. Through its interface, users can search for a gene of interest, or a collection of genes, and retrieve the loss-of-function phenotypes observed, in human cells, by suppressing the expression of the selected gene(s), through RNA interference (RNAi), across independent phenotypic studies. Similarly, users can search for a phenotype of interest and retrieve the RNAi reagents that have caused such phenotype and the associated target genes. Information about specific RNAi reagents can also be obtained when searching for a reagent ID.

EELS Data Base

Electron energy loss spectroscopy Data Base

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The EELS database is a public interactive consultable web repository of outer-shell and inner-shell excitation spectra from Electron Energy Loss Spectroscopy and X-Ray experiments, which forms a reference catalog of fine structures for materials. Each spectrum is available with a full set of recording parameters providing a complete overview of the working conditions. The database must also be seen as a research tool for EEL spectroscopists, theoreticians, students, or private firms and a central “location” for the growing EELS community.

EMDataResource

formerly: EMDataBank

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Cryo electron microscopy enables the determination of 3D structures of macromolecular complexes and cells from 2 to 100 Å resolution. EMDataResource is the unified global portal for one-stop deposition and retrieval of 3DEM density maps, atomic models and associated metadata, and is a joint effort among investigators of the Stanford/SLAC CryoEM Facility and the Research Collaboratory for Structural Bioinformatics (RCSB) at Rutgers, in collaboration with the EMDB team at the European Bioinformatics Institute. EMDataResource also serves as a resource for news, events, software tools, data standards, and validation methods for the 3DEM community. The major goal of the EMDataResource project in the current funding period is to work with the 3DEM community to (1) establish data-validation methods that can be used in the process of structure determination, (2) define the key indicators of a well-determined structure that should accompany every deposition, and (3) implement appropriate validation procedures for maps and map-derived models into a 3DEM validation pipeline.

The Cell Vision

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TheCellVision.org is a freely available and web-accessible image visualization and data browsing tool that serves as a central repository for fluorescence microscopy images and associated quantitative data produced by high-content screening experiments. Currently, TheCellVision.org hosts images and associated analysis results from two published high- content screening (HCS) projects focused on the budding yeast Saccharomyces cerevisiae. TheCellVision.org allows users to access, visualize and explore fluorescence microscopy images, and to search, compare, and extract data related to subcellular compartment morphology, protein abundance, and localization. Each dataset can be queried independently or as part of a search across multiple datasets using the advanced search option. The website also hosts computational tools associated with the available datasets, which can be applied to other projects and cell systems, a feature we demonstrate using published images of mammalian cells. Providing access to HCS data through websites such as TheCellVision.org enables new discovery and independent re-analyses of imaging data."

Yeast Resource Center

Yeast Resource Center Public Data Repository

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The Yeast Resource Center provides access to data about mass spectrometry, yeast two-hybrid arrays, deconvolution florescence microscopy, protein structure prediction and computational biology. These services are provided to further the goal of a complete understanding of the chemical interactions required for the maintenance and faithful reproduction of a living cell. The observation that the fundamental biological processes of yeast are conserved among all eukaryotes ensures that this knowledge will shape and advance our understanding of living systems.

Cell Centered Database

CCDB

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>>> !!!!! The Cell Centered Database is no longer on serice. It has been merged with "Cell image library": https://www.re3data.org/repository/r3d100000023 !!!!! <<<<

Yeast Resource Center Public Image Repository

YRC Public Image Repository

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The Yeast Resource Center Public Image Repository is a database of fluorescent microscopy images and their associated metadata/experimental parameters. The images depict the localization, co-localization and FRET (fluorescence energy transfer) of proteins in cells, particularly in the budding yeast Saccharomyces cerevisiae as a model organism. Users may download the entire datasets to improve their research.

Rotterdam Ophthalmic Data Repository

ROD-REP

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The Rotterdam Ophthalmic Data Repository (ROD-Rep) contains data sets related to ophthalmology that the Rotterdam Ophthalmic Institute has made freely available for researchers worldwide. This portal is an initiative of the Rotterdam Ophthalmic Institute, which is the research institute of the Rotterdam Eye Hospital. It provides the datasets from ophthalmic research (includes measurements such as visual fields and various imaging modalities, grades, etc.) for sharing and re-use to accelerate multi-disciplinary research, resulting in better ophthalmic care. The portal is the successor of the ORGIDS (or Open Rotterdam Glaucoma Imaging Data Sets site); which was an initiative of Koen Vermeer, Hans Lemij and Netty Dorrestijn and initial financial support was provided by Stichting Glaucoomfonds (The Netherlands).

BioImage Archive

BIA

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The BioImage Archive stores and distributes life sciences imaging datasets. It supports deposition of biological imaging data associated with publications for the whole research community, as well as reference imaging datasets. All data deposited to the BioImage Archive is made openly accessible to the scientific community.

The Cell Image Library

The Cell

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This library is a public and easily accessible resource database of images, videos, and animations of cells, capturing a wide diversity of organisms, cell types, and cellular processes. The Cell Image Library has been merged with "Cell Centered Database" in 2017. The purpose of the database is to advance research on cellular activity, with the ultimate goal of improving human health.

Journal of Cell Biology - JCB DataViewer

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>>>!!!<<< Data originally published in the JCB DataViewer has been moved BioStudies. Please note that while the majority of data were moved, some authors opted to remove their data completely. >>>!!!<<< Migrated data can be found at https://www.ebi.ac.uk/biostudies/JCB/studies. Screen data are available in the Image Data Resource repository. http://idr.openmicroscopy.org/webclient/?experimenter=-1 >>>!!!<<< The DataViewer was decommissioned in 2018 as the journal evolved to an all-encompassing archive policy towards original source data and as new data repositories that go beyond archiving data and allow investigators to make new connections between datasets, potentially driving discovery, emerged. JCB authors are encouraged to make available all datasets included in the manuscript from the date of online publication either in a publicly available database or as supplemental materials hosted on the journal website. We recommend that our authors store and share their data in appropriate publicly available databases based on data type and/or community standard. >>>!!!<<<

EBRAINS

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EBRAINS offers one of the most comprehensive platforms for sharing brain research data ranging in type as well as spatial and temporal scale. We provide the guidance and tools needed to overcome the hurdles associated with sharing data. The EBRAINS data curation service ensures that your dataset will be shared with maximum impact, visibility, reusability, and longevity, https://ebrains.eu/services/data-knowledge/share-data. Find data - the user interface of the EBRAINS Knowledge Graph - allows you to easily find data of interest. EBRAINS hosts a wide range of data types and models from different species. All data are well described and can be accessed immediately for further analysis.

MyTardis

Tardis

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MyTardis began at Monash University to solve the problem of users needing to store large datasets and share them with collaborators online. Its particular focus is on integration with scientific instruments, instrument facilities and research lab file storage. Our belief is that the less effort a researcher has to expend safely storing data, the more likely they are to do so. This approach has flourished with MyTardis capturing data from areas such as protein crystallography, electron microscopy, medical imaging and proteomics and with deployments at Australian institutions such as University of Queensland, RMIT, University of Sydney and the Australian Synchrotron. Data access via https://www.massive.org.au/ and https://store.erc.monash.edu.au/experiment/view/104/ and see 'remarks'.

GigaDB

GigaScience Database

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GigaDB primarily serves as a repository to host data and tools associated with articles published by GigaScience Press; GigaScience and GigaByte (both are online, open-access journals). GigaDB defines a dataset as a group of files (e.g., sequencing data, analyses, imaging files, software programs) that are related to and support a unit-of-work (article or study). GigaDB allows the integration of manuscript publication with supporting data and tools.

Plant Genomics and Phenomics Research Data Repository

PGP Repository

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The Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) and German Plant Phenotyping Network (DPPN) has jointly initiated the Plant Genomics and Phenomics Research Data Repository (PGP) as infrastructure to comprehensively publish plant research data. This covers in particular cross-domain datasets that are not being published in central repositories because of its volume or unsupported data scope, like image collections from plant phenotyping and microscopy, unfinished genomes, genotyping data, visualizations of morphological plant models, data from mass spectrometry as well as software and documents.

European Zebrafish Resource Center

EZRC

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The EZRC at KIT houses the largest experimental fish facility in Europe with a capacity of more than 300,000 fish. Zebrafish stocks are maintained mostly as frozen sperm. Frequently requested lines are also kept alive as well as a selection of wildtype strains. Several thousand mutations in protein coding genes generated by TILLING in the Stemple lab of the Sanger Centre, Hinxton, UK and lines generated by ENU mutagenesis by the Nüsslein-Volhard lab in addition to transgenic lines and mutants generated by KIT groups or brought in through collaborations. We also accept submissions on an individual basis and ship fish upon request to PIs in Europe and elsewhere. EZRC also provides screening services and technologies such as imaging and high-throughput sequencing. Key areas include automation of embryo handling and automated image acquisition and processing. Our platform also involves the development of novel microscopy techniques (e.g. SPIM, DSLM, robotic macroscope) to permit high-resolution, real-time imaging in 4D. By association with the ComPlat platform, we can support also chemical screens and offer libraries with up to 20,000 compounds in total for external users. As another service to the community the EZRC provides plasmids (cDNAs, transgenes, Talen, Crispr/cas9) maintained by the Helmholtz repository of Bioparts (HERBI) to the scientific community. In addition the fish facility keeps a range of medaka stocks, maintained by the Loosli group.

Protein Data Bank in Europe

PDBe

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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.

Worldwide Protein Data Bank

wwPDB

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The Protein Data Bank (PDB) is an archive of experimentally determined three-dimensional structures of biological macromolecules that serves a global community of researchers, educators, and students. The data contained in the archive include atomic coordinates, crystallographic structure factors and NMR experimental data. Aside from coordinates, each deposition also includes the names of molecules, primary and secondary structure information, sequence database references, where appropriate, and ligand and biological assembly information, details about data collection and structure solution, and bibliographic citations. The Worldwide Protein Data Bank (wwPDB) consists of organizations that act as deposition, data processing and distribution centers for PDB data. Members are: RCSB PDB (USA), PDBe (Europe) and PDBj (Japan), and BMRB (USA). The wwPDB's mission is to maintain a single PDB archive of macromolecular structural data that is freely and publicly available to the global community.

The Human Protein Atlas

HPA

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The Swedish Human Protein Atlas project has been set up to allow for a systematic exploration of the human proteome using Antibody-Based Proteomics. This is accomplished by combining high-throughput generation of affinity-purified antibodies with protein profiling in a multitude of tissues and cells assembled in tissue microarrays. Confocal microscopy analysis using human cell lines is performed for more detailed protein localization. The program hosts the Human Protein Atlas portal with expression profiles of human proteins in tissues and cells. The main objective of the resource centre is to produce specific antibodies to human target proteins using a high-throughput production method involving the cloning and protein expression of Protein Epitope Signature Tags (PrESTs). After purification, the antibodies are used to study expression profiles in cells and tissues and for functional analysis of the corresponding proteins in a wide range of platforms.