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Found 17 result(s)

caNanoLab

cancer Nanotechnology Laboratory

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caNanoLab is a data sharing portal designed to facilitate information sharing in the biomedical nanotechnology research community to expedite and validate the use of nanotechnology in biomedicine. caNanoLab provides support for the annotation of nanomaterials with characterizations resulting from physico-chemical and in vitro assays and the sharing of these characterizations and associated nanotechnology protocols in a secure fashion.

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."

NCBI Datasets

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NCBI Datasets is a continually evolving platform designed to provide easy and intuitive access to NCBI’s sequence data and metadata. NCBI Datasets is part of the NIH Comparative Genomics Resource (CGR). CGR facilitates reliable comparative genomics analyses for all eukaryotic organisms through an NCBI Toolkit and community collaboration.

mentha

the interactome browser

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mentha archives evidence collected from different sources and presents these data in a complete and comprehensive way. Its data comes from manually curated protein-protein interaction databases that have adhered to the IMEx consortium. The aggregated data forms an interactome which includes many organisms. mentha is a resource that offers a series of tools to analyse selected proteins in the context of a network of interactions. Protein interaction databases archive protein-protein interaction (PPI) information from published articles. However, no database alone has sufficient literature coverage to offer a complete resource to investigate "the interactome". mentha's approach generates every week a consistent interactome (graph). Most importantly, the procedure assigns to each interaction a reliability score that takes into account all the supporting evidence. mentha offers eight interactomes (Homo sapiens, Arabidopsis thaliana, Caenorhabditis elegans, Drosophila melanogaster, Escherichia coli K12, Mus musculus, Rattus norvegicus, Saccharomyces cerevisiae) plus a global network that comprises every organism, including those not mentioned. The website and the graphical application are designed to make the data stored in mentha accessible and analysable to all users. Source databases are: MINT, IntAct, DIP, MatrixDB and BioGRID.

HIstome

The Histone Infobase

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HIstome: The Histone Infobase is a database of human histones, their post-translational modifications and modifying enzymes. HIstome is a combined effort of researchers from two institutions, Advanced Center for Treatment, Research and Education in Cancer (ACTREC), Navi Mumbai and Center of Excellence in Epigenetics, Indian Institute of Science Education and Research (IISER), Pune.

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.

Edinburgh DataShare

DataShare

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Edinburgh DataShare is a digital repository of research data produced at the University of Edinburgh, hosted by the Research Data Service in Information Services. Edinburgh University researchers who have produced research data associated with an existing or forthcoming publication, or which has potential use for other researchers, are invited to upload their dataset for sharing and safekeeping. A persistent identifier and suggested citation will be provided.

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.

DEPOD

DEPhOsphorylation Database

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DEPOD - the human DEPhOsphorylation Database (version 1.1) is a manually curated database collecting human active phosphatases, their experimentally verified protein and non-protein substrates and dephosphorylation site information, and pathways in which they are involved. It also provides links to popular kinase databases and protein-protein interaction databases for these phosphatases and substrates. DEPOD aims to be a valuable resource for studying human phosphatases and their substrate specificities and molecular mechanisms; phosphatase-targeted drug discovery and development; connecting phosphatases with kinases through their common substrates; completing the human phosphorylation/dephosphorylation network.

Clinical Proteomic Tumor Analysis Consortium Data Portal

CPTAC Data Portal

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The CPTAC Data Portal is the centralized repository for the dissemination of proteomic data collected by the Proteome Characterization Centers (PCCs) for the CPTAC program. The portal also hosts analyses of the mass spectrometry data (mapping of spectra to peptide sequences and protein identification) from the PCCs and from a CPTAC-sponsored common data analysis pipeline (CDAP).

Molecular INTeraction Database

MINT

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Starting September 2013, MINT uses the IntAct database infrastructure to limit the duplication of efforts and to optimise future software development. Data manually curated by the MINT curators can now be accessed from the IntAct homepage at the EBI. Data maintenance and release, MINT PSICQUIC and IMEx services are under the responsibility of the IntAct team, while curation effort will be carried by both groups. The MINT development team now focuses on two new developments: mentha that integrates protein interaction information curated by IMEx databases and SIGNOR a database of logic relationships between human proteins. MINT is a public repository for molecular interactions reported in peer-reviewed journals.IT is a collection of molecular interaction databases that can be used to search for, analyze and graphically display molecular interaction networks and pathways from a wide variety of species. MINT is comprised of separate database components. HomoMINT, is an inferred human protein interatction database. Domino, is database of domain peptide interactions. A new component has been added called VirusMINT that explores the interactions of viral proteins with human proteins.

Autophagy Database

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The goal of the Autophagy Database is to provide up-to-date relevant information including protein structure data to researchers of autophagy, and to disseminate important findings to a wider audience so that their ramifications can be appreciated. For this purpose, we strive to make the database to contain as much pertinent information as possible and to make the contents freely available in a user-friendly format.

Top Down Proteomics Repository

TDPR

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This database will provide a central location for scientists to browse uniquely observed proteoforms and to contribute their own datasets. Top-down proteomics is a method of protein identification that uses an ion trapping mass spectrometer to store an isolated protein ion for mass measurement and tandem mass spectrometry analysis.

APID

Agile Protein Interactomes DataServer

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APID Interactomes is a database that provides a comprehensive collection of protein interactomes for more than 400 organisms based in the integration of known experimentally validated protein-protein physical interactions (PPIs). Construction of the interactomes is done with a methodological approach to report quality levels and coverage over the proteomes for each organism included. In this way, APID provides interactomes from specific organisms that in 25 cases have more than 500 proteins. As a whole APID includes a comprehensive compendium of 90,379 distinct proteins and 678,441 singular interactions. The analytical and integrative effort done in APID unifies PPIs from primary databases of molecular interactions (BIND, BioGRID, DIP, HPRD, IntAct, MINT) and also from experimentally resolved 3D structures (PDB) where more than two distinct proteins have been identified. In this way, 8,388 structures have been analyzed to find specific protein-protein interactions reported with details of their molecular interfaces. APID also includes a new data visualization web-tool that allows the construction of sub-interactomes using query lists of proteins of interest and the visual exploration of the corresponding networks, including an interactive selection of the properties of the interactions (i.e. the reliability of the "edges" in the network) and an interactive mapping of the functional environment of the proteins (i.e. the functional annotations of the "nodes" in the network).

Plant Organelles Database 3

PODB3

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<<<!!!<<< This repository is no longer available. >>>!!!>>> The Plant Organelles Database Version 3 (PODB3) is a specialized database project to promote a comprehensive understanding of organelle dynamics, including organelle function, biogenesis, differentiation, movement, and interactions with other organelles. This database consists of 6 individual parts, 'The Electron Micrograph Database', 'The Perceptive Organelles Database', 'The Organelles Movie Database', 'The Organellome Database', 'The Functional Analysis Database', and 'External Links to other databases and Web pages'. All the data and protocols in these databases are populated by direct submission of experimentally determined data from plant researchers.

FlowRepository

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FlowRepository is a web-based application accessible from a web browser that serves as an online database of flow cytometry experiments where users can query and download data collected and annotated according to the MIFlowCyt standard. It is primarily used as a data deposition place for experimental findings published in peer-reviewed journals in the flow cytometry field. FlowRepository is funded by the International Society for Advancement of Cytometry (ISAC) and powered by the Cytobank engine specifically extended for the purposes of this repository. FlowRepository has been developed by forking and extending Cytobank in 2011.

Screening Unit Berlin-Buch

Screening Unit Jens Peter von Kries

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The mission of the platform is to enable access for academic projects towards experiments in high-throughput without loss of IP and on a cost basis, which does not restrict access towards HTS usage. The FMP hosts the central open access technology platform of EU-OPENSCREEN, the ChemBioNet and theHelmholtz-Initiative für Wirkstoffforschung, the Screening Unit. The Unit serves for systematic screening of large compound or genome-wide RNAi libraries with state-of-the-art equipment like automated microscopes and microfluidic systems. The Screening Unit is part of the Chemical Biology Platform of the FMP also supported by the MDC. See also: https://www.mdc-berlin.de/screening-unit