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hPSCreg / human Pluripotent Stem Cell registry
A public registry and data portal for human embryonic and induced pluripotent stem cell lines (hESC and hiPSC). The Registry provides comprehensive and standardized biological and legal information as well as tools to search and compare information from multiple hPSC sources and hence addresses a translational research need. To facilitate unambiguous identification over different resources, hPSCreg automatically creates a unique standardized name for each cell line registered. In addition to biological information, hPSCreg stores extensive data about ethical standards regarding cell sourcing and conditions for application and privacy protection.
IDR / Image Data Resource
Links experimental perturbations to public genetic or chemical databases, and cell and tissue phenotypes to controlled vocabularies expressed as ontologies. IDR collects and integrates imaging data acquired using many different imaging modalities including high-content screening, super-resolution microscopy, timelapse imaging and digital pathology, and links them in a single resource. This database integrates image data and metadata from several studies into a single resource. The current IDR web user interface (WUI) is based on the open source OMERO web application.
Assists users to understand the functional role of yeast genes. PROPHECY is an online database that clusters information about phenotypic characteristics in yeast and permits the exploration of the growing field of phenome bioinformatics. It can display quantitative phenotypic data at different levels of abstraction. Moreover, this database provides several specific tools for alternative data visualization and mining, such as the visualization of gene dispensability for components in protein complexes.
SCMD / Saccharomyces Cerevisiae Morphological Database
Facilitates the analysis of abnormal cells. SCMD provides micrographs and quantitative data using the image-processing software for shapes of the daughter and mother cells, the localization of the nuclear DNA and the morphology of the actin patches. To search for mutants with similar morphological traits, the system outputs a list of mutants ranked by similarity of average morphological parameters. The SCMD system is intended as a resource that complements existing sequence and gene-expression databases.
JCB DataViewer
A web-based, multi-dimensional image data-viewing application. JCB DataViewer is a tool for visualization and simple analysis of original image data files associated with JCB articles. Image data are archived by the Journal and may be freely accessed by readers using the JCB DataViewer. Download of author-provided image data and associated metadata in OME-TIFF format is also possible with author permission, allowing for independent analysis of image data irrespective of acquisition or viewing software.
Maps validated gene and protein expression, phenotype and images related to cell types. The data allow characterization and comparison of cell types and can be browsed by using the body browser and by searching for cells or genes. All cells are related to more complex systems such as tissues, organs and organisms and arranged according to their position in development. CellFinder provides long-term data storage for validated and curated primary research data and provides additional expert-validation through relevant information extracted from text.
Digital development
Provides a comprehensive, curated, multidimensional database for developmental phenotypes, cell-specific gene functions, differentiation trajectories and a multiscale model of lineage differentiation in the C. elegans embryo. Digital development stores data from recent systematic studies of cell lineage differentiation in the C. elegans embryo containing ∼200 conserved genes, 1400 perturbed cell lineages and 600 000 digitized single cells. Users can conveniently browse, search and download four categories of phenotypic and functional information from an intuitive web interface. This information includes lineage differentiation phenotypes, cell-specific gene functions, differentiation landscapes and fate choices, and a multiscale model of lineage differentiation. Digital Development provides a comprehensive, curated, multidimensional database for developmental biology. The scale, resolution and richness of biological information presented here facilitate exploration of gene-specific and systems-level mechanisms of lineage differentiation in Metazoans.
ProTraits / PROkaryotic TRAITS
Describes environmental preferences of microbes, interactions with other organisms, biochemical phenotypes, resistance to chemicals and other stressors. ProTraits recognizes 424 phenotypic traits and covers 3,046 bacterial or archeal species. Overall, it provides 545,081 annotations (less than 10% of false discovery rate (FDR), tallying both the positive and the negative labels), of which 503,308 are novel. Moreover, the ProTraits pipeline can infer phenotypes using five independant sources of genomic data, while providing estimates of FDRs that agree with manual curation.
CIL / Cell Image Library
Compiles images, videos and animations of cells from multiple organisms, cell types, and processes, normal and pathological. CIL-CCDB is an open-source database including about 9250 images from 358 different species. Each submission is evaluated and annotated with terms from 14 different ontologies in 16 different fields. It also contains a basic description and technical details. Searches can be made by keywords, image attributes, license, biology, imaging methods or anatomy. This tool is available on mobile application.
SSBD / Systems Science of Biological Dynamics
Stores and shares quantitative biological dynamics data. SSBD currently provides 311 sets of quantitative data for single molecules, nuclei, and whole organisms in a wide variety of model organisms from Escherichia coli to Mus musculus. The data are provided in Biological Dynamics Markup Language (BDML) format and also through a REST API. In addition, SSBD provides 188 sets of time-lapse microscopy images from which the quantitative data were obtained and software tools for data visualization and analysis. SSBD supports, promotes, and contributes to advances in systems biology and various interdisciplinary research fields, and facilitate data-driven biology.
2D model of olfactory bulb gamma oscillations
Provides biophysical model of the olfactory bulb (OB) network. 2D model of olfactory bulb gamma oscillations is based on a two-layer model of cholinergic neuromodulation in the OB. It supports the diverse phenomena observed in OB neurophysiological recordings. This dataset contains the following phenomena: (1) patterned spiking activity in mitral and projecting tufted cells (MCs) and granule cells (GCs); (2) tolerance to a wide range of afferent MC excitation levels; and (3) tolerance for substantial changes in MC-GC synaptic weights, between other.
Maize Cell Genomics Database
A public database, developed to organize a large data set of confocal images generated from the maize marker lines, for studying native gene expression in specific cell types and subcellular compartments using fluorescent proteins. Maize Cell Genomics Database represents two types of data: (i) information which describes fluorescent-tagged gene constructs used for maize marker line generation; and (ii) confocal images representing spatial and temporal expression of the fluorescent markers in the maize marker lines.
PheMaDB / Phenotype Microarray DataBase
Simplifies the sharing of data. PheMaDB consists of web-based database management system that provides investigators with the ability to manage OmniLog™ data and strain metadata. It allows users to share data via the web user interface and may serve to promote the public sharing of phenotype data. This database enables users to load and store the data, query across datasets, perform statistical analyses, and produce publication quality figures.
Allows to search and browse experiments and explore analyses for the Stem Cell Genomics database. StemBase stores gene expression data derived from Affymetrix expression microarrays and Serial Analysis of Gene Expression (SAGE) libraries. Experimental data are organized into groupings of “samples” which represent different conditions in a given experiment. Samples contain a set of “replicates” made using the same sample under the same experimental conditions and associated with one or more “files” containing the raw expression data.
Provides a molecular atlas of the developing lung. LungMAP includes mouse and human data for cross correlation of developmental processes across species. This online resource is available through a web portal for presentation of results and public sharing of data sets. It establishes a repository of young human lung tissues obtained through organ donor organizations. It also develops a comprehensive lung ontology that incorporates the latest findings of LungMAP consortium. The database contains transcriptomic, proteomic, and lipidomic data sources.
IN Situ Gene Expression Image Database
Gathers information for 14 pigment cell-expressed genes of the developing melanocyte and Ribulose-phosphate 3-epimerase (RPE) lineages. IN Situ Gene Expression Image Database consists in an online resource that supplies method to describe complexities underlying differential gene expression within the context of pigment cell lineages. This methodology can be applied to other genes with expression in pigment cell lines, allowing a standardized description of the expression of pigment cell genes.
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