1 - 21 of 21 results

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.


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.

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.

SOCR / Statistics Online Computational Resource

Aims to design, validate and disseminate knowledge. SOCR is a technique that enables investigation of biological mechanisms related to morphological changes in cell nucleus through quantitative analysis of changes in its size and shape. It provides portable online aids for probability and statistics education, technology based instruction, statistical computing, and predictive big data analytics. Its tools and resources include a repository of interactive applets, computational web application and graphing tools, instructional and course materials.

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.


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.

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.

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.

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.

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.