A Closer Look at 3-D Cell Cultures

Organization: Lawrence Berkeley National Laboratory (U.S. Dept. of Energy)
Co-Developer(s): Bahram Parvin, Principal Developer, Cemal Bilgin, Hang Chang, Gerald Fontenay, Ju Han
Year: 2014

2014 R&D 100 Winner

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It’s well known that compared with 2-D cell culture models, 3-D cell culture models have different patterns of development, respond differently to therapeutic targets and have different patterns of gene expression. Lawrence Berkeley National Laboratory’s BioSig3D is the only computational platform that provides Web-based delivery of image-based bioinformatics technology from 3-D cell culture models that are imaged in full 3-D using either confocal or deconvolution microscopy. The computational platform is database-centric using PostgreSQL. All resources and processes are registered, invoked and monitored by the database. Such resources also include Web pages and an embedded workflow model that prompts the client for experimental design and annotation.

The system has six conceptual components that are tightly integrated through controlled vocabularies (CVs), where the CVs have been borrowed and extended from existing ontologies. The Resource Manager (RM) maintains an inventory of cell lines, reagents, antibodies and small molecule inhibitors. The Experimental Design Manager (EDM) interacts with the RM, via querying the database, to design an experiment utilizing a series of templates and CVs. The Data Load Manager supports three functionalities: uploading data in a variety of input formats into the image server, linking data with associated experimental factors and individual wells in a multiwall plate format and providing utilities for downloading images and computed representations. Visualization modules support three distinct services: a thumbnail viewer of an image stack, volume visualization and surface rendering of processed samples.

Technology Computational platform for 3-D cell culture

DevelopersLawrence Berkeley National Laboratory

Development Team

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Lawrence Berkeley National Laboratory's BioSig3D development team.














The BioSig3D Development Team from Lawrence Berkeley National Laboratory Bahram Parvin, Principal DeveloperCemal BilginHang ChangGerald FontenayJu Han