Developing a Database Supporting Cell Biology Modeling

University Of Connecticut, Storrs CT

Investigators

Abstract

Interest in computational cell biology has expanded in recent years. A good indicator is the attendance at a workshop on the topic, at the Biophysical Society meeting last year, which drew 600 scientists. In Japan, the E-CELL project is attempting to incorporate the entire genome of a unicellular organism into a model. In contrast, this database emphasizes models as building blocks for understanding cell biological events. Models are a collection of hypotheses and facts that are brought together in an attempt to understand a phenomenon. VCELLDB, the Virtual Cell Database, will be a web-accessible electronic repository of physiological models. Built on a prototype that already includes intracellular calcium dynamics, nuclear envelope breakdown, mitochondrial respiration and RNA trafficking, employing easy-to-use interfaces, the expanded database would include computational and data resources, such as a thesaurus, links to other databases and built-in math functions so that scientists could create consistent models. It will also have a community data curation feature that will permit the database to expand with a peer review mechanism, a sort of online publication mechanism that would lead to a self-sustaining public electronic model repository.