The cell cycle DB: a systems biology approach to cell cycle analysis

Abstract

The cell cycle database is a biological resource that collects the most relevant information related to genes and proteins involved in human and yeast cell cycle processes. The database, which is accessible at the web site http://www.itb.cnr.it/cellcycle, has been developed in a systems biology context, since it also stores the cell cycle mathematical models published in the recent years, with the possibility to simulate them directly. The aim of our resource is to give an exhaustive view of the cell cycle process starting from its building-blocks, genes and proteins, toward the pathway they create, represented by the models.

Figure 1.

Architecture of the Cell Cycle Database. The core of the resource is a data warehouse system which collects data from the most relevant bioinformatics resources (Data Sources) and provides links to external resources (Linked Resources). The Cell Cycle Database comprises user-friendly interfaces which show information and, in general, provide the functions of the resource, even relying on third party free software (SW).

Figure 2.

Model of Bai et al 2003 [15]. Examples of two objects shown by the user friendly interfaces in the “models section” of the Cell Cycle Database: (A) the ordinary differential equations as they appear on the web interface; (B) plot of time courses of three state variables of the model.