Cell cycle database (CellCycleDB)

Cell cycle database (CellCycleDB) provides integrated gene, protein, protein–protein interaction and mathematical model data for yeast and mammalian cell-cycle systems to support systems-biology analysis and ODE-based dynamical simulation.

Key Features:

• Data Integration: Comprehensive annotations of genes and proteins involved in the cell cycle for yeast and mammalian cells are consolidated in the database.
• Protein Interaction Networks: Catalogues protein–protein interactions relevant to cell-cycle regulation to support network-level analysis.
• Mathematical Modeling: Supports ordinary differential equation (ODE) systems to represent dynamic behavior of cell-cycle components.
• Model Simulation and Dynamical Analysis: Enables simulation of ODE models and analysis aimed at identifying stable steady states and oscillations.
• Mathematical Pipeline: Implements a pipeline to handle the mathematical aspects of models and to incorporate new mathematical data for simulations.

Scientific Applications:

• Systems biology: Facilitates study of emergent properties and systemic behavior of the cell cycle by integrating structural and dynamical model information.
• Cancer research: Supports analysis of molecular cell-cycle mechanisms and dynamic properties that are relevant to cancer biology.
• Model component analysis: Enables retrieval of model components and examination of their dynamic properties across different models.

Methodology:

Integration of gene and protein annotations; representation of dynamics with ordinary differential equation (ODE) systems; simulation of ODE models; analysis to identify steady states and oscillations by coupling structural and dynamical information; an implemented pipeline to handle mathematical aspects of models.