The Cell Cycle Browser: An Interactive Tool for Visualizing, Simulating, and Perturbing Cell-Cycle Progression.

Area of Science:

• Molecular Biology
• Cell Biology
• Computational Biology

Background:

• Cell cycle progression relies on tightly regulated molecular events.
• Understanding these dynamics is crucial for cell biology research.
• Existing tools lack integrated simulation and prediction capabilities.

Purpose of the Study:

• To develop an interactive web interface, the Cell Cycle Browser (CCB).
• To facilitate visualization, organization, simulation, and prediction of cell cycle perturbations.
• To integrate real-time reporter data from proliferating human cells.

Main Methods:

• Developed the Cell Cycle Browser (CCB) as an interactive web interface.
• Utilized real-time reporter data from proliferating human cells.
• Incorporated computational models for simulating cell cycle dynamics and phase transitions.
• Enabled users to adjust molecular parameters and predict outcomes.
• Implemented virtual assays (e.g., growth curves, flow cytometry) for comparison.

Main Results:

• The CCB allows visualization of multi-layered timelines of molecular activities from individual cell data.
• Users can simulate cell cycle dynamics by adjusting parameters like expression levels.
• Predictions of cell cycle behavior can be made through virtual experiments.
• Familiar outputs from virtual assays facilitate comparison between data and simulations.

Conclusions:

• The Cell Cycle Browser (CCB) unifies understanding of cell cycle dynamics.
• It provides a platform for hypothesis generation via virtual experiments.
• CCB enhances the exploration of molecular perturbations in the cell cycle.