Cell Cycle Browser (CCB)

Cell Cycle Browser (CCB) visualizes, simulates, and predicts cell-cycle dynamics using real-time reporter time-series from proliferating human cells to analyze temporal coordination among molecular activities.

Key Features:

• Time-series visualization: Visualizes and organizes time-series traces from individual proliferating human cells across the cell cycle.
• Multi-layered timeline: Constructs multi-layered timelines of molecular events to represent temporal coordination among activities driving the human cell cycle.
• Computational modeling: Simulates dynamic interactions and phase transitions using computational models of molecular activities.
• Model manipulation: Adjusts expression levels and modifies strengths of molecular relationships within models to predict effects on the cell cycle.
• Virtual assays: Generates virtual growth curves and flow cytometry outputs for comparison between experimental data and simulation results.
• Prediction and hypothesis testing: Predicts potential outcomes of perturbations and supports hypothesis generation through simulation-based comparisons.

Scientific Applications:

• Molecular mechanism analysis: Investigates molecular mechanisms underlying cell-cycle regulation by comparing time-series data and model simulations.
• Perturbation studies: Assesses effects of genetic or environmental perturbations on cell-cycle dynamics via model manipulation and virtual assays.
• Therapeutic strategy development: Evaluates potential interventions targeting cell cycle–related pathways using simulated perturbations and assay outputs.
• Comparative data-model analysis: Compares experimental reporter data from proliferating human cells with simulations to validate or refine hypotheses.

Methodology:

Uses real-time reporter time-series traces and computational models that capture dynamic molecular interactions and phase transitions, with parameter adjustments (expression levels and molecular-relationship strengths) and generation of virtual growth curves and flow cytometry outputs.