We have developed a software system that simulates chemotaxis-based cell aggregation in 2D. The model implemented within the system consists of such cell behaviors as chemical diffusion/detection, motility, proliferation, adhesion and life cycle stages. Each virtual cell detects the state of the environment, and responds to the environment based on a pre-defined "program" and its own internal state. Cells are discrete units that are located on a grid, exist in discrete states (e.g. active or dying) and perform discrete tasks (e.g. divide and attach), but they also contain and are affected by continuous quantities (e.g. chemoattractant concentrations, gradients, age and velocities). This paper provides an overview of our chemotaxis-based aggregation model and details the algorithms required to perform chemotaxis-based cell aggregation simulation. A number of biological studies are being conducted with the system. They include fine-tuning the model parameters to reproduce in vitro PC12 cell aggregation experiments and parametric studies that demonstrate the effect that the model's components have on cell aggregation dynamics.