CompuCell3D

Molecular modeling is a fascinating scientific foray into the depths of the human organism, which can yield important answers to some of our most fundamental questions. Fortunately, scientists have benefited greatly from the steady increase of computational power, as more and more applications are dedicated to helping them unravel biological mysteries. CompuCell3D is just one such program that can be employed by highly trained professionals to accurately simulate and model cell behavior.

The scientific utility employs cellular Potts models, specifically Glazier-Graner-Hogeweg (GGH) algorithms to model and describe the behavior of single or multi-cells tissues, organs or organisms. This lattice-based approach ensures models are exactly solvable and generated simulations and cell representations adequately scale up to the actual mechanisms.

Creating a simulation requires that users define the actual cells, as well as design their interactions. This is performed by setting new properties to the entries in the “Model Editor”. Just as with any programming environment, scientists can adjust any properties of the simulation elements, including physical dimensions, volumes and cell types.

For any viable research to occur, one must also define the amplitude of fluctuations and the degree of variation. The initial configuration of the cells must also be defined and users can import these latter items from any simple data files. After all these steps have been completed, simulation is performed by simply clicking on the “Run” button.

However, more tech-savvy users will find the application's support for Python scripts and C++ extensions highly valuable, as it allows one to build more sophisticated and accurate biological models. During the simulation, screenshots can be taken and one can also generate PIF files from the VTK outputs.

All things considered, CompuCell3D is a powerful solution for anyone active in the field of biological modeling, at the cell level. The GGH algorithm is used to model single or multi-cell tissues or organisms accurately and advanced users can also insert Python scripts to generate improved analyses.