CompuCell
biological network data management/visualization software
CompuCell is a very user friendly, fully open-source environment for modeling biological systems and complex fluids. Programmers and scientists from the University of Notre Dame and Indiana University, Bloomington, are collaborating to make CompuCell a tool accessible to all.
Starting with a simple-to-write configuration file, a researcher from any field should be able to run complex simulations which evolve in a natural way. Currently, CompuCell employs an algorithm inspired from statistical-mechanics. However, the algorithm has been extended to incorporate an infinite variety of physics, including biological properties of cells.
In the configuration file, the user sets basic simulation parameters such as cell adhesivity, secretion rates, chemotaxis rates, mitosis rate, etc. From there, everything is done through the CompuCell3d player: the user simply selects the configuration file and presses play, watching the results emerge. The user controls views, display options, and data storage.
The CompuCell player is also a useful debugging tool in its own right. Montecarlo simulations can be difficult to debug without being able to view the entire state of the lattice. The CompuCell player provides an easy, low-overhead way to do this.
Another part of the CompuCell package is an xml-based language called BIO-LOGO which enables the user to generate partial differential equation (PDE) solvers which are compiled and linked to the main program at run time. What makes BIO-LOGO special is that the user only needs to write out the PDE in simple terms, such as
CompuCell does the rest. A python-based scripting language is also under development which will transform CompuCell from a program to a complete programming and development environment (such as MATLAB).
Although it is flexible and powerful in its current implementation, as we add more algorithms and features to CompuCell it will open doors for researchers to run complex simulations with a minimum of programming fuss. We are currently parallelizing the code to increase speed, and adding other new features daily.