Introduction

If you have been already using CompuCell3D you probably have realized the limitations of CC3DML (CompuCell3D XML model specification format). Simulations written CC3DML are “static”. That means you specify initial cellular behaviors, and throughout the simulation those behaviors descriptions remain unchanged. If your goal is to run simple cell-sorting or grain coarsening simulations CC3DML is all you need. However if you are seriously thinking about building complex biological models you have to look beyond markup-languages. Fortunately, CompuCell3D provides easy to use and learn Python scripting interface which allows users to build complex simulations without writing low-level code which requires compilation. If you have used Matlab or Mathematica you are familiar with such approach – somebody writes all number-crunching functions and provides you with scripting language which you use to “glue” those functions together to build mathematical models. This approach is very successful because it allows non-programmers to enter the arena of mathematical modeling. Python scripting available in CompuCell3D offers modelers significant flexibility to construct models where behaviors of individual cells change (according to user specification) as simulation progresses. In case you wonder if using Python degrades performance of the simulation we want to asure you that unless you use Python “unwisely” you will not hit any performance barrier for CompuCell3D simulations. Yes, there will be things that should be done in C++ because Python will be way to slow to handle certain tasks, however, throughout our two years experience with CompuCell3D we found that 90% of times Python will make your life way easier and will not impose ANY noticeable degradation in the performance. Based on our experience with biological modeling, it is by far more important to be able to develop models quickly than to have a clumsym but over-optimized code. If you have any doubts about this philosophy ask any programmer or professor of SoftwareEngineering about the effects of premature optimization. With Python scripting you will be able to dramatically increase your productivity and it really does not matter if you know C++ or not. With Python you do not compile anything, just write script and run. If a small change is necessary you edit source code and run again. You will waste no time dealing with compilation/installation of C/C++ modules and Python script you will write will run on any operating system (Mac, Windows, Linux). However, if you still need to develop high performance C++ modules, CompuCell3D andT wedit++ have excellent tools which make even C++ programing quite pleasurable (Hint: look at CC3D C++ menu in the Twedit++)