14.6. Editing MDLs and Analysis with Python

MCell can be thought of as a simulation engine for CellBlender. In other words, after you design your model in CellBlender, it is MCell which actually carries out the simulation itself (i.e. the diffusion and reaction of molecules). And MDL (Model Description Language) is the file format which MCell uses. With the help of CellBlender, some users may never need to hand-edit an MDL or even know that they exist. But for the users who need that extra flexibility and control, editing MDLs or even writing them from scratch can be invaluable. And for those with a programming background, the syntax might be familiar as it shares some similarities with C-style languages. Don’t worry if you are not a programmer however; MDL is not that difficult to understand. In the following tutorials, you will learn about MDL, checkpointing, and how to do some simple analysis using Python and matplotlib.


It is assumed that you have already gone through tutorials 1-5 prior to attempting these.