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5. Additional tools

ChemCell is designed to be a computational kernel for performing reaction/diffusion computations. Additional pre- and post-processing steps are typically needed to setup and analyze a simulation.

Our group has written and released a separate toolkit called Pizza.py which provides tools for doing setup, analysis, plotting, and visualization for ChemCell simulations. Pizza.py is written in Python and is available for download from the Pizza.py WWW site. Images and movies created by Pizza.py are displayed on the ChemCell WWW site.

Pizza.py has a "cdata" tool with many sub-commands for reading and creating regions, surfaces, particles. The resulting geoemtries can be visualized with other Pizza.py tools: "gl", "vcr", "raster", "svg", etc.

Similarly, Pizza.py has a "dump" tool which reads in ChemCell dump files and allows particles to be selected, visualized, and animated, along with the ChemCell geoemtry (regions, triangulated surfaces) via the same Pizza.py tools.

Pizza.py also has a "clog" tool which reads in ChemCell log files and allows the species concentration statistics to be plotted either via GnuPlot ("gnu" tool) or MatLab ("matlab" tool).

If you write additional tools (either stand-alone or as part of Pizza.py) that you think are generally useful for setting up or analyzing ChemCell simulations, send us an email; we can include them as part of the ChemCell or Pizza.py packages.