Cellzilla Quick Start Cellzilla2D Home

  1. Download and Install Cellzilla2D

    Download and installation instructions are given here.

  2. Create a Cellerator model

    Cellzilla needs a model of a network in a single compartment; this model is then automatically reproduced on a template that you will specify. Quick start instructions for xlr8r are here.

  3. Create a geometric template

    The template consists of a representation of a two dimensional tissue composed of cells, stored in a data structure called a Tissue. Each cell is a separate compartment in this data structure.

    You can use a pre-defined template, such as the ones picture here; look in the index on main Cellzilla web page for functions starting with the name Template to generate one of these.

    You can also define the tissue directly from an external template by formatting the data structure as described here, or by reading from a PLY file or flat file tissue description.

  4. Populate your model to the template (static simulations)

    The easiest way to do this is with the function CelleratorNetwork, which is used to generate simulations on non-growing, static tissue.

  5. Run a simulation on the Static Tissue

    Run a simulation and plot the results, e.g., with RunSim and SimPlot. You may want to plot your results on a template with SimAnimate.

    A simple example that does all of the above steps on a rectangular template using coupled simple harmonic oscillators is given here

    The results of static simulations - e.g., the values of variables as a function of time - are computed entirely in memory and will be forgotten when you quit Mathematica. If you will need them in the future they can be saved with the built-in Mathematica function Save.

  6. Incorporate growth and cell division

    The function grow incorporates the functionality of CelleratorNetwork and RunSim when cell growth and/or cell division is going to occur. (Note that cell growth and division are included only starting in Version 3.)

    Because the tissue is constantly changing the entire system is recomputed after each cell division. This leads to a heavy demand on computer resources. Consequently, rather than saving the solution internally in memory, it is written to disk after each cell division. These files can easily be recovered for later examination and plotting. Several functions such as GetSavedFile, SimAnimate, ShowTissue and SimPlot have interactive features that allow you to select the desired file and perform these functions.

[2012-11-08 ]