Getting Started With Cellzilla Cellzilla2D Home

  1. Pre-requisites

    1. Mathematica - Cellzilla2D has been tested with Mathematica 8,9 and 11.

    2. Cellerator- Download and install the latest version (e.g. Cellerator-xxx) from Github. Earlier versions at Sourceforge and Launchpad probably will not work.

    3. xSSA - is not strictly required except for stochastic simulations. Download the lastest version of xssalite-xxx from Github and install it. Then after installing it, rename the file xSSAlite.m to xSSA.m. (It will be located in the Applications subfolder of the $UserBaseDirectory folder To determine the location of ,span class="function">$UserBaseDirectory on your operatimg system, type $UserBaseDirectory into any cell in Mathematica and press enter.)

  2. Download and install Cellzilla

    To get the latest stable version, download the latest Cellzilla file release Cellzilla-xxx" from the Github web site.

    To install Cellzilla:

    1. Unzip the download.
    2. Open the file installer.nb in Mathematica.
    3. From the Mathematica menu bar select Evaluate > Notebook and follow the instructions on the pop-up menu.

    [ Advanced users may wish to fork their own version of the repository, which is located here. Altrnatively, incremental versions of the code can be downloaded from the repository.]

  3. 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. Cellerator arrows are illustrated here. In addition, Cellzilla arrows that can also be included in the model are indicated here.

  4. 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.

  5. 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.

  6. 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.

  7. 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.

[ 20 June 2017 ]