models/chapter7

The ArtCell object contains components for simulating cell growth and performning statistical analysis on populations of cells grown according to various rules.

The growth rules are specified by a ArtCellParameters object which sets the growth duration, parameters of the branching rule, and the probability distributions for the branching power, the growth rate first segment length, and the terminal diameter. Optionally the growth rate and branching may be modulated during the growth of the cell by setting Profile objects for the growthRateHist and branchingHist fields. If set, these are assumed to be percentages of the default values.

The CellGrower object takes a set of growth parameters and makes a single instance of a cell according to these parameters. One can specify the timestep and maximum number of points to allow. Normally neither of these should affect the results: they only have an effect if the timestep is so large that some branching events are missed, or the branching law is such that the cell would end up with more than maxPoints branches.

There are a number of display options, including a skeleton dendrogram, and one where the sections are drawn with their real width. For the latter, the dgram-yskip variable is useful for setting the vertical spacing in the dendrogram so branches are not drawn on top of each other. The freezeSeed option allows the same seed to be used for the random number generator each time. This sometimes makes it easier to see the effect of parameter changes on the branching.

The CMLINK(PopulationGrower) makes a whole set of cells according to a particular set of growth rules and shows histograms of various derived quantities.

singleCellGrowth	Growth rules for a single cell. The growth parameters are shown on the left. The branching probability per unit time is bpa * exp [-bpb * ord] /nterm^bpc where ord is the order of a segment, defined as the number of branch points between it and the origin. The next three fields are probability density functions for the first segment length, exponent in the Rall branch diameter relation, and the growth rate. To edit these, select the "floating frames" option and click the corresponding buttons. By default they use gamm distributed random variables, but you can also use Gaussion random variables. The branching and growth are assumed to proceed with uniform probability for the duration of the growth period unless Profile objects are set for growthRateHist or branchingHist fields. If set these are interpreted as percentages of the default values to be applied at given times.
populationGeneration	Population synthesis. The growth parameters are shown on hte far left. The PopGrower object grows ncell random cells according to these parameters and measures their geometrical properties. The raw measurements for the different cells are shown in the upper right graph, and the properties are summarised below. On theright, the mean and standard deviation of each measurement is shown. Since each has a different scale, a different range is used for each, with the upper limit shown on the right. To the left is a histogram showning one set of results, as selected with the hgram field, in detail. The default display shows simply the number of cells per bin. With the normalize option set, it shows the fraction of the to total per unit along the abscissa such that the total area of the graph is 1.