CryptSim
http://www.cs.unm.edu/~dlchao/cancer
September 2008

This directory contains the Java source code for the "frontier model" described in 
"Pre-neoplastic lesion growth driven by the death of adjacent normal stem cells".
The simulation can be run by compiling all the java sources in the directories
lib, sim, and ui, then running PNASDriver.  PNASDriver takes one command line
argument, which is an experiment number that corresponds to a set of parameters
used in the paper.  For some experiments (7-9), a second command line argument is 
used to supply the parameter "lambda".  Output from the experiments go to
stdout, with some status messages going to stderr.

The experiment numbers are as follows:
  1. survival advantage growth (Figure 1A, Figure 2)
  2. reproductive + survival advantage growth (Figure 1B, Figure 2)
  3. reproductive advantage without survival advantage (mentioned in Results)
  4. no advantages
  5. survival advantage mutant border shape (Table 1)
  6. reproductive advantage mutant border shape (Table 1)
  7. "p53 mutants" that do not die (set lambda to 0.08 to get Figure 3C)
  8. "p53 mutants" that die at 40% of the normal rate (set lambda to 0.11 to get Figure 3D)
  9. "p53 mutants" that die at 14% of the normal rate (not used in the paper)
  11. "p53 mutants" that do not die, lambda=0.02 (not used in the paper, but compare with Figure 3C)
  12. "p53 mutants" that do not die, lambda=0.04 (not used in the paper, but compare with Figure 3C)
  13. "p53 mutants" that do not die, lambda=0.06 (not used in the paper, but compare with Figure 3C)
  14. "p53 mutants" that do not die, lambda=0.08 (Figure 3C)
  15. "p53 mutants" that do not die, lambda=0.10 (not used in the paper, but compare with Figure 3C)
  16. "p53 mutants" that do not die, lambda=0.12 (not used in the paper, but compare with Figure 3C)
  17. "p53 mutants" that die at 40% of the normal rate, lambda=0.02 (not used in the paper, but compare with Figure 3D)
  18. "p53 mutants" that die at 40% of the normal rate, lambda=0.04 (not used in the paper, but compare with Figure 3D)
  19. "p53 mutants" that die at 40% of the normal rate, lambda=0.06 (not used in the paper, but compare with Figure 3D)
  20. "p53 mutants" that die at 40% of the normal rate, lambda=0.08 (not used in the paper, but compare with Figure 3D)
  21. "p53 mutants" that die at 40% of the normal rate, lambda=0.10 (not used in the paper, but compare with Figure 3D)
  22. "p53 mutants" that die at 40% of the normal rate, lambda=0.12 (not used in the paper, but compare with Figure 3D)
  23. "p53 mutants" that die at 40% of the normal rate, lambda=0.14 (not used in the paper, but compare with Figure 3D)

The "ui" directory contains a GUITissueDriver program, which uses the
same underlying model but allows the user to input parameters in a 
dialog box and watch an animation of lesion growth.
