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DOI

STEM-SIM

Multi-scale simulation of neoplasm formation.

Requirements

Ant

Ant is an open source software building tool available at ant.apache.org.

Java 1.5

StemSim is pure Java and requires Java 1.5 or later. Java is available at java.sun.com.

Building StemSim

To build StemSim, cd into the StemSim directory and type: ant.

Running a StemSim Simulation

  1. Modify the run.properties file as needed

    • the default run.properties is set up to run a default simulation
    • review each parameter and change as needed

  2. To run the simulation:

    • cd StemSim
    • ./bin/sim run.properties

StemSim will create a directory named after the time the simulation was kicked off. All files created by the simulation will be found in this directory.

Computing Statistics

StemSim cancer statistics are computed after the runs have completed from the XML simulation files. To generate the statistics:

./bin/stat <sim xml directory>

The stat command will create files with names based on the XML directory.