• All needed libraries (including PeerSim) should already be in the lib/ directory. The primary prerequisite is for Apache Ant, which is used for the build scripts. A relatively recent version of Java is also needed.

• To compile, simply run ant compile from the root. The unchecked conversion warnings from PeerSim can be safely ignored.

• A convenience script is used to launch the simulation. This script, run, is a Bourne shell script, and will only work on UNIX-like systems. If you are using Myconet on Windows, you will need to create an equivalent run.bat or run.cmd file by using this file as a guide for how to set the Java classpath.

• The configuration for an individual experiment is performed using a text file. Relevant parameters can be found in the example-*.txt files in the root of the repository. Additional discussion can be found in the docs/ subdirectory.

Once you run the simulation with the visualizer enabled, you will see a number of buttons. Note that the position of the nodes on the screen does not represent their actual location…it is a layout algorith that attempts to make the neighbor relationships clear, which is the significant aspect. With the basic VisualizerTransformers enabled, small blue circles are biomass, red triangles are extending hyphae, yellow squares are branching hyphae, and green pentagons are immobile hyphae.

The JUNG layout code has a couple of bugs in it, which results in an occasional race condition and null pointer exception (halting the layout update algorithm). Should this occur, just kill the simulation and restart.

• freeze pauses the layout algorithm, which can be useful when you are letting the simulation run for a number of rounds and don't care about what's happening in between. Clicking the button again restarts the layout engine.

• capture takes a picture of the displayed graph and saves it to the capture/ directory using the basename specified in the config file.

• pause stops a running or walking simulation.

• step advances the simulation by one cycle

• walk starts the simulation advancing with a short delay between each cycle. If this delay is too short, you'll need to change it in the code.

• run starts the simulation running without pausing between cycles. If you click run (say, because you want to get to round 80, fast), it's best to freeze the layout to reduce the chance of the null pointer error.