To download and install Netlogo, please go to:

https://ccl.northwestern.edu/netlogo/download.shtml

and follow the download and install instructions. My version was 6.2.0, which can be selected in the dropdown. This should be quick on current computers. It should then load on your machine. 

###OR you can use the Web application at (running 6.2.1, which has been tested with models):

http://netlogoweb.org/launch#http://netlogoweb.org/assets/modelslib/Sample%20Models/Chemistry%20&%20Physics/GasLab/GasLab%20Gas%20in%20a%20Box.nlogo

Then click "Choose file" (top right) and upload one of the files.

Info on Netlogo commands can be found here:

https://ccl.northwestern.edu/netlogo/docs/dictionary.html 

There are four models provided with this file, which reference for which figures they were used in their titles.

#For online:

To run the models, click "Setup". Then "Go/Pause"
Parameters can be adjusted using the sliders. They are described in the methods (or results for EvoModel). 
SDwithconversion model has an additional slider which allows users to alter the rate of senescent cells. 

To access or view the code directly, go to the tab at the bottom of the page.

#For installed:

Once Netlogo is installed, double click should open these on a Windows machine.
On Linux, open Netlogo then open file with File -> Open.

To run the models, click Setup on the Interface tab (which should show on opening).
Then "Go/Pause"
Parameters can be adjusted using the sliders on the Interface tab. 

To access or view the code directly, please go to the "Code" tab.

Expected outputs:
The sliders are set up at the starting variable conditions. Increasing Fill should accelarate AS mutant takeover. Increasing Kill, AR mutant takeover.
At the mutation rate of 1 and replication error of 2.5, running the model takes about 2 days to reach the 120,000 cycles used. 
However, for demo purposes, increasing mutation rate and replication error each to ten should allow for unidirectional takeover (to either AS or AR) in minutes.