Files to run the model and generate the data in Fig 5 for the wildtype (WT) model phenotype:

1. adaptation.sh 	- shell script for running simulations in parallel
2. LPSVar1.m 		- sample MATLAB file generated by adaptation.sh
3. runsim.m 		- this file runs the simulation, called by MATLAB files generated by adaptation.sh
4. params.m 		- this file contains all model parameters
5. odefn.m 		- this file contains the ODE model
6. Microgliavariation00x.bin 	- (note. x = 1 to 10) data files generated by running adaptation.sh
7. AnalyzeAdaptationData.m 	- file for integrating .bin files and processing the data
				- this file outputs the processed data into baseline_noDelay.txt
8. baseline_noDelay.txt 	- data generated by AnalyzeAdaptationData.m for subsequent plotting

Instructions

Run the followung command from a unix shell with MATLAB installed:

	sh adaptation.sh

To analyze the resulting data, open MATLAB and enter:

	>> AnalyzeAdaptationData