To install: 
1. Run the application \\OptimizationScenarios-DOAssess\OptimizationDOassessAppInstaller_mcr.exe
2. This will install the application on the default C-drive (you can specify another location as well):
	C:\Program Files\Ecology\Optimization_DOAssessment
3. This will also install Matlab runtime files (necessary to run the application). Again you can speficy the location for the runtime files
 	C:\Program Files\MATLAB\MATLAB Runtime\v98
4. Create a shortcut on your desktop, if you wish


To Run:
This script will process one scenarios for a given year and provide planview maps and Excel tables
1. Point to scenario and reference netcdf file. The script will also use the associated .mat file
2. Run the application using the shortcut or the application: 
	C:\Program Files\Ecology\Optimization_DOAssessment\application\Optimization_DOAssessment.exe
3. If it does not work on your machine, right-click the application or shortcut and run it as an administrator:
	a. Wait for matlab resources to load up. This will take sometime.
	b. Choose the default location for matlab temporary file or select another location.
	c. Choose year of simulation
	d. Choose location where maps and tables will be saved
	e. Open a scenario.nc and reference.nc files when prompted
	f. Min DO for each layer of each cell are extracted from hourly data for all scenarios
	g. DO noncompliance calculations are done
	h. planview maps are made
	i. A table of max magnitude and dates of noncompliance AND total cumulative days of noncompliance a generated