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1. Unzip the protege package in your chosed chosen directory
2. Run the bat or sh file
3. Do NOT immediate accept download of plugins.  
   1. Go to Launcher/Preferences then the plugins tab.  Make sure you are pointed to the correct plugins location.
   2. Go to File/Check for plugins and select all plugins
   3. Restart protege
4. Set up Lucene - Go to File/Preferences and choose Lucene as in tne General tab
5. Set up Pellet - Go to File/Preferences, the Reasoner tab and the Pellet sub-tab.  
   1. Select Remote as the reasoner type
   2. Enter the server address for pellet
6. Optional - restart Protege
7. Choose File Open from Protege Server.  Enter the credentials and wait.
8. Profit