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• As long as no changes have been made to the behavior of the startup scripts, the following files and scripts should be copied over from the old Protégé.Server version to the new folder:
  

     codegen.dat (the seed number will also need to be changed to 101000.  This can be accomplished by typing 'vi                    codegen.dat.'  Once in the vi editor, type 'shift + insert' and modify the seed number.  Press 'esc', then ':wq' to save and exit the vi editor).
     codegen.properties
     run_rmiregistry.sh
     run_protege_ server_nci.sh
     shutdown_protege_server.sh

• If you do need to use new scripts, make sure to adjust the memory upwards from the default in the run_protege_server_nci.sh script.  Appendix G presents a table dsisplaying The following table dsisplays how much memory to allocate for each script, per tier.  You will also need to adjust the rmi.registry and rmi.server ports, the hostname and the metaproject location in this same file.  Please view Appendix A for port information for each tier.For the examples/server/nci_metaproject, you might need to export it to an OWL file in the previous version, and then create a new project using the OWL for the new version.  This depends on whether significant changes have   been made to the data interface. 

• As long as no changes have been made to the behavior of the startup scripts, navigate to the Protégé.Client folder and transfer the following script:

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• Enter all requested database info and click finish.  BiomedGT and NCIThesaurus data are stored in different databases (Please view Appendix A to view specific database info for each instance). Conversion can take anywhere up to 2 hours, if a file from production is being used 

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• After conversion of the project file, you can verify that the database has been created by utilizing a database GUI tool (DB Visualizer) to view if the table has been created.  Once verified, the project is now ready to be configured from the GUI.

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• Open the nci_metaproject.pprj located at /app/protégé/data/<PROTÉGÉ INSTACE>/Meta/.  Click on the project tab underneath the SYSTEM-CLASS tab on the left-hand side menu.  Select the 'Instances' tab at the top of the page. You will notice an 'Instance Browser' section, and an 'Instance Editor' section. The instance browser specifies the display name of your project, and the Instance Editor specifies the path of your database project.  Click on the dispay project name and set the correct path to your project files.
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• Within the metaproject, the changes ontology projects (annotation files) should also not be made invisible visible to users when trying to access a project on the server.  To configure the project display list, please view the DisplayInList setup instructions.

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