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1. Allocate a decent max_heap_size. (default is set to 12gigs, however, less memory can be used for test machines (i.e. 8GB for QA)).
2. Enusre that the explanation server is pointing to the correct Protege.Server folder: (protege_install=/path/to/new/Protege server folder). This allows the Explanation server to use jars found in the Protege.Server folder.
3. Make sure the path to the java server is correct (replace <PATH TO JRE BIN> with the actual jre/bin/java.exe location.
4. The command to connect the explanation server to a database project: './start_explanation_server.sh --port <PORT> --protege-standalone /path/to/databaseProject.pprj'. The command to connect to a raw OWL file:  *'./sh start_explanation_server.sh --urls file:///home/user/path/to/file.owl'*
5. The Explanation Server is ready when you see "Jena, Classification, and Extracting' as well as a final
   'Server started, listening on port ....' message. The Explanation Server should be allowed to start completely before starting the Protege Server.

Protégé Server Folder

run_rmiregistry.sh

1. JAVA_HOME must be set in the script.
2. The very last line has a port number that will need to match the Protégé Server: $JAVA_PATH/rmiregistry <PORT> &

run_protege_server.sh

1. JAVA_HOME must be set.
2. Set MAX_MEMORY to a suitable size to run adequately (i.e. NCI Production - 7.5 GB, QA - 7GB, Dev - 3GB).
3. Ensure RMI_REG_PORT number matches port number in 'run_rmiregistry.sh' script.
4. Set RMI_SERV_PORT to any desired open port.
5. HOSTNAME_PARAM=-Djava.rmi.server.hostname=<hostname> should be edited with the actual server hostname where the rmi registry server will be running. The "localhost" address will not work properly, it needs to be the actual server name.
6. Set METAPROJECT with the location of the Metaproject file.

codegen.properties

The codegen.seed number should be set at a figure higher than the highest concept number in your vocabulary. The codegen prefix and codegen.suffix values are optional. The optional codegen delimeter will set the character to be inserted between prefix and code or code and suffix. Example: prefix=B, delimiter=-, suffix=cs, seed=100. The first code generated will be B-100-cs. A 'codegen.dat' file will then be generated within the Protégé server folder and will be updated to "100" and will iterate the concept code number from that point.

PromptNCIPlugin.properties

Verify correct database information for saving to the evs_history table. This information should match the PromptNCIplugin info residing in the Protégé client folder:

nci.prompt.ipAddress=<hostname>:<port>
nci.prompt.dataBaseName=<db name>
nci.prompt.dbEVSHistoryTable=<tablename>
nci.prompt.userName=<username>
nci.prompt.password=<password>

protege.properties

Verify that the protege.properties file points to the correct Protégé server as well as the URL for the explanation server:

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