1. BEL Framework Exercise August 2012 This work is licensed under the Creative Commons Attribution 3.0 Unported License. To view a copy of this license, visit http://creativecommons.org/licenses/by/3.0/ or send a letter to Creative Commons, 444 Castro Street, Suite 900, Mountain View, California, 94041, USA.

2. Goals Download sample BEL knowledge from GitHub Run Compiler Run Compiler without Phase III List KAMs in KAM Store Export a KAM to XGMML Remove KAM from KAM store Start Server and access KAMs from KAM Navigator (Cytoscape) © 2012, Open BEL Community2

3. Download sample knowledge Go to https://github.com/OpenBEL/openbel- framework-resources/tree/master/knowledgehttps://github.com/OpenBEL/openbel- framework-resources/tree/master/knowledge Select full_abstract1.bel Click Raw Right click and select Save Page As – Make sure it gets saved as a.bel file! Save to a location you will remember © 2012, Open BEL Community3

4. Run BEL Compiler (adjust directions as needed for Linux or OS X) Open Command Prompt Navigate to BEL Framework Directory belc.cmd -h – Provides list of compiler/assembler options belc.cmd -f path\full_abstract1.bel -k testKAM –d "test KAM" -v – Your KAM should begin compiling – Verbose mode provides extra information about each step – Complation should take a few minutes © 2012, Open BEL Community4

5. Run Compiler without Phase III Repeat previous step, with two changes – Use different KAM name (testKAM2) – Add --no-phaseIII Phase III should be skipped Compilation should be faster © 2012, Open BEL Community5

6. List KAMs in KAM Store Change directory to tools KamManager.cmd -h – This will list the options for KamManager KamManager.cmd --list – Your Available KAMs will be listed – Should have testKAM and testKAM2 © 2012, Open BEL Community6

7. Export a KAM to XGMML KamManager.cmd --export -k testKAM2 -t XGMML – Your KAM will be exported and saved as an XGMML file © 2012, Open BEL Community7

8. Remove a KAM from the KAM Store KamManager --delete -k testKAM – testKAM should be removed from your KAM store KamManager --list – Confirm deletion of testKAM © 2012, Open BEL Community8

9. Start Server and Access KAM from Cytoscape Return to BEL Framework Folder startServer.cmd – A Tomcat window should launch – A success message should provide the WebAPI WSDL url http://localhost:8080/openbel-ws/belframework.wsdl Launch Cytoscape – Configure KAM Navigator to use the above WSDL – Open a new empty network – Select Add KAM nodes – 'testKAM2' should appear in the KAM pulldown menu Remember to stop the server – stopServer.cmd © 2012, Open BEL Community9