Physio_MIST Mark Caral, Sara Cummins, BarbaraJoy Jones

REQUIREMENTS JDK 6 Update 17: http://java.sun.com/javase/downloads/index.jsp The directory containing jvm.dll must be in the user's PATH environment variable. NUnit: http://www.nunit.org/index.php Open Physio_MIST.sln in Visual Studio and build the project.

QUERY REQUIREMENTS MySQL 5.0 and the JDBC: http://dev.mysql.com/downloads/connector/j/5.0.html Make a database named "fma_owl_3" Make a MySQL user "fma_test" with the password set to "test" with full privileges on the FMA database. Unzip the fma3.0.owl.zip file in the QuerySystem directory and run DB_Builder.java Building the database can take a significant amount of time, but only needs to be done once.

LOADING MODELS Select File->Load from the main menu. Browse for the desired file (either an MML text file or an XML file conforming to the Physio_MIST schema) and click the Open button. A sample model (meal_model.xml) is located in the source directory.

SAVING MODELS Select File->Save from the main menu. Enter the desired file name and click the Save button.

EDITING MODELS Select an item in either the Parameter or Variable tables and click the Edit button. Input must conform to the MML standard, except for the Anatomical Structure and the Description fields.

QUERYING Select the desired structure in the ontology tree. Right click and select "Find Related Structures..." then select the desired relationship type and click the Run Query button.