Putting some notes in here that relate to SQL Server specific isssues. On linux boxes, accessing MS SQL is easiest using 'sqsh' a command-line Transact-SQL client. On the primary MS SQL server provided by the UHL, we have configured the following: {{{ create database i2b2metadata create database i2b2demodata create database i2b2workdata create database i2b2metadata2 create database i2b2demodata2 create database i2b2workdata2 create database i2b2_b1_metadata create database i2b2_b1_data create database i2b2_b1_workdata create database i2b2hive create database i2b2pm }}} Links This is useful on rebuilding indexes: http://www.sqldbpros.com/2010/11/sql-server-rebuild-indexes-the-fastest-way/