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/