BII-Manager is a standalone java application, that validates ISA-Tab formatted reports and persist encoded information to database backend. It relies on Hibernate Object persistence broker framework to convert objects into HQL statement for persistence. It is therefore necessary to provide BII-Manager with database connection information, a location where to write the database index and move the data files associated with ISA-Tab formatted metadata.

BII Web application is the database front-end, accessible via an Internet browser (e.g. Firefox, Safari, InternetExplorer, Chrome). The web application requires Jboss Seam web application server to installed and properly configured to run. The web application also requires database connection information, access to the database Lucene index and to the data file locations. Those parameters are shared with the BII-Manager.