The SIGNATURE interface in GenePattern is context-sensitive. To develop interfaces that can be sensitive to context, such as the state of a database or expertise of the user, we have extended GenePattern to support Interface Generators. These are add-ons to standard GenePattern modules that are responsible for producing the interface for the module at run time. Interface Generators can serve as brokers between GenePattern and other databases across the network. An Interface Generator is used for the Score Signatures module. In the simplest form of a Score Signatures analysis, the only parameters necessary are the RMA and MAS5 normalized versions of the data set, and an option for which signatures to include in the analysis (left). However, experienced users may wish to tune the analysis, and in response, the interface presents the user with an advanced interface that allows tuning of every parameter. On the right, a user has chosen to tune the parameters for the AKT signature.
Chang et al. BMC Bioinformatics 2011 12:443 doi:10.1186/1471-2105-12-443