The Scene is initially empty and you start with creating a schema on it:
schema
A schema is a visual representation of the query that would be used to analyze a nucleotide sequence. It consists of elements.
element
An element of a schema. There are two types of elements: algorithm elements and constraint elements.
algorithm element
An element of a schema that represents an algorithm used to analyze a nucleotide sequence.
constraint element
An element of a schema used to impose constraints on the results obtained from algorithm elements.
Your first step is to add necessary algorithm elements to the Scene by dragging them to the Palette.
The next step is to add constraints on the algorithms results.
Read Manipulating Element chapter to learn the details or check the section below on how to create and run a schema.