The on-instrument applications for the GS FLX+ System consist principally of the GS Sequencer application, which provides a graphical user interface used to control the GS FLX+ Instrument; and the GS Run Browser, which allows the raw or processed data from the sequencing Run to be viewed. They can both be accessed by double-clicking their respective application icons on the GS FLX+ Instrument computer desktop (Figure 1). System Start and System Stop icons are also available on the desktop to start and stop the GS FLX+ Instrument background processes. In addition, Run data processing can be performed on-instrument by embedding it in a sequencing Run (or by launching the GS Run Processor software via the GS Run Browser), although only the first part of this, image processing, is normally carried out on the instrument. The GS Run Processor and associated software are described in Part B of this manual.

The main functionalities of the GS Run Browser, to view sequencing Run and data processing results, are presented in detail in Part B, Section 3, of this manual. Part A of the manual focuses on the implementation and usage of the GS FLX+ on-instrument applications; this includes using the GS Run Browser application to launch processing jobs through the GS Run Processor Manager Tool, as discussed in Section 4.