Screenshot of the results for the Ion Torrent validation case. The flow value is the sequencing flow for which the signal was measured (experiment) or simulated. The darker horizontal and vertical regions in these flow signal plots represent the signal-value and flow-number windows, respectively. These regions enclose the experimental/measured signal values that were included in the optimization process. In addition, the green vertical line(s) in the Flow Signal Plot window delineate the signal regions associated with each of the reads within the spot (technical, biological, etc.). In order to provide more clarity on the user interface, a demonstration is provided in the Supplementary Material, available online ay doi:10.5402/2012/371718.