Screenshot of the Pegasys GUI showing the three pane design. The visible pane is the canvas pane which allows the user to create a workflow by clicking and dragging icons corresponding to the programs available to the system. The icons can be connected to each other through edges. The parameters used for the execution of each program can be set by double clicking the icon and filling in the dialogue box that appears (see Figure 5). Expected inputs and outputs for the edge can be set by double clicking the edge and filling in the dialogue (see Figure 6). This workflow will run RepeatMasker on the sequence specified in the File node and write the results to a text file whose path is specified in the text output node. The RepeatMasker analysis itself is run on the compute server and the results are communicated back to the client.