Vineeta (V) is a lab-bench biologist and Xing (X) is a computational biologist. Vineeta would like to analyze her data in her own time, but finds it hard to use run Xing's script directly in a terminal because she is not familiar with the command-line syntax for running his program, so Xing agrees to make an interface using BioMate to generate the command-line syntax.
Xing logs onto BioMate to generate the interface.
Xing types the name "monte carlo" into the text box for searching for the script to run. As no script with the name 'monte carlo' is found, he has the option of adding a new script with that name, which he selects.
Xing then has to construct the command chunk-by-chunk. The syntax for the command is "perl montecarlo.pl -v input.txt | less". This is composed of four chunks: "perl montecarlo.pl" (static text) "-v" (flag) "input.txt" (required parameter) and "| less" (static text). Xing adds each chunk sequentially.
Xing also has the option of pressing "Notes" and adding notes for Vineeta to read. An example of a note he might include is "the output of this command appears in the terminal window itself. Come see me if you would like to write the output to a file." (the inclusion of this note is not shown in the storyboard).
After Xing is done, Vineeta contacts Xing and mentions she would like to have the option of manually configuring the number of iterations. This means Xing must edit his command line structure to include the "-n numiterations" optional parameter, which he does.
Xing then shares the script with Vineeta by choosing her from his contact list.
Vineeta logs into BioMate to run the script.
Vineeta selects "monte carlo" from a dropdown list. She is then presented with the interface to enter her parameters. The fields are filled in (with pending delete) by the default values that the programmer had decided on earlier. Vineeta can hover over the question mark next to any field to get more information on what the field is. By default, any values she enters into the fields will be saved to the autocomplete for that field. For the flags (dubbed "settings"), Vineeta has the option of saving a particular combination of flags or loading a previously saved combination of flags.
Vineeta enters her desired parameters and presses "generate command". The copies and pastes the generated command into her terminal window. After observing the results, she makes a note to herself that she likes 1000 iterations.
The next time Vineeta logs into BioMate, her previous parameter values will have been saved to the autocomplete for the individual parameters.