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.
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.
