Vineeta (V) is a lab-bench biologist and Xing (X) is a computational biologist. Vineeta tells Xing via e-mail that she needs to use a Monte Carlo script which he wrote. Xing then logs into BioMate to create an interface for this script for Vineeta to use. Xing then clicks on the "My Scripts" folder on the computational biologist landing page shown below and subsequently chooses to create a new script (not shown here).
Xing, now at the page for creating new scripts, fills out the necessary information for his Monte Carlo script. In particular, he is able to simply specify the general format of the command in the "Command Format" text field and that string is parsed to yield suggested fields as shown on the right-hand side of the first wireframe below (under Heading 2.1). Next, Xing can edit the parsed commands if he has any issue with the computer-generated suggestions. Finally, Xing saves his script interface and shares it with Vineeta.
After being notified that Xing has shared the Monte Carlo script with her, Vineeta logs into BioMate to view the interface which Xing created for the script. However, Vineeta notices that there is no option available to specify the number of iterations for the script, something critical to the analysis she hopes to perform. Vineeta then e-mails Xing back requesting that he update the Monte Carlo script interface to allow her to specify the number of iterations.
Xing then logs back into BioMate, clicks on "My Scripts" on the landing page and selects the Monte Carlo script he just created (not shown here). Then, Xing edits the script interface and adds a new parameter for the number of iterations. Finally, Xing saves the updated script and re-shares it with Vineeta.
Having been notified that Xing has updated the Monte Carlo script, Vineeta logs back into BioMate and comes to the landing page for lab-bench biologists shown below. She sees that the "Shared With Me" folder has a notification telling her that there are new scripts shared with her.
After clicking on the "Shared With Me" folder, Vineeta looks for the Monte Carlo script shared by Xing. It is the first script presented to her since it has just been shared by Xing and she hasn't viewed its interface yet.
Vineeta then arrives at the interface for the Monte Carlo script which Xing has designed for her. She sees that there is now an option allowing her to specify the number of iterations for the script per her request. She enters the desired number (500 iterations) and notes the command generated for her, which now includes the number of iterations (prefixed by "-n" as specified by Xing).
Vineeta then uses the command shown to run her data analysis in the command-line. Vineeta's analysis was successful using 500 iterations, so she'd like to make a note of this. Returning to the Monte Carlo script interface in BioMate, Vineeta elects to create a note reminding her that 500 iterations worked well for the particular analysis she was doing.
Several weeks later, Vineeta wants to re-run Xing's Monte Carlo script, but this time using a different input file. Vineeta logs back into BioMate and clicks on the History icon on her landing page.
After clicking on the History icon, Vineeta is presented with a list of scripts which she has recently viewed. The last time she logged onto BioMate was when she ran Xing's Monte Carlo script, so this is presented as the first option. Note that to find the Monte Carlo script, Vineeta could have also gone back to the folder of shared scripts or searched for the script directly by name, function, or author.
Now, Vineeta has returned to the interface for Xing's Monte Carlo script and selects her desired parameters, this time with a new input file name. Vineeta then obtains the command she needs for her analysis and logs out. Overjoyed with BioMate's ease of use, Vineeta continues on to have a happy and productive day.
