As a graduate student, not only gain more advance education, but also prepare for applying those theses in the near future. If students can spend time getting the main idea of the software, they might have chance to improve the result by setting different initial conduction. As a result, only read the instructions on using the software cannot gain the big picture of the whole concept. After students really understand the meaning of program, they would find out that a lot of difficulties have to be overcome during hands-on section. Otherwise, they might use the software to check their consequence; it would not achieve the maximum of software.
Students would like to apply those theories in the industry, and they have the advantage of good educations. When they follow the concept, they might be able to think about new solution. It is good to use the software program as a tool, and they would not spend time on those routine procedures. As long as they can connect the education to the application, the industry would welcome those intelligent students. For example, MADLAB is a useful product in math works. Both engineering and science students might use it all the time, but only plug those giving data into the program will not help students to understand the meaning of the concept.