The microbiology concept inventory can be used to access learning gains in many different ways. It's most common usage is as a pre- post-test of an entire course to determine where your students are learning, and where they are not. From this information, you can make adjustments to your instructional methods to address any shortcomings. The MCI can also serve to measure various teaching methods and determine what makes an impact and what doesn't.
If you are giving the MCI, you want to do a pre-test before any instruction. For large classes, using a survey site, such as Qualtrics is extremely useful. If you do use Qualtrics, here are two important gotchas I ran across while using it.
After treatment, administer the MCI as a post-test. When you are finished, you can upload your results to this site and the analysis will be done for you.