The downtown area of Guanajuato is fairly compact and most of the places where you are likely to find accommodation will be within a twenty-minute walk of the main square, Guanajuato University and all the main social hubs.
For longer distances within the city limits, there is an extensive and cheap bus service, but timing can be unreliable, and some routes are less well-served than others. Since the Valenciana area which is home to CIMAT is located in the mountains on the outskirts of the city, the frequency of the service is only around one bus per hour. So, if you—as many students do—choose to live downtown, this can sometimes prove inconvenient.
Nevertheless, if your bus does not show up on time, Guanajuato has many taxis. However, these are not metered, and if you are evidently not familiar with the city, some drivers may seek to exploit this. The common local practice is to tell the driver where you are going before you get in and ask what the charge would be, and—once you know the city a little better—understand whether the fare is reasonable.
Alternatively, if you would prefer not to haggle with drivers, Guanajuato also has an Uber taxi network which, though not yet as widely available as conventional taxis, will specify the fare before you confirm the ride.