How do we clear codes the computer module properly?

We recently had the transmission and battery replaced in our Buick. But, now the Computer is acting crazy. My husband and the repair guy say that its because the battery was completely drained. They tried resetting the computer however, it now cranks, runs for about 3 minutes then shuts off. They say its the Security device and that the computer module may have to be reset or even replaced by a dealership. I CANNOT afford that and cringe at the thought of what the cost might be. IS it at all possible to reset the Computer module or security part of the computer ourselves?