How to shrink/purge ibdata1 file in MySQL

I am using MySQL in localhost as a "query tool" for performing statistics in R, that is, everytime I run a R script, I create a new database (A), create a new table (B), import the data into B, submit a query to get what I need, and then I drop B and drop A.

It's working fine for me, but I realize that the ibdata file size is increasing rapidly, I stored nothing in MySQL, but the ibdata1 file already exceeded 100 MB.

I am using more or less default MySQL setting for the setup, is there a way for I can automatically shrink/purge the ibdata1 file after a fixed period of time?