There are multiple schools of thought on where one should go to get a bike: go with a local, co-op, smaller-selection option (The Missing Link), get a used bike (many, but try The Bent Spoke, and maybe avoid the shady Karim Cycle), or a try more traditional bike store (Mike's Bikes, REI, Solano Ave Cyclery, or Performance Bike). Hank and Frank has the added bonus that they will service your bike for life for free, if you are willing to trek to north Oakland.

General advice for biking safely and avoiding bike theft.

License your bike on campus

Here are some excellent maps of bike routes in the East Bay.