From Caltrain's terminus at 4th & King in San Francisco, Gary planned to ride his bike to the Ferry Building to catch the Vallejo Ferry. After hanging out in Vallejo for a little while, he planned to return to San Francisco via the Ferry and then figure out his options. He didn't know if he wanted to go down the East Bay using BART (and then using AC Transit to connect to VTA Light Rail for a ride back to Diridon Station) or just return to the South Bay using Caltrain.
Gary planned to complete this entire circuit before the 1p.m. deadline, when the ferries, BART, Caltrain and ACE would no longer be free.
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Do those trains have bike racks? Any pictures you can provide? In St. Louis, we have a brand new light rail train but although bikes are permitted, they must share the aisles with the passengers. Jack
Caltrain has a dedicated compartment on each trainset that can carry up to 32 or 16 bikes, depending on the car.
California Amtrak commuters and the Altamont Commuter Express also have bike compartments. ACE can carry up to 34 bikes per train, depending on how the train is configured. Amtrak commuter trains have dedicated room for 3 bikes per car.
Santa Clara County light rail has bike hooks. Each train has at least 4 and up to 8 hooks in it. Cyclists can also store bikes near the doors if the hooks are full so max realistic capacity can be something like 16 bikes per train, depending on how many cars are on the train.
Here's a photo of my bike on VTA light rail: http://www.flickr.com/photos/bike/266597211/
BART permits bikes on board (with some restrictions), but there's no dedicated bike storage for the bikes. You just bring them on board and hold them in the aisle. Here's a photo of a bike on BART that's pretty typical: http://www.flickr.com/photos/turkisdach/174257061/
I avoid taking my bike on BART -- it's kind of a pain in the neck because the system is very heavily used.