On other systems, folding bicycles such as Bike Friday or Brompton are usually permitted. BART allows bicycles except during peak commute hours, and CalTrain has dedicated bike cars for bike commuters. Consider leaving your bike in a locker at a BART or rail station, so you don't have to carry it with you. Use a bell to let a pedestrian or cyclist know you are approaching, but to signal drivers who can't see you, you'll need a horn. Carry a pump, patch kit, and spare tube for your wheels.
Many people simply switch to a good tube and patch a punctured tube later at home.
Practice fixing a flat or have a fellow cyclist teach you before you find yourself stranded. Keep your chain and gears oiled and free of dirt and grit buildup. Eventually you'll gain strength, improve your balance, enhance your breathing, sleep better and on and on. In short, your fitness will improve, simply by commuting to and from work every day. As you become more aware of safe cycling issues, consider local bike advocacy groups, which work for better cycling conditions.