First, there's prevention. If you're overpronating, strengthen the muscles of your feet. Concentrate on supporting yourself with the four corners of your feet (big toe mound, pinky toe mound, and the two corners of the heel) rather than with the center arch. If you're landing with a forefoot strike and toeing off, concentrate on landing with a midfoot strike and using your core muscles to move your legs. If you're ankling on the bike, concentrate on driving through your heels; you may need to re-position your saddle down and/or rearward for a better fit.

Then, there's treatment. Be sure to stretch your calf muscles after every run. Work out the trigger points by drawing your calf along the bent knee of the opposite leg, starting at the ankle and working toward the knee. Do 6-12 strokes on each leg, several times a day, pausing to work out trigger points that you find. And/or use The Stick, roller balls, or other myofascial release tools.

I'm sure others will have more to add...