Put the beans in a large pot and cover them with water. Bring them to a boil and take them off the heat. This breaks the capsules surrounding the beans and allows stachyose, verbascose and raffinose, the gas-causing sugars, to escape into the water. Stir about half a teaspoon of baking soda into the soaking water (to make it more alkaline) and let the beans soak overnight.
Drain the soaking water off the beans and rinse them thoroughly.
Place the beans in a large pot and cover them with plenty of water (about 2″ or more over the top of the beans). Bring to a boil over high heat, then reduce the heat to just under boiling and cook the beans until they are soft. Cooking time will vary with the variety of the beans and the length of time they have been in storage (older beans take longer to cook). Check the package for cooking time recommendations, which can range from 45 minutes for lentils to two hours or more for large varieties such as red kidney beans. Undercooked or raw beans should not be eaten.
Canned beans should not be a problem since they are prepared using a method similar to this. I often use canned beans in my healthful recipes; the choice is yours.
If you are just starting to add beans to your healthful diet, start out gradually and build up the amount you eat over several weeks. You will gradually build up colonies of healthful bacteria that help to break down the gas-causing sugars that are new to you.
