Worm muscle contraction simulation(involved many individual muscle pieces)

Not really an answer, but too long to fit into comments:

"Skeleton" animation (technical term: bones) usually starts with a human-created set of movements on a stickman. Either by an artist, of motion capture. So any muscle action is never computed -- either faked (artist) or observed (mo-cap.)

The bipedal skeleton system is then about playback, or synching forward motion with foot motion (avoid moonwalking.) It generally assumes you have a pre-done set of motions.

Say you had a "boned" worm, (no animation needed.) It would be a little like a radio-controlled set of connected motorized rods, wrapped in wormed-shaped clay. If you did all the math yourself, you could use the bones to internally bend the worm in the correct way. So, instead of maybe having a set of spheres for the body, which would "bend," by moving spheres, you could have a continuous body which would flex.