Is it possible to insert a keyframe to a metaball element? I think everything is in the title : I want to deform my metaball object during animation.

Let's explain a bit more : I have several metaball objects in my scene, each of them composed of several metaball elements.

mball = bpy.data.metaballs.new("my_ball") 
obj = bpy.data.objects.new("my_object", mball)
elem1 = mball.elements.new(type="BALL")
elem1.co = Vector((0,0,0))
elem2 = mball.elements.new(type="BALL")
elem2.co = Vector((2,0,0))
bpy.context.scene.objects.link(obj)


(There are also stiffness, radius... that I didn't wrote for the sake of clarity)

This object can move/rotate with 

obj.location = Vector((1,2,3))
obj.rotation = Quaternion((1,2,3,4))


and be animated simply with 

obj.keyframe_insert(data_path="location"/"rotation", frame = 1)


Also, it must be able to fusion with other objects, so those objects are named "my_object.001", "my_object.002", ...

Now, the problem is that I want to deform the object during the animation :

elem2.co = Vector((0,2,0))
obj.keyframe_insert(data_path="location", frame = 100) # Of course, it doesn't work


One solution would be to use only objects with one metaball element each, and use lists of metaball objects for my (semantic) objects. But it will be particularly difficult to handle rotations...
With obj.keyframe_insert you are adding a keyframe for the object, not the element.

To set keyframes for elem2 you want to use elem2.keyframe_insert

elem2.co = Vector((2,0,0))
elem2.keyframe_insert(data_path="co", frame = 10)

elem2.co = Vector((0,2,0))
elem2.keyframe_insert(data_path="co", frame = 100)