Muscles simulations are very very very complex… and to make things even more complex, Blender has no concept of muscles. You can approximate the effect of muscles with shapekeys but you have a lot to learn before to reach that point.
Now, the somewhat traditional way to animate a character is to first make the character, its “skin” which is usually referred as the mesh. In general, in order not to waste your CPU power, the mesh includes only the visible skin and the clothes. This character mesh is usually built in T-pose or a pose very similar. Standing on its feet with the arms extended on both sides… Well, if your character is human. It can be anything, like a car, a robot, a snake, a spider, or what-not. It all cases, you build your character with its limbs/parts extended and not tangled because it’s easier down the line.
Once you character is at 99% in its definite shape, you can start building a hierarchical skeleton inside the mesh with bones from join to join. (Bones are simple objects, nothing to “code”… and you don’t need to rebuild the whole human skeleton.) This skeleton is called a “rig”. It can be very simple or extremely sophisticate. You can build it so that the legs fold automatically when you lower the pelvis or else that the arm follows when you pull a hand, that kind of fancy stuff… And I won’t even speak about the complexity required to give facial expressions to your character.
Two expressions you need to know: “Inverse Kinematic” (IK) and “Forward Kinematic” (FK). To simplify, let’s say that IK is what allows you to make an arm follow the hand, while FK allows you to move the bones independently.
And a third one: “Bone Constraints”. You can add constraints to the bones so that they don’t allow you to exceed the possibilities of the body of your character… or not. In that case, it’s up to you not to animate your character beyond what’s possible. (BTW, IK is also a bone constraint… amongst the large family of bone constraints.)
When the support skeleton is done, you can associate it with the mesh through parenting and weight painting. Weight painting is a process to associate bones with parts of the mesh so that, for example, only the left arm moves when you move its bones and not the right leg.
The whole process of building the rig and associating it with the mesh throught weight painting is called “rigging”. (You’ll find plenty of tutorials about this subject on the web.)
To finish, the curse word of all the animators: “Bone roll!”