How much energy does it take to simply run forward? I'm interested in tracking as much data about my runs as I can in an effort to get faster, and while I can easily estimate energy expenditure during an uphill run due to the change in elevation, I can't estimate energy expenditure due to the requirements of just keeping in motion. I could estimate wind resistance, creating a simple cylindrical model and estimating drag, but obviously it would take energy to move forward on a flat surface in a vacuum as well.
Where would I start for this? What would be my variables? I know for a bicycle it's pretty simple to account for rolling friction, but I'm not sure what I'd need to account for. The question: What makes running so much less energy-efficient than bicycling? seems to downplay the importance of vertical motion in energy dissipation.
I guess to further boil down the question I'd ask: where does the energy go when you run?
 A: If you ignore air resistance, and assume the surface is hard and absorbs no energy that you need to care about, then the remaining energy must be absorbed as heat in your body (and shoes). If your temperature is steady then you will lose energy through heat radiation and convection at the rate you use it.
There will be many different chemical and mechanical process that generate heat in your body  as you run. I'm not going to try to list them and that would be biology rather than physics.
If you run on a soft inelastic material then energy will be converted into heat within the material - e.g. by friction as grains of sand rub against each other if you run on sand.
A: Most of the energy of running is used to move the legs of the runner. This isn't very efficient because the legs are heavy and are being quickly accelerated and deaccelerated from the running speed. The leg muscles are very powerful but runners hit a maximum speed when most of the power of their muscles is used up moving their legs back and forth. Bicycling is much more efficient because the legs don't have to be accelerated nearly as much, and the gearing makes better use of the power of the muscles. 
A: Energy (other than air resistance and shoe friction) is consumed by movements of body parts like legs and arms muscles and movement of internal organs - like when they move up/down, back/for as part of running, breathing activity, and heart pumping blood faster than normal and joint movements. Even the head bounces little bit on every step. Same way all the fluid in the body including blood bounces little bit. The radiated energy comes out of these activities only. Would be pretty hard to calculate I guess because it would also depend upon your style of running which impacts all the activities mentioned above.
But calculating this energy is pretty much of no use unless you plan to compete as a professional. In normal running, the purpose actually, is that all these activities do happen in order to give body more varied activity.
