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The quark gluon plasma (QGP) is one of the most interesting forms of matter providing us with insight on quantum chromodynamics (QCD) and the early universe. It is believed that the heavy-ion collision experiments at the Relativistic Heavy Ion Collider (RHIC) and the Large Hadron Collider (LHC) have created the QGP medium by colliding two heavy nuclei at nearly the speed of light. Since the collision happens really fast, we can not observe the QGP directly. Instead, we look at the hundreds or even thousands of final hadrons coming out of the collision. In particular, jet and heavy flavor observables are excellent probes of the transport properties of such a medium. On the theoretical side, computational models are essential to make the connections between the final observables and the plasma. Previously studies have employed a comprehensive multistage modeling approach of both the probes and the medium. In this dissertation, heavy quarks are investigated as probes pf the QGP. First, the framework that describes the evolution of both soft and hard particles during the collision is discussed, which includes initial condition, hydrodynamical expansion, parton transport, hadronization, and hadronic rescattering. It has recently been organized into the Jet Energy-loss Tomography with a Statistically and Computationally Advanced Program Envelope (JETSCAPE) framework, which allows people to study heavy-ion collision in a more systematic manner. To study the energy loss of hard partons inside the QGP medium, the linear Boltzmann transport model (LBT) and in medium DGLAP evolution (implemented in the MATTER model) are combined and have achieved a simultaneous description of both charged hadron, D meson, and inclusive jet observables. To further extract the transport coefficients, a Bayesian analysis is conducted which constrains the parameters in the transport models.