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Efforts to scale-up quantum computation have reached a point where the principal limiting factor is not the number of qubits, but the entangling gate infidelity. However, the highly detailed system characterization required to understand the underlying error sources is an arduous process and impractical with increasing chip size. Open-loop optimal control techniques allow for the improvement of gates but are limited by the models they are based on. To rectify the situation, we provide an integrated open-source tool-set for Control, Calibration and Characterization, capable of open-loop pulse optimization, model-free calibration, model fitting and refinement. We present a methodology to combine these tools to find a quantitatively accurate system model, high-fidelity gates and an approximate error budget, all based on a high-performance, feature-rich simulator. We illustrate our methods using simulated fixed-frequency superconducting qubits for which we learn model parameters with less than 1% error and derive a coherence limited cross-resonance (CR) gate that achieves 99.6% fidelity without need for calibration.