This paper presents a methodology to determine the energy and reserve schedules with consideration of power system uncertainties. Unlike contingency analysis, the requirements of operating reserves based on the stochastic optimal power flow are not predefined. Instead, the reserve requirement is generated to meet both the system reliability and economic efficiency under system uncertainties. The stochastic optimal power flow with reserve determination is proposed and studied with different types of uncertainties, including variation of system demand, outages of transmission lines and generation units, and intermittent generation. This study emphasizes the impact of the intermittent generation on the energy schedule and reserve determination, and so provides a new methodology for addressing emerging system issues with the emergence of renewable energy. Exploring a variety of cases reveals the differences between contingency analysis and risk-based motivations for reserve.