A medical infusion pump system, comprising: a portable pump housing configured to receive medicine for dispensation to a user, the pump housing at least partially containing a pump drive system to dispense the medicine through a flow path to the user; and a controller that controls the pump drive system to dispense the medicine from the portable pump housing according to a closed-loop delivery mode in which the controller autonomously provides insulin dosages to the user in response to feedback information of a user's blood glucose level, wherein the controller is configured to, in response to receiving input indicative of a user-prompted bolus dosage, temporarily interrupt the closed-loop delivery mode by dispensing from the infusion pump system the user-prompted bolus dosage, wherein a calculated dosage amount of the user-prompted bolus dosage is calculated by the infusion pump system based upon both user input and an amount of insulin dispensed during the closed-loop delivery mode over a selected time period immediately prior to the user-prompted bolus dosage, wherein said amount of insulin dispensed during the closed-loop delivery mode over the selected time period comprises an effective-insulin-on-board amount calculated as follows: Effective Insulin-on-Board = [∑(Dosage n * Duration Factor(t) n)] - Estimated Basal Rate, where Dosage n represents the quantity of any insulin dosage among n number of dosages delivered to the user during the selected time period, where n is any positive whole number, and where Duration Factor(t) n, represents a factor discounting the dosage based on an amount of time (t) since its delivery, and wherein the estimated basal rate represents an estimate of the user's background insulin needs. a portable pump housing configured to receive medicine for dispensation to a user, the pump housing at least partially containing a pump drive system to dispense the medicine through a flow path to the user; and a controller that controls the pump drive system to dispense the medicine from the portable pump housing according to a closed-loop delivery mode in which the controller autonomously provides insulin dosages to the user in response to feedback information of a user's blood glucose level, wherein the controller is configured to, in response to receiving input indicative of a user-prompted bolus dosage, temporarily interrupt the closed-loop delivery mode by dispensing from the infusion pump system the user-prompted bolus dosage, wherein a calculated dosage amount of the user-prompted bolus dosage is calculated by the infusion pump system based upon both user input and an amount of insulin dispensed during the closed-loop delivery mode over a selected time period immediately prior to the user-prompted bolus dosage, wherein said amount of insulin dispensed during the closed-loop delivery mode over the selected time period comprises an effective-insulin-on-board amount calculated as follows: Effective Insulin-on-Board = [∑(Dosage n * Duration Factor(t) n)] - Estimated Basal Rate, where Dosage n represents the quantity of any insulin dosage among n number of dosages delivered to the user during the selected time period, where n is any positive whole number, and where Duration Factor(t) n, represents a factor discounting the dosage based on an amount of time (t) since its delivery, and wherein the estimated basal rate represents an estimate of the user's background insulin needs.