1. A computer-implemented method for iteratively refining a seed schedule for a network of transportation resources, the method comprising: identifying a first seed schedule including a plurality of segments, with each segment connecting two markets and having at least one of a corresponding departure time or a corresponding arrival time, the first seed schedule further including paths to be traversed by a particular transportation resource, each path including a plurality of sequentially connected segments; defining at least one of additional candidate departure windows or additional candidate arrival windows for at least one segment in the first seed schedule; generating additional candidate paths with the computer from a set of available segments, each additional candidate path including a different plurality of sequentially connected segments than the paths in the first seed schedule, wherein the set of available segments includes at least a portion of the segments in the first seed schedule and at least a portion of the segments having at least one of additional candidate departure windows or arrival windows; using the computer to generate a composite score using mathematical programming for the first seed schedule and at least one possible alternative schedule, wherein the at least one possible alternative schedule includes a different combination of candidate paths than the first seed schedule; and identifying a replacement schedule with the computer by comparing the composite scores for the at least one possible alternative schedule and the first seed schedule.