A Simulated Annealing Algorithm for Resource Allocation and Scheduling with Precedence Constraints in the GLECLUBS/eGLECLUBS Pipelines

We present a heuristic algorithm for solving a series of resource allocation and scheduling problems. Given a resource of fixed size in a system, the problems are to schedule jobs with resource requirements, release and due dates, and priorities, so as to maximize the throughput, make span, or average completion time. The models have a wide range of applications such as bandwidth allocation for sessions in communication networks and resource reservations in cluster computing systems. Particularly, in order to speed up two bioinformatic pipelines "GLECLUBS" and "eGLECLUBS\´\´ we designed recently, which are used to predict {em cis}-regulatory motifs in a large scale of prokaryotic genomes simultaneously, we employ the heuristic to schedule the packages in the pipelines for a genome or a group of genomes. Our heuristic algorithm is simple, efficient, and based on simulated annealing.