MOTIVATION Post-sequencing DNA analysis typically consists of read mapping followed by variant calling. Especially for whole genome sequencing, this computational step is very time-consuming, even when using multithreading on a multi-core machine. RESULTS We present Halvade, a framework that enables sequencing pipelines to be executed in parallel on a multi-node and/or multi-core compute infr...

We model and solve the problem of sequencing a set of jobs with specified processing times and tool requirements on a set of identical parallel machines. Decisions concern the assignment of jobs to machines, their sequencing, and the allocation of tools on each machine. The objective function minimizes the makespan. We propose an adaptive large neighborhood search metaheuristic in which the des...

Designing a scheduling competition to attract researchers from the several fields interested in scheduling problems seems a challenging, and highly worthwhile effort. In this paper, we propose a design for one possible track of this proposed scheduling competition. Specifically, we propose a track aimed at one machine sequencing problems. We argue that any such track must include problems with ...

We discuss the problem of sequencing precedence-constrained jobs on a single machine to minimize the average weighted completion time. This problem has attracted much attention in the mathematical programming community since Sidney’s pioneering work in 1975 (Sidney, J. B. 1975. Decomposition algorithms for single machine scheduling with precedence relations and deferral costs. Operations Resear...

The problem of sequencing and scheduling airplanes landing and taking off on a runway is under consideration. We propose a new family of valid inequalities which are obtained from the study of the single machine scheduling problem polytope.

This paper considers a different version of the parallel machines scheduling problem in which the parallel jobs simultaneously requirea pre-specifiedjob-dependent number of machines when being processed.This relaxation departs from one of the classic scheduling assumptions. While the analytical conditions can be easily statedfor some simple models, a graph model approach is required when confli...

Nested Patch polymerase chain reaction (PCR) amplifies a large number (greater than 90) of targeted loci from genomic DNA simultaneously in the same reaction. These amplified loci can then be sequenced on a second-generation sequencing machine to detect single nucleotide polymorphisms (SNPs) and mutations. The reaction is highly specific: 90% of sequencing reads match targeted loci. Nested Patc...