Using workflow management in DNA sequencing

Abstract

DNA fragment assembly is an area which makes intensive use of computers. However, computer users in this field are typically not experts in computer science, but build their working environment on an ad-hoc basis. In this situation, it seems appropriate to offer a kind of support which can contribute to a better organization of working environments, and a better exploitation of computer hardware and software. The authors describe an approach in this direction based on the emerging paradigms of workflow modeling and management. In particular they offer three contributions: first, they discuss why workflow management can be fruitfully adopted in DNA fragment assembly, and describe one way to perceive and model sequencing processes as workflows. Second, they outline an architecture of a system intended to support sequencing applications, whose core component is a workflow management system. Finally, they sketch their experience of building a prototype using commercial workflow management technology.