Engineering Sequence Analysis Algorithms and Workflows for Parallel Computing

Mohamed Abouelhoda

art der veranstaltung


Part I: Introduction
Review of sequence data types and formats: focus on NGS data types
Review of sequence Analysis Algorithms and indexing data structures

Part II: Engineering software tools
Parallel Index construction: I. on multi-core machines
Parallel Index construction: II. on computer cluster
Parallel string matching: I. shared index distributed queries
Parallel string matching: II. distributed index
Chaining algorithms: sequential and parallel
Use of GPUs: Case studies
Task scheduling: Single program multiple data

Part II: Engineering workflows
Introduction to workflow systems
Task scheduling and management in workflow systems
Data management in workflow systems

Part III: Emerging platforms
Use of Hadoop/ Map-Reduce
Use of cloud Computing

Lehrsprache Englisch

Fri Dec 19 10:54:56 CET 2014