Seminar: Improving Bioinformatic Methods via Enhancing and Scaling Up Workflows

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Workflows have proved to be an excellent medium for representing scientific methods in general and especially also in the areas life sciences and chemistry. In the last 20 years quite a few mature workflow engines and workflow editors with diverse foci and strength have been developed to support communities in managing workflows. More recent trends for enhancements of workflow systems address the usability of workflows and optimizations of their efficiency. The talk will go into detail for three methods and concepts concerned with these topics. The first topic consists of meta-workflows for quantum-chemical applications applied in the project MoSGrid (Molecular Simulation Grid) and its science gateway developed on top of WS-PGRADE. The second one addresses scaling up bioinformatic workflows with dynamic job expansion and our case study using Galaxy and Makeflow. The talk concludes with a model for balancing thread-level and task-level parallelism for data-intensive workloads on clusters and clouds on the example of aligners for next-generation sequencing data.

Sandra Gesing, Ph.D. (University of Notre Dame)

Sandra Gesing is a research assistant professor and a computational scientist at the University of Notre Dame, USA. Her research focuses on science gateways, workflows and distributed and parallel computing. Prior to the position at Notre Dame, she was a research associate at the University of Edinburgh, UK and in the Applied Bioinformatics Group at the University of Tübingen, Germany. Additionally, she has perennial experience as a project manager and system developer in industry. She received her German diploma in computer science from extramural studies at the FernUniversität Hagen and her PhD in computer science from the University of Tübingen, Germany