Increasing the Efficiency of Workflows: Use Cases in the Life Sciences

Speaker:

Dr Sandra Gesing, University of Notre Dame, USA.

Abstract:

Workflows have proved to be an excellent medium for representing scientific methods in general and especially also in the areas of 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, re-usability, sustainability and optimisations 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.

Biography:

Dr Sandra Gesing is a research assistant professor at the Department of Computer Science and Engineering and a computational scientist at the Center for Research Computing at the University of Notre Dame, USA.

Prior to the position at Notre Dame, she was a research associate in the Data-Intensive Research Group at the University of Edinburgh, UK, in the area of data-intensive workflows and in the Applied Bioinformatics Group at the University of Tübingen, Germany, in the area of science gateways and grid computing.

Additionally, she has perennial experience as a project manager and system developer in industry. As head of a system programmer group, she has led long-term software projects (e.g. infrastructure on web-based applications).

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.

Her research interests include science gateways especially for bioinformatics applications and distributed and parallel computing.

She is heavily involved in the US Science Gateway Community Institute, where her role focuses on outreach and community engagement. The successful European workshop series IWSG (International Workshop on Science Gateways) was founded by her in 2009 and she has guided it since. IWSG is the partner workshop series of the US workshop series on science gateways that has existed for more than 10 years and the Australian IWSG-A, which was founded in 2015.

The significance of science gateways was also recognized by IEEE and Dr Gesing chairs and coordinates the IEEE technical area on science gateways.

Supporting open-access initiatives, she is an academic editor of the open-access journal PeerJ Computer Science.