eSI Visitor Seminar: "Workflow-Engines in a Bioinformatic Portal " by Sandra Gesing

29 March, 2007 04:00 PM - 05:00 PM

e-Science Institute, 15 South College Street, Edinburgh

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Any slides or other material generated as a result of this event can be found at: www.nesc.ac.uk/action/esi/contribution.cfm?Title=780

Sandra Gesing
PhD student
The Division for Simulation of Biological Systems (http://www-bs.informatik.uni-tuebingen.de/)
University of Tuebingen

The e-Science Institute is delighted to host a seminar with Sandra Gesing. The seminar is open to all interested parties in academia and industry. There is no need to register for this event and those attending the seminar are invited to join us for tea and coffee at 15:30.


Sandra Gesing

Abstract

The area of bioinformatics covers a broad range of rather different topics. In all these fields an enormous number of complex and sophisticated algorithms and tools has been developed to aid the research activities. These tools often require specific computational resources and rather advanced computational skills for the installation and use of the software. However, scientists of the disciplines biology, biochemistry, and biomedicine want to focus on their specific question, combing all kinds of different approaches, but do not want to deal with the unpleasant details of software installation and practicability.

To enable efficient interaction with existing tools and to allow various combinations, we are designing a workflow-enabled portal. The specific characteristics of workflows for bioinformatics are among others challenging large data set sizes, heterogenity of data, diversity of data formats and long running tasks (from hours up to weeks). However, the workflows themselves are not very complicated from a structural point of view. The presentation will introduce to existing workflow engines and a generic user interface to submit workflows for enactment.

Biography

Sandra Gesing is a German PhD student in the group of Prof. Kohlbacher in the Division for Simulation of Biological Systems (http://www- bs.informatik.uni-tuebingen.de/), University of Tuebingen. She took up this position shortly after completing her extramural studies in computer science with a focus on computational geometry and software engineering at the FernUniversitaet Hagen. Since completing her Gymnasium diploma, she has always worked full-time in the IT area (as project manager and systems programmer), while also serving an apprenticeship and doing her diploma as an extramural student. For the last year she has been working on the TueBiGrid project (The Tuebingen Bioinformatics Grid). The goal of this project is the design and implementation of a grid infrastructure for parallel and distributed applications in the area of bioinformatics, particularly in the field of proteomics and systems biology.

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