Sandra Gesing

Publications

• Special Issue: Portals for life sciences - Providing intuitive access to bioinformatic tools.

  Sandra Gesing, Jano I. van Hemert, Péter Kacsuk, Oliver Kohlbacher

  Concurrency and Computation: Practice and Experience. 01/2011; 23:223-234.

• TOPP goes Rapid - The OpenMS Proteomics Pipeline in a Grid-Enabled Web Portal

  Sandra Gesing, Jano van Hemert, Jos Koetsier, Andreas Bertsch, Oliver Kohlbacher

  CCGrid 2010, 10th IEEE/ACM International Conference on Cluster, Cloud and Grid Computing, 2010, Melbourne, Australia; 01/2010

  Proteomics, the study of all the proteins contained in a particular sample, e.g., a cell, is a key technology in current biomedical research. The complexity and volume of proteomics data sets produced by mass spectrometric methods clearly suggests the use of grid-based high-performance computing for... [more] Proteomics, the study of all the proteins contained in a particular sample, e.g., a cell, is a key technology in current biomedical research. The complexity and volume of proteomics data sets produced by mass spectrometric methods clearly suggests the use of grid-based high-performance computing for analysis. TOPP and OpenMS are open-source packages for proteomics data analysis, however, they do not provide support for Grid computing. In this work we present a portal interface for high-throughput data analysis with TOPP. The portal is based on Rapid, a tool for efficiently generating standardized portlets for a wide range of applications. The web-based interface allows the creation and editing of user-defined pipelines and their execution and monitoring on a Grid infrastructure. The portal also supports several file transfer protocols for data staging. It thus provides a simple and complete solution to high-throughput proteomics data analysis for inexperienced users through a convenient portal interface.
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  Impact points

  Simultaneous alignment of short reads against multiple genomes.

  Korbinian Schneeberger, Jorg Hagmann, Stephan Ossowski, Norman Warthmann, Sandra Gesing, Oliver Kohlbacher, Detlef Weigel

  Genome biology. 09/2009; 10(9):R98.

  ABSTRACT: Genome resequencing with short reads generally relies on alignments against a single reference. GenomeMapper supports simultaneous mapping of short reads against multiple genomes by integrating related genomes (e.g., individuals of the same species) into a single graph structure. It consti... [more] ABSTRACT: Genome resequencing with short reads generally relies on alignments against a single reference. GenomeMapper supports simultaneous mapping of short reads against multiple genomes by integrating related genomes (e.g., individuals of the same species) into a single graph structure. It constitutes the first approach for handling multiple references, and introduces representations for alignments against complex structures. Demonstrated benefits include access to polymorphisms that cannot be identified by alignments against the reference alone. Download GenomeMapper at http://1001genomes.org.

• Simultaneous alignment of short reads against multiple genomes

  Korbinian Schneeberger, Jörg Hagmann, Stephan Ossowski, Norman Warthmann, Sandra Gesing, Oliver Kohlbacher, Detlef Weigel

  Genome Biology 2009 10:R88. 10(9):R98.

  Genome resequencing with short reads generally relies on alignments against a single reference. GenomeMapper supports simultaneous mapping of short reads against multiple genomes by integrating related genomes (e.g., individuals of the same species) into a single graph structure. It constitutes the ... [more] Genome resequencing with short reads generally relies on alignments against a single reference. GenomeMapper supports simultaneous mapping of short reads against multiple genomes by integrating related genomes (e.g., individuals of the same species) into a single graph structure. It constitutes the first approach for handling multiple references and introduces representations for alignments against complex structures. Demonstrated benefits include access to polymorphisms that cannot be identified by alignments against the reference alone. Download GenomeMapper at http://1001genomes.org.