Vanted and MetaCrop for Computational Systems Biology and Plant Metabolic Modelling
16/04/2013 - Room C209 at 14:00 - External Seminar
Prof. Falk Schreiber
(Bioinformatics Leibniz Institute of Plant Genetics and Crop Plant Research (IPK))
Systems biology comprises the iterative cycling between experimental and computational approaches with the aim of generating a holistic understanding of biological systems. The complexity of experimental datasets is continuously increasing thereby elevating the requirements for respective computational tool support for the analysis, integration, and visualization of multiple large-scale datasets.
Motivated by an example from modeling and analysis of barley seed metabolism [1, 2] this talk will discuss requirements and components of software support for systems biology. It will present a framework for computational systems biology consisting, among others, of the Vanted system  and related extensions as well as the MetaCrop information system . Computational tasks will be discussed and some further application examples from different areas will be presented.
1. E. Grafahrend-Belau, F. Schreiber, D. Koschützki and B. H. Junker: Flux balance analysis of barley seeds: a computational approach to study systemic properties of central metabolism. Plant Physiology 149: 585-598, 2009.
2. H. Rolletschek, G. Melkus, E. Grafahrend-Belau, J. Fuchs, N. Heinzel, F. Schreiber, P. M. Jakob and L. Borisjuk: Combined non-invasive imaging and modelling approaches reveal metabolic compartmentation in the cereal endosperm. Plant Cell 23(8): 3041-3054, 2011.
3. H. Rohn, A. Junker, A. Hartmann, E. Grafahrend-Belau, H. Treutler, M. Klapperstück, T. Czauderna, C. Klukas and F. Schreiber: Vanted v2: a framework for systems biology applications. BMC Systems Biology 6: 139, 2012.
4. F. Schreiber, C. Colmsee, T. Czauderna, E. Grafahrend-Belau, A. Hartmann, A. Junker, B. H. Junker, M. Klapperstück, U. Scholz and S. Weise: MetaCrop 2.0: managing and exploring information about crop plant metabolism. Nucleic Acids Research 40 (1): D1173-D1177, 2012.