Integrative bioinformatics---network modelling, analysis, and visualisation with examples from crop plant metabolism

Falk Schreiber (Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), and Institute of Computer Science Martin Luther University Halle-Wittenberg )

CSIRO ICT CMIS

DATE: 2010-11-26
TIME: 11:00:00 - 12:00:00
LOCATION: CSIRO Seminar Room S206 Bld 108 ANU
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ABSTRACT:
Modern technologies used in the life sciences produce huge amounts of data about the building blocks of organisms, such as genes, transcripts, proteins, and metabolites, as well as on phenotype data. For an integrative, systems biology directed approach it is not sufficient to consider the biological entities alone but is necessary to study their interactions and link the experimental data to the underlying biological processes. The key to this integration is biological networks in their spatial and temporal environments and the development of methods for the modelling, analysis, simulation, and visualisation of these networks and related multimodal and multidimensional data.

After an introduction to the integrative analysis of such complex data and an overview of the group's work (network analysis, visual computing, visualization) this talk focuses on two aspects: firstly MetaCrop is presented, a database that contains manually curated information about metabolic pathways in crop plants ranging from global overviews to fine details including location information, transport processes, and reaction kinetics. MetaCrop contains high quality information for about 40 major metabolic pathways in several monocotyledon and dicotyledon crop plants with emphasis on the metabolism of agronomically important organs. It provides the basis for data integration, data analysis, and simulation of metabolic processes which will also be discussed in this talk. Secondly SBGN (Systems Biology Graphical Notation) is presented, a new set of standards for graphically representing biological information, the biology equivalent of the circuit diagram in electronics. SBGN as a visual language should make it easier to exchange complex information, so that models are accurate, efficient, and readily understandable. Methods and tools which support editing, transforming, and validating SBGN maps will also be discussed.

BIO:
My research focuses on two areas: the representation, modelling, analysis, and visualisation of biological networks in their spatial and temporal embedding; and visualisation and visual analytics of multimodal, multidimensional as well as network-related data. Goal of these research activities is to support the knowledge generation process in the life sciences. As coordinator of the Bioinformatics research of the IPK Gatersleben, one of the major plant research institutes in Germany, I am particularly interested in plant bioinformatics and plant systems biology. However, I also have close collaboration with scientists from several other fields, especially medicine.