title: Visualizing multi-omics data in metabolic networks with the software Omix: a case study.
abstract: Systems Biology is a multi-disciplinary research field with the aim of understanding the function of complex processes in living organisms. These intracellular processes are described by biochemical networks. Experimental studies in alliance with computer simulation lead to a continually increasing amount of data in liaison with different layers of biochemical networks. Thus, visualization is very important for getting an overview of data in association with the network components. Omix is a software for the visualization of any data in biochemical networks. The unique feature of Omix is: the software is programmable by a scripting language called Omix Visualization Language (OVL). In Omix, the visualization of data coming from experiment or simulation is completely performed by the software user realized in concise OVL scripts. By this, visualization becomes most flexible and adaptable to the requirements of the user and can be adapted to new application fields. We present four case studies of visualizing data of diverse kind in biochemical networks on metabolic level by using Omix and the OVL scripting language. These worked examples demonstrate the power of OVL in conjunction with pleasing visualization, an important requirement for successful interdisciplinary communication in the interface between more experimental and more theoretical researchers.
authors.affiliation: Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Germany.
authors.forename: Peter
authors.initials: P
authors.lastname: Droste
authors.forename: Stephan
authors.initials: S
authors.lastname: Miebach
authors.forename: Sebastian
authors.initials: S
authors.lastname: Niedenführ
authors.forename: Wolfgang
authors.initials: W
authors.lastname: Wiechert
authors.forename: Katharina
authors.initials: K
authors.lastname: Nöh
mesh_terms: D003198:Computer Simulation; D048230:Corynebacterium glutamicum / Q000378:metabolism; D004926:Escherichia coli / Q000378:metabolism; D020600:Gluconobacter oxydans / Q000378:metabolism; D053858:Metabolic Networks and Pathways; D055442:Metabolome; D055432:Metabolomics / Q000379:methods*; D012984:Software; D059467:Transcriptome