Abstract
Modelling and analysis of metabolic processes is an established research field in Computational Systems Biology and Medicine. There are many different approaches for modelling as well as for visualization, but often these methods ignore the subcellular localization of proteins, enzymes and transporters involved in the metabolic processes.
Over the recent years, we developed two tools: CELLmicrocosmos 4 PathwayIntegration (CmPI) and VANTED. CmPI is used to analyse, visualize and explore potential subcellular localizations in a cell environment. CmPI provides import capabilities for metabolic pathways and simple visualization of directed networks showing the enzyme-compound relationships inside this environment in 2D as well as 3D. VANTED allows to analyse and visualize biological networks, to integrate data into these networks and simulate their dynamics.
Here, we will discuss future perspectives of these approaches and how to extend the capabilities of CmPI's localization method to provide a) complex modelling, visualization and exploration of metabolic networks in combination with -omics data, and b) immersive analytics of the spatially distributed networks using different Virtual Reality-based technologies. We discuss the prototypic integration of CmPI with VANTED and the large display visualization framework Omegalib in combination with a semi-immersive monitor zSpace™ and CAVE2™.
About the authors
Björn Sommer is a Research Fellow with the Department of Computer and Information Science of the University of Konstanz. He studied Media Informatics and Media Sciences at Bielefeld University, Germany, and made his PhD in Bioinformatics. Then, he was working at the Bio-/Medical Informatics Department at Bielefeld as a lecturer and researcher. Over the years, he developed together with his students the CELLmicrocosmos project which consists of a number of sub projects. The different software tools support researchers in modeling, visualizing and analyzing cell-related models, such as molecular membranes and vesicles, intracellular interaction and localization data. From 2015 to 2016, he was working as Research Fellow at Monash University, Melbourne, in the Immersive Analytics initiative, where he was working on three-dimensional human computer interaction, as well as small-to-large scale stereoscopic data exploration.
University of Konstanz, Computational Life Sciences, PO Box 76, 78457 Konstanz, Germany
Falk Schreiber graduated, obtained a PhD and a habilitation in Computer Science from the University of Passau (Germany). He worked as a Research Fellow and Lecturer at the University of Sydney (Australia), research group leader at the IPK Gatersleben (Germany), professor of Bioinformatics at the Martin Luther University Halle-Wittenberg (Germany) and professor at the Monash University Melbourne (Australia). In 2016 he was appointed professor for Practical Computer Science and Computational Life Sciences at the University of Konstanz. He is an adjunct professor at Monash University Melbourne (Australia). Prof. Schreiber is researching topics in Bioinformatics and Computational Systems Biology since more than 20 years. His main interests are visual computing and immersive analytics of biological data, analysis of structure and dynamics of biological networks, integrative omics data analysis, graphical standards for systems biology, as well as modeling and investigation of metabolism.
University of Konstanz, Computational Life Sciences, PO Box 76, 78457 Konstanz, Germany; and Bielefeld University, Bielefeld, Germany; and Monash University, Melbourne, Australia
Acknowledgement
We thank the anonymous reviewers for their helpful comments regarding the original submission.
©2016 Walter de Gruyter Berlin/Boston
