Research

In recent years group members have been awarded millions of dollars in ARC Discovery and Linkage Grants and significant investment through industry sponsored research.

Click any individual project to learn more. View active, proposed and completed projects.

Visualisation of large, complex networks through small, beautiful diagrams

Networks are everywhere—Google's Knowledge Graph, Facebook's social networks and the Semantic Web. We will develop a new approach to visualise and understand these networks.

Funding: ARC Discovery Project — DP140100077

Flexible user-guided network layout for biomedical applications

This project will develop techniques for automatic layout of biological network diagrams, allowing users to guide the layout while satisfying any required placement constraints and drawing conventions. As part of the project, these methods will be integrated into several real-world systems biology applications for network browsing and authoring.

Funding: ARC Discovery Project — DP110101390

CIDER: A component-based toolkit for creating smart diagram environments

Smart Diagram Environments (SDEs) are software applications that use structured diagrams to provide a natural visual interface that behaves as if the computer "understands" the diagram. Unfortunately, despite their potential usefulness, SDEs are not easy to build. We present CIDER a Java toolkit for building SDEs which greatly simplifies this task. CIDER is a generic component-based system which is designed to be easily embedded in Java applications. It provides automatic interpretation of diagrams as they are constructed and manipulated, structure preserving manipulation, and a powerful transformation system for specifying diagram manipulations and user interaction. CIDER's main innovation is its component-based approach to SDE development which provides substantially increased architectural flexibility to the application programmer.

CELLmicrocosmos

The CELLmicrocosmos (Cm) project aims at the spatial analysis and visualisation of intracellular interactions. For this purpose, different software applications were developed. Biological pathways or other protein-/gene-related networks can be localized in the context of different three-dimensional cell models by using the Cm PathwayIntegration. For this purpose, content of different biomedical databases is queried. For the generation of molecular structures the Cm MembraneEditor is used, which is able to generate membrane and vesicular structures using PDB files. Originally developed at Bielefeld University, these tools will be extended and optimized in the context of the Immersive Analytics group by using advanced virtual reality techniques and bridging the gap between 2D and 3D representations. For this purpose, new stereoscopic technologies are explored and a comprehensive integration with network and data analysis tools, such as VANTED, is in development.

VANTED

VANTED stands for Visualization and Analysis of Networks containing Experimental Data. This system enables users to load and edit networks, which may represent biological pathways or functional hierarchies. A core feature is to map experimental datasets onto networks for visualisation of time series data, data of different genotypes or environmental conditions, as well as differential expression data, in the context of a the underlying biological processes. The program supports comprehensive tools for analysing network structures, network layout, as well as statistic functions, allow a fast evaluation of the data (e.g. t-Test or correlation analysis) and its underlying network.