Immersive Exploration of Cell Localization Scenarios Using VR, Spatialized Video Communication, and Integrative Bioinformatics

We published a new book chapter in the Springer book: "Integrative Bioinformatics"!

The cell models we used as the base in this chapter were created with the Cm 4.2 PathwayIntegration!

Bjorn Sommer, Ayn Sayuti, Chang Hee Lee, Zidong Lin, Jenny Hu & Ashley Hall

Integrating spatially localized molecular networks into virtual cell environments is an approach which is only provided by a very small number of tools. As this task requires the combination of a set of Biotechnology/Bioinformatics-related information sources, it can be seen as an appropriate example for Integrative Bioinformatics research. Here, we want to show new immersive perspectives for cytological pathway integration by combining recent explorative technologies with the software CELLmicrocosmos 4 PathwayIntegration. A mesoscopic-localized metabolic pathway—i.e. the citrate cycle and the glycolysis—is localized based on database entries onto an abstract cell environment of Arabidopsis thaliana. The created cell model is used in three different contexts providing different degrees of immersion:

  1. Web-based 2D exploration of 3D Scenarios (using,
  2. Exploration and Annotation in a VR Design Application (using Gravity Sketch), and
  3. Large-Scale VR Visualization and Navigation (using the CAVE2 and zSpace).

All these examples promise to be very useful in the context of Integrative Bioinformatics-related education as well as communication.