XML3D based Molecular Structure Visualization using BALLView and Ballaxy (PDF)

Bachelor Thesis from the year 2014 in the subject Computer Science - Applied, grade: 1,3, Saarland University, language: English, abstract: The field of molecular visualization is an important part of biology, chemistry, medical computer science and bioinformatics. Molecular visualizations can help scientists to gain a better understanding of underlying mechanisms of molecular structures, even for large sets of data. With this thesis, we aim at bringing molecular visualizations to the browser. In order to achieve this goal, this thesis introduces a new online visualization tool for the web-based molecular structure analysis system ballaxy. Ballaxy is a customized version of the popular molecular data analysis and workflow system Galaxy and relies on the Biochemical Algorithms Library (BALL) framework. This framework provides molecular modeling functionality for structural bioinformatics.

This new ballaxy tool equips scientists with a small and handy application to visualize molecular structures directly in the browser without forcing them to use any additional tools or browser plugins. It makes use of the HTML extension XML3D to render molecular visualizations in the browser and optimizes the already existing XML3D export feature available in BALL and its accompanied molecular visualization tool BALLView.

The implementation of this optimization exploits XML3D features, which have been added to the XML3D library only recently. It removes many redundancies in the resulting documents and adds new features, like animations or additional information about the visualized molecules.

This thesis provides an initial implementation of the tool mentioned above and also extends BALLView with all newly developed features. Furthermore, it proofs that the newly introduced optimizations of the XML3D renderer have a significant positive impact on the browser rendering performance and the general usability of this solution.

Our approach shows that native 3D visualizations of molecular structures in the browser are a feasible option for displaying and analyzing molecular structures. The solutions developed for this thesis can already be used by scientists for their everyday work.