A hybrid visualization system for molecular models

Abstract

Figure 1: Visualization of a large protein molecule[Chen and Williamson 2013], using ribbon diagram (left) and ball-and-stick model (right) with ParaViewWeb. AbstractNowadays, 3D visualization is part of our everyday lives and remains an important tool for understanding complex structures, dynamic simulations, and research discoveries. In the meantime, the complexity of the visualization often requires specific hardware, including visualization clusters, as well as dedicated software tools. Several efforts, such as WebGL and remote visualization, have been pushing visualization to the web browser. However, technical limitations have constrained the adoption of web browsers as a means of rendering 3D datasets. To surpass these limitations, prospective action has been recently initiated with the development of a web application based on two innovative technologies: WebGL and ParaViewWeb. This application combines the benefits of local and remote rendering, therefore allowing a user to visualize small to massive 3D molecular datasets on a large number of devices. To demonstrate this approach a prototype has been developed, and in this paper we present the hybrid architecture of the proposed system, the initial implementation experiment, and a comparison with current technologies. Finally, we discuss the future work and potential improvements of the application.

Molecular simulations and visualization: introduction and overview

“…For example, tools that are traditionally dedicated to areas such as the video game industry or the film industry may be used for molecular visualization [ 63 , 64 , 65 ] or animation [ 66 , 67 , 68 ]. The availability of such tools has enabled the use of molecular visualization in collaborative structural biology, for example using TV-based [ 69 ] or web-based [ 70 ] solutions. A similar cross-fertilization is observed for GPUs, originally used in the consumer graphics market and nowadays omnipresent in high performance computing and scientific visualization.…”

Bringing 3D visualization into the online research article

“…This mapper combines two rendering techniques: impostors and geometry instancing. Impostors are usually implemented to lower the number of triangles rendered in a scene by rendering the image of an object instead of rendering the object geometry [20]. To trick the user, the semi-transparent image of the object (the billboard) is drawn on a quad and then dynamically oriented to face the camera.…”