The BioBrowser Software

Using Advanced Graphic Technologies to Visualize Biomolecular Information

  • Fig. 1: Current visualizations of the BioBrowser: Ball and Stick, Ribbon, Spacefill and SticksFig. 1: Current visualizations of the BioBrowser: Ball and Stick, Ribbon, Spacefill and Sticks
  • Fig. 1: Current visualizations of the BioBrowser: Ball and Stick, Ribbon, Spacefill and Sticks
  • Fig. 2: The BioBrowser GUI uses the Microsoft Fluent UI for intuitive access to the visualization features. A: Switching visualization styles. B: The output pane contains info about loaded files. C: Molecule files can be downloaded and displayed automatically just by typing the PDB ID. D: Tool to generate large (print quality) images within seconds.
  • Andreas Halm, Graduate Student; Eva Eggeling, PhD, Head of the Fraunhofer Austria Visual Computing Group

Structural biology allows research on the causes of diseases as well as to increase the effectiveness of medicine. By doing research on the structure of molecules, a hardly comprehensible and understandable amount of data is generated. The software BioBrowser translates this data into pictures and allows the researcher to understand active parts of molecules. The 3D models of the proteins can be zoomed in and looked at from all directions. Detailed information can be gathered this way for research as well as medical applications.

Molecules Visualized in Three Dimensions


Lately tools for interactive molecular visualization have taken big steps forward, and more and more molecular biologists recognize that. As the function of a protein is closely related to its 3D structure, using 3D visualizations is essential for the daily work of researchers. The software "BioBrowser" has been developed as a project funded by the German Research Foundation (Deutsche Forschungsgemeinschaft (DFG)). Computer scientists and researchers of structural biology worked together to achieve a level of image quality that was not seen in interactive tools before.
The size of the molecules that BioBrowser can handle is not limited, 50,000 and more atoms are no problem. The BioBrowser can load standard PDB files as well as download them from the RCSB Protein Data Bank directly (www.rcsb.org) , given the PDB ID. The user can switch between the most often used visualization styles (ball and stick, sticks, spacefill, ribbons and sas). While zooming, moving around and rotating the display always stays pin sharp.

Scene Graph Architecture

A scene graph system can be described as some kind of hierarchical management software processing objects and abstract links between them. A simple 3D model of a car, for example, could consist of the car body and the four wheels. The car body would be implemented as one node in the scene graph and the four wheels being child nodes. Moving the car body does also move the wheels, but when turning right, the wheels need to move independently for steering.

Internally, the scene graph system would only store one 3D model of a wheel and use that model four times. This allows storing complex models in a very memory efficient way.
The main reason to implement molecular visualization using a scene graph system is that they are very similar. Molecules are hierarchically structured, especially in organic chemistry. A small number of atoms make up an amino acid. A number of amino acids whose three dimensional organization follows a special rule make up a so called secondary structure, for example a helix or a sheet. Some of these secondary structures form a chain, and a molecule is composed of one or more (usually similar) chains. Such a strictly hierarchical structure is perfectly suited for processing using a scene graph system.
The data structure that is used inside the BioBrowser is a component called BioSG. All data management functionality is implemented there as well as the visualization algorithms. It is based on the C++ Open Source scene graph system OpenSG. Using OpenSG as the basis has a lot of benefits, as it is very easy to support distributed rendering, for example. Medical applications would be possible, since doctors can zoom into the human body until molecular level. BioSG can also be used for scientific computing as distributed computation is very easy to implement (like cloud computing). This will support interdisciplinary research in the future, for example with vaccines development. Additionally BioSG can be added to any application using OpenSG very easily. This opens a whole new field of possibilities.

Graphics

One problem of existing applications is the visual quality when navigating interactively and the time it takes to generate high quality (print-quality) images. Graphics quality in programs like chimera or rasmol is below of what current standard graphics hardware is capable of. This makes them unusable for presenting research results.
Displaying big molecules, consisting of thousands of atoms, is the strong point of the BioBrowser. It makes use of modern graphics algorithms - billboards, depth sprites, level-of-detail meshes and pixel shaders, just to name a few. For most of the visualizations, more than one display algorithm is implemented and one is chosen automatically depending on hardware capabilities. This results in fast and detailed visualization of molecules. A press of a button generates an image file with a resolution of up to 32 megapixels within seconds.

Embedding Information

The fact that the BioBrowser is based on a scene graph system makes it the optimum base for information management. As in every scene graph system, not only 3D objects can be attached to nodes, but also all kind of information. Possibilities are currently investigated for attaching information not only to molecules, but to the various substructures of a molecule, like helices or amino acids. This information can be anything, from simple notes to complete research results. Also links to online information would be possible as well as links to other molecules.

Possible Applications

Molecular visualizations can be useful in various areas, for example medical, biological or chemical applications.
The BioBrowser can be used to visualize research results in the fields of biology or chemistry at conferences because of the high quality display even on low end computers, like laptops.
A lot of simulations have to be run to find out how effective a specific vaccine is or to test the aggressiveness of a poison. Such simulations can be controlled by a BioSG-derived application, allowing visualizing the intermediate simulation results while the underlying scene graph architecture simplifies distributed computation.

Test BioBrowser Now

A demo version of the BioBrowser, showing its graphic capabilities, is available for download. Scientist interested in testing the software should contact Fraunhofer Austria via the button email 'request' noted below.

References
[1] Halm A. et al.: Biobrowser: A framework for fast protein visualization. EuroVis05: Joint Eurographics - IEEE VGTC Symposium on Visualization (pp. 287-294). Leeds, United Kingdom: Eurographics Association (2005)
[2] Halm A. et al.: Visualization of complex molecular ribbon structures at interactive rates. Eighth International Conference on Information Visualisation (pp. 737-744). Washington, DC, USA: IEEE Computer Society (2004)

 

Authors

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Fraunhofer Austria Research GmbH
Inffeldgasse 16c
8010 Graz
Austria

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