BioBlender visualization

BioBlender is a software package built on the open-source 3D modeling software Blender. BioBlender version 1.0 for Windows and Linux was released on July 12, 2013. The first beta version of BioBlender (v 0.1) was presented in September 2010.



BioBlender is the result of a collaboration, driven by the SciVis group at the Institute of Clinical Physiology (CNR) in Pisa, Italy, between scientists of different disciplines (biology, chemistry, physics, computer sciences) and artists, using Blender in a rigorous but at the same time creative way.

With BioBlender users can handle proteins in the 3D space, displaying their surface in a photorealistic way, and elaborate protein movements on the basis of known conformations. Scientists all over the world study proteins at atomic level and deposit information in the public repository Protein Data Bank, where each molecule is described as the list of its atoms and their 3D coordinates.

BioBlender can be used for:

  • import and visualize Protein Data Bank (PDB) files (The PDB file format is a textual file format describing the three dimensional structures of molecules held in the Protein Data Bank)
  • simulate molecular dynamics and optimize protein motion
  • visualize complex protein surface properties  (e.g. MLP and EP surface properties)

A BioBlender tutorial was published by Raluca Andrei, Mike Chen Pan and Monica Zoppè, in the BlenderArt magazine N.31 in December 2010.

WebGL – OpenGL for the Web

WebGL brings plugin-free 3D to the web, implemented right into the browser. Major browser developpers Apple (Safari), Google (Chrome), Mozilla (Firefox), and Opera (Opera) are members of the WebGL Working Group.

WebGL is a cross-platform, royalty-free web standard for a low-level 3D graphics API based on OpenGL ES 2.0, exposed through the HTML5 Canvas element as Document Object Model interfaces.  It stays very close to the OpenGL ES 2.0 specification, with some concessions made for what developers expect out of memory-managed languages such as JavaScript.

WebGL  is developped by the Khronos Group, a not for profit, member-funded consortium focused on the creation of royalty-free open standards for parallel computing, graphics and dynamic media on a wide variety of platforms and devices. The Khronos Group was founded in January 2000 by a number of leading media-centric companies, including 3Dlabs, ATI, Discreet, Evans & Sutherland, Intel, NVIDIA, SGI and Sun Microsystems.

A guide how to get a WebGL implementation is available at the Khronos wiki website.

The current stable version of the Google Chrome 8 browser can be WebGL enabled by entering about:flags in the address bar and enabling the feature. A better (default) support of WebGL is provided with the Google Chrome Canari browser (the development version 10.0.614.0).

The following links point to websites with useful informations, tutorials, tools and ressources about WebGL :