Do-it-yourself 3-D Bioscience Modelling

Feb 17 2011 Published by under Art & Science

A picture's worth a thousand words.  Sometimes even more.  I think that's especially true when trying to imagine microscopic organisms and molecules, that simply can't be seen with the naked eye. And even better than a flat picture is a three-dimensional model that you can move and manipulate.

I have on good authority that it used to be that if you wanted to create a 3D image on your home computer you would have to invest in expensive software and wait seemingly forever for models to be processed or rendered.  But almost a decade ago, Blender - a free open source 3D modeling application - was released to the public. And over the years personal computers have gotten fast enough that it doesn't take days to render your images.

Blender has been used to make some pretty amazing animated shorts. But it's uses aren't limited to entertainment and commercials.

Blender Image Rendering

Blender rendering a microbe image.

Issue #31 (December 2010) of BlenderArt Magazine takes a look at how Blender can be used "Under the Microscope" to demonstrate scientific principles and visualize microrganisms and microscopic cellular components.

Biomolecular visualization specialists Raluca Mihaela Andrei, Mike Pan and Monica Zoppè, write about how to use BioBlender.  BioBlender is a Windows application used to view and manipulate 3D protein models using data from the  RCSB Protein Data Bank (pdb files).

An example of their work is  the video Protein Expressions (there is a stereo version on their web site):

In the same issue, physicist Enrique Sahagún describes how he animated a kinesin protein motor transporting a vesicle down a microtubule.  The result:

The magazine includes some full-page images that demonstrate  nicely that  biological visualizations on the microscopic level can be both powerful science and beautiful art.

You can download Issue 31 of BlenderArt Magazine- along with sample .blend files. - for free at BlenderArt.org. The issue are also includes a couple of articles about creating physics visualizations, if bioscience isn't your thing.

If you are in the Boston area, you might want to consider attending the BioBlender workshop at the VizBi (Visualizing Biological Data) conference  on March 19th at the Broad Institute in Cambridge.

3D Models created with Blender:

Virtual worm @ WormBase

• IFC-CNR Scientific Visualization Unit videos and blender files

Firing Neurons, the Cell Dance 2010 Public Outreach Video Winner

•  XVIVO's Powering the Cell (I don't know that they used Blender, but it's fantastic animation)

Molecular Shots Portfolio

Online tutorials :

Jonathan Williams demonstrates how to use Blender to model a Microscopic Virus

Frederik Steinmetz shows how to construct a "Microcosm" using Blender 2.5

BioBlender

The image at the top is one of the Blender Magazine sample images in the process of rendering. I actually don't have any experience making 3D animations myself.  Thanks to Brian (who does use Blender) for pointing the magazine out to me!

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