Play Game, Do Science

August 6, 2010 //
3

And finding a cure for cancer is definitely lvl 80.

My daily reading usually does not include anything from Science or Nature, but this article stood out among all the other academia mumble-jumbos.  In a nut shell, the paper described a software that evaluates protein conformations faster than any existing computer.  How?  By taking advantage of human brain’s immense cognitive power.  Researchers found that even a casual player (non-biochemist) can solve complex protein folding problems much faster than a computer.  (Ars has some very good background info explaining the biology aspect of the paper, take a look if you are unfamiliar with terms like amino-acid and hydrophilicity)

So a game called FoldIt is devised to takes advantage of of people’s boredom.  A series of incrementally difficult scenarios teaches players the basic mechanics of the game, then real data is streamed from online for player to solve.  Results are sent back for cumulative analysis.  So far, the result looks wonderfully promising.  It turns out, our monkey brains can easily out-perform a cluster of Intel i7s, both in accuracy and speed.

In the US, 200,000 Million (200Billion) hours are spent in front of a television, each year.  A total of 500 million hours were spent in Second Life in 2009, and a mere 100 million hours was spent in creating the entire Wikipedia.  Perhaps we can cure cancer in a week if we all just skip our weekly quota of Grey’s Anatomy?

Blender Workshop

July 23, 2010 //
2

We just wrapped up a full-day Blender workshop yesterday under the blazing sun of Pisa, Italy.  The seminar went smoothly and was well received.  A total of 35 attendees showed up despite the fact that the event was announced only a week prior.

In the morning, the attendees got a high level overview of what Blender can do, followed by a crash course on scientific visualization as applied to cellular biology and biochemistry as well as an extensive Python lesson.  In the afternoon, we moved to the computer lab and covered some of the Blender fundamentals, giving a lot of the attendees their first hands-on experience with Blender.

Even though this is my third time running such an event, there is still lots of rooms for improvement.  (For example, Blender 2.5′s UI was corrupt on some of the machines running older Ubuntu installations and Intel graphics chip, which made running the tutorials very challenging)

Photos of the event are on Pisaca.  Special thanks to the Pisa Linux User Group, without them, this workshop would not have been possible.

Biochemical Visualization Using Blender

June 25, 2010 //
8

Here at the Scientific Visualization Unit of the National Research Council in Pisa, Italy, we have been using Blender since 2008 for doing some very interesting bio-molecular visualization at the sub-cellular level.  I myself joined the team just over 3 months ago, and am eager to share some of our work with the Blender community now that the Italian soccer team can stop embarrassing themselves in South Africa.

We use Blender to visualize protein motions and interactions, as well as making short animations that show the inside of a cell in a way that had never been seen with the unaided eye.  Because one key focus of the project is scientific accuracy, a lot of time is spent to ensure that the visualization is not only nice-looking, but also scientifically accurate. The process involves using numerous third-party programs to convert the input data (atomic coordinates of a protein) into something Blender can read. We use Python extensively to help facilitate data conversion between different formats.  The result is this video:

To really appreciate the video, it helps to understand the science going on behind it.  If you are a bit lost, have a look at the explanatory note associated with the video.  The video is made and rendered with Blender in 1080p HD, we also toyed with stereoscopic rendering with some very good result.  You can download the HD stereo version from the SciVis site.

Currently, we are working to build an interactive protein viewer inside Blender.  Using Blender 2.5 as the platform, we built an interface that will allow biologist to load a text description of any protein (a PDB file), and Blender will display the imported file in an intuitive interactive viewer. (As shown below)

Why Blender? Blender is especially suitable for this task for several reasons. Its python support allows us to accomplish a lot of custom features in relatively very little coding.  Having a game engine and a physics engine built-in means we can use do realtime visualization all from one software package.  Its open source nature allows us to easily modify (at least have access to) the source code if needed.

Above is our BioBlender interface for Blender 2.5.  The protein on the right is MLCK backbone, a 1845 residue long protein.

There is still a lot of work to be done.  Blender is currently having a hard time handling large proteins that contains thousands of amino acid groups, the interface turns sluggish with as the number of object increases.   Surprisingly, the game engine performance is very fast, it manages to maintain 20fps on a laptop even with a fancy ambient occlusion shader.

Sintel Movie coloring test

June 13, 2010 //
12

Blender Institute just released a bunch of test renderings from their upcoming movie Sintel, and I couldn’t help it but try my hands on giving those wonderful images some aggressive color-grading.  I’ve included the before, after and a short justification for my choice of grading.  Criticisms welcome!

The Sintel team simply isn’t doing a good enough job, they are doing a GREAT job, and I am sure color grading is a planned part of their pipeline.  I just got carried away a bit playing with these images :D

Even though snow should be white, it doesn’t hurt to give it some tone to communicate the extreme coldness.  Blue works well in this case.

Wow, the team is doing a great job with facial animation.  This looks like a very somber scene, so it calls for some gloomy color.  I also added a dark gradient from the top, anime style.  Split toning is used to maintain the skintone while pushing the background to a cool blue.

I am speculating here, but I wanted to create a contrast between the safety of the warm tent and the harsh cold outside.  So things close to the fire is made warmer, things further away is pushed to a chilling blue.  The histogram is also very left-biased (dark), so I brightened up the image a bit.

Here, our main character isn’t emphasized enough in this (what I assume would be) high motion scene due to the similarity in color. I added a warming filter to highlight Sintel to convey the classic warm-vs-cold, good-vs-evil, light-vs-dark concept.

Just added some warmth to make the image look a bit more organic and less CG.

Everything is done in Lightroom, which is an awesome postprocessing package for photos, but the same effect can be easily achieved in Blender’s composite engine.  But seriously, Sintel is going to be amazing.

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