The Twisting Tale of DNA

Wed 19th Dec 2012, by Paul Hellard | Peoplestudios

CGSociety :: Technology Focus

19 December 2012, by Meleah Maynard

Accuracy is the goal in the science and medical animation world, so there isn’t much call for fun and whimsy. But when Cameron Slayden approached TED-Ed about doing some animation for their educational video series, he soon found himself covering a complex scientific subject in a whole new way.

“We don’t do analogy or character animation, but TED-Ed likes to incorporate an element of whimsy into their videos,” explains Slayden, founder and creative director of the science and medical animation studio, Cosmocyte. “There was definitely a mental adjustment to be made, but once we figured out what the visual storytelling would be, we were able to create something beautiful and engaging.”

TED-Ed provided Slayden with a script and an audio file, and gave him four weeks to create animations for a video called The Twisting Tale of DNA. Using Maxon’s CINEMA4D, Adobe After Effects and Amazon’s Elastic Compute Cloud supercomputer, Slayden did all of the animations himself, starting with a storyboard that was quickly approved. “They were pretty hands off, and there wasn’t much wiggle room with the script, so I was happy that I got the feel of the piece right the first time,” he recalls.

Telling DNA’s story

Slayden was able to find inexpensive models online of the various creatures and characters that appear in the video. To animate them, he used the new rigging tools in C4D’s R13. “With only two days to rig and animate the movements of all the creatures in the piece, being able to quickly figure out how things operated was essential,” he says.

In this shot, a single “ladder rung” of DNA is viewed as a molecule with the deoxyribose backbone highlighted. The DNA molecule is visible in the background.

TED-Ed specifically requested the standard ball-and-stick representation of DNA, which may not be that imaginative, Slayden explains. “But it does help make clear how many atoms are involved.” To create the DNA ladder, he cloned the rungs along a spline with a tracer set to connect elements to form a backbone.

The twist of the ladder was accomplished with a step effector. “If you know how to use the IK-spine tag to make splines move without flipping their point coordinates, you can animate a DNA chain of any length and have it do whatever you want,” Slayden says, pointing out that it’s important to make sure the ladder spins the right way—bottom left to top right.

Interestingly, the cartoon representation of single-stranded DNA seen in the video doesn’t exist in nature, but it was used for clarity. In reality, Slayden notes, DNA that exists as a single strand will twist back on itself “like a tangled phone cord in shapes called hairpin loops.”

Slayden used MoGraph to build this single strand of DNA.

Animating the cell was the trickiest part of the four-week project. Rendered with a blurry transparency, best anti-aliasing and a high polygon count in HD, the transparency effects alone took the equivalent of 256 hours to render 10 seconds of the final footage at 24 frames per second on an 8-core machine with 60 gigs of RAM. (More on the rendering process later.)

Part of what made the creation of the cell difficult is the complexity of the cellular environment, Slayden says. “Cells are in the neighborhood of 80 percent water, and there is a staggering number of proteins inside a cell. If the proteins inside the animation’s cell were opaque, they would be so dense they would have blocked the nucleus from view.

Proteins within a cell were created with the free ePMV molecular viewer plug-in

After doing some research to ensure he was making the right types of proteins inside the cell, as well as their relative proportions, Slayden generated the proteins with the open-source plug-in, embedded Python Molecular Viewer (ePMV), which allows users to run molecular modeling software inside 3D animation applications. “I figured out which proteins I wanted, grabbed their structures and had ePMV make a spline for their backbones,” he explains. “Because all proteins are essentially a squiggly chain of amino acids, all that was really needed to accurately visualize them at the size in the animation was the overall shape.”

Visualizing complex concepts

Explaining complicated concepts visually can be challenging in a number of ways, and this is where analogy comes in handy. To help make clear what a gene is, TED-Ed asked Slayden to come up with a visual treatment to express the idea that DNA is like a library and genes are like books. This sounds easy enough, but it turned out to be extremely difficult.

MoGraph came in handy for creating the mountains of books standing in for genes.

“I couldn't have held an entire mountain of books on screen without making my graphics card cry,” Slayden recalls. So he used an extremely low-poly stack of books, which was actually an elongated cube with carefully extruded parts to make it look like book covers. Knowing he wanted to have the absolute minimum number of polygons possible, Slayden cloned the stack over a landscape object to make a hollow mountain shape. “It worked like a charm, but one regret is that I didn’t have time to separate the books and make sure they didn’t clip into each other.”

To make the books move and pile up properly, Cosmocyte used a classic trick they call the switcheroo in which they swap geometrically or calculationally dense objects with much simpler ones once their higher functionality is no longer needed. “When the cloners were finished doing their work, I swapped them for a version that had been made editable so that part of the cloner could be keyframe animated,” he says.

Books stand in for genes throughout Cosmocyte’s TED-Ed video.

Rendering in the cloud

Over the last couple of years, Cosmocyte has been building their own render farm, but they’ve also been looking into render services. While most turned out to be to be expensive enough to discourage the experimental nature of rendering, Slayden was impressed with Amazon’s Elastic Compute Cloud (EC2), which allows users to rent time on Amazon’s supercomputer. “They have the fifth largest supercomputer in the world currently and they let you rent from them, and you can adjust the processing power and ram to suit your needs,” he explains.

This complex cell interior was rendered at one hour per frame.

After doing the calculations, Cosmocyte figured out that they could get the equivalent of an 8-core machine with 60 GB of ram for around 30 cents and hour. “There’s a lot of computational power in those machines, and I think it’s definitely the future of small studio rendering, possibly even for large studios,” says Slayden. “Our in-house farm is great for the everyday projects, but sometimes time is critical and we don't want to sacrifice production value or resolution.”

"Render farm services can be a bit expensive, but if you don't mind setting up your own account on Amazon and turning on your own virtual machines, you can save a bundle, Slayden says. To help, he’s written a tutorial offering step-by-step instructions artists can use to create their own on-demand C4D render farms. Cosmocyte has also made their pre-configured virtual machine available in the tutorial, further simplifying implementation. See it all on the Cosmocyte web site HERE.

Meleah Maynard is a Minneapolis-based writer and editor. Visit her website at

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