Visualizing DNA in a virtual reality (VR) science game

A simple image search of ‘DNA’ or ‘DNA structure’ makes it clear that there are myriad ways, both inaccurate and accurate, of representing DNA in science illustrations and medical animations. For a Virtual Reality (VR) science game AXS Studio is developing internally, called Guardians of the Genome, we had the challenge of meeting various requirements in our own depiction of the ubiquitous double helix.

Science and learning requirements: The game features DNA mismatch repair, with players (as nanobots) identifying incorrectly paired bases, excising them, collecting correct bases, and ligating them in place.

We want players to gain an intuitive understanding of how DNA is constructed: i.e., two strands, each with a backbone and a sequence of bases; each base paired to a base on the opposite strand (A with T, and C with G). The bases should be easily recognizable so that mismatches can be identified. The DNA should be accurate with respect to the 3D spatial arrangement of components ( and handedness).

Nucleotides showing Watson-Crick base-pairing using a geometric representation
Stylistic requirements: DNA is a complex molecule, and we wanted to provide enough information without overwhelming the player with visual detail, as the expansive and immersive VR environment is already visually rich.In contrast to the players’ mechanical nanobots and robot tools, we also wanted the DNA to feel natural and part of a living organism.
Gameplay requirements: One early gameplay decision was to make the DNA very large, with nucleotides larger than players, to afford the movable and immovable states of the bases. Large objects are harder to move in real life, so large DNA suggests how it can (and can’t) be manipulated during gameplay.

Because the player would be physically interacting with nucleotides (excising, replacing, ligating), we wanted to allow some space to work in and around the bases, without frustrating collisions or clipping through geometry.

There also needed to be clear locations on the nucleotides for certain operations to take place (e.g. ligating the backbone).

Smooth surface nucleotide models with “ghosted” stick representation

Technical requirements: Because there would be hundreds of nucleotides in an interactive VR environment being rendered in real-time in stereo at high frame-rates, the geometry should have a relatively low poly-count.

Geometric model of DNA’s double helix
One proposed representation was a geometric style, demarcating the parts of the sugar-phosphate backbone and bases, including hydrogen-bond donor/receiver components to make the base-pairing mechanism clear. Typically geometric shapes are reserved for simple 2D illustrations of DNA, and are often a student’s first introduction to the building blocks of DNA.
A 3D version of this style may help clarify the components of a nucleotide and the method of base pairing, however the various components in both the backbone and the base resulted in high visual complexity, particularly when viewed as a full double-helix, which might hinder the ability to assess each base (and base pair) as a single unit from a distance.
Work in progress model using a geometric DNA representation

Furthermore, there was some debate about where the representation sat on the stylistic spectrum between “mechanical” and “organic”. The geometric style ultimately placed visual emphasis on structural features that were less important to attend to during the identification stage of gameplay.

Smooth surface model of a DNA strand with “ghosted” stick representation
So we went back to the drawing board and thought about how, as the objectives of the user change throughout the course of the game, so must the direction of our visuals. For identification, we arrived at a smoothed surface representation, where from a distance, we let color be the primary differentiator between bases.

We also wanted to help players appreciate how the backbone connects the bases together, so we added a stick representation of atomic bonds which appears inside the surface representation at key points in the gameplay, during excision and ligation.
Final Representation: We feel these two representations combined fit our various requirements. Do you agree?
In-game footage of nanobot flying into “nuclear arena” and inspecting our final DNA representation

In the end, there’s no single best style of DNA, and even in a single project, sometimes multiple representations are beneficial. As long as the outcome is science-based and driven by learning objectives, there are plenty of styles to explore.

Top 10 Game Jam tips. Developing fun science games in a hurry

AXS Studio science game developers Joyce Hui, Mike Kent, Susan Park and Brendan Polley recently stormed the Royal Ontario Museum (ROM) annual Game Jam for a sleep-deprived weekend of art and coding. Given 2 days to finish a space-themed video game, they rocked it. Rogue Rovers is an addictive, super-fun multiplayer game of discovery (and smashing) on the surface of Mars.
Rogue Rovers start screen
Rogue Rovers gameplay

Tips

Here, the team shares their Top 10 Tips for creating science games under pressure:

  1. Define team member roles before not during the Jam.
  2. Plan ahead so you’re only actually building at the Jam.
  3. Prioritize the must-haves and nice-to-haves.
  4. HYDRATE!
  5. Match game goals to learning goals. If the game is meant to be educational make sure these goals are compatible.
  6. Be prepared to change things on the fly and go with the flow.
  7. Take risks. Play to your strengths, but don”t be afraid to try a new technique or software feature.
  8. Get up and move occasionally. No one wants a DVT at the game jam!
  9. Small is beautiful. Keep your scope small and focused; and make it excellent.
  10. TEST! TEST! TEST! Does it work and, more importantly, is it fun?!

June is brain injury awareness month

Brain Injury Awareness Month highlights the importance of understanding the effects and causes of brain injury.

Together with the Florida Institute for Neurologic Rehabilitation (FINR), AXS Studio created 2 digital resources to help the families of patient understand the causes, effects and treatments of common brain injuries:

Understanding Brain Injury: Acute Hospitalization, an interactive iBook that includes descriptions of brain injury assessment options and common ICU equipment utilized, transition to the acute hospitalization setting, common adjustment issues and methods to cope and the roles and responsibilities of treatment team members.

FINR Brain Atlas enables users to explore brain anatomy and common injuries using an interactive 3D model. Detailed descriptions cover normal structure/function, changes due to injury and their effects. This is a helpful resource for people in need of a quick primer on the causes and effects of brain injury.

While not all brain injuries are preventable, many are. Wear a helmet and be safe!

Talking science visualization in the classroom

Last week I had the pleasure of speaking to a class of wonderful grade 5’s about medical science visualization. They’re learning about the human body and invited me talk about the amazing things we get to do at AXS studio, with a short lesson on the respiratory system thrown in. It was super fun. Kids are so awesome: so curious and funny and keen to learn.

We started with ‘what we’re all made of’, tracing our composition from organs to tissues to cells, molecules and atoms. We talked about how medicine is increasingly happening at the molecular level and that’s the realm where many medical artists now work. I showed animations that move from organs, through cells to molecules and demonstrate how they interact with one another to ‘make us work’.

We then discussed how similar we humans are to many other animals — we have many of the same parts and many species start out much the same at the embryonic stage. To demonstrate, I showed our Chick embryo: 10 years to hatching animation which got a spontaneous round of applause! 

Chicken Embryo Development

A highlight for the kids was the models I brought in: casts of a dolphin and human brain (thanks Professor Lumsden!), human skulls, molecular (CPK) models of common substances, and 3 sets of lung models, courtesy of Joel Bathe from InterMune.

We ended with a quiz — to see who was really paying attention. The correct answers were ‘lymph node’, ‘alveolus’ and ‘capillary’ (see if you can guess the questions). I got some hilarious responses, but ultimately the right ones and 3 clever kids went home with AXS calendars.


Thanks to Ms Netley, Ms. Balane and the grade 5s at Maurice Cody Public School.

Tips for talking science with kids

  • Make it interactive. Don’t simply talk to them, but make it a dialogue with lots of Q & A.
  • Use models. many kids are hands-on learners; they like to touch and feel the subject.
  • Use pictures and video — lot’s of them. A soon as I start to lose kids while talking, I switch to a new image and, bing, they refocus.
  • Relate the subject to everyday experience, so it’s meaningful. When discussing the importance of respiration and gas exchange in the alveoli of the lungs, I relate it to the discomfort of holding your breath, or being winded after a run.
  • If you’re talking about anatomy, ask if anyone gets queasy, then give them a heads-up before showing pictures of anatomy. I take for granted that the inside of a body is fascinating. Not so for everyone.
  • Make it fun! Science is about curiosity and discovery.