Interactive biotechnology learning and design using games and remote-control labs

April 22, 2015

Stanford Engineering | Ingmar Riedel-Kruse, an assistant professor of bioengineering at Stanford, and his team have created three related projects that begin to define the new field of interactive biotechnology.

Stanford bioengineers have developed a new approach to teaching and experimenting, using “interactive biotechnology,” with  “Biotic processing units” (BPUs) that allow for remotely interacting with biological materials and performing experiments.

“Biotechnology today is very similar to where computing technology used to be,” said Ingmar Riedel-Kruse, an assistant professor of bioengineering at Stanford. “Biological labs are housed in big buildings and the technology is hard to access,”

Riedel-Kruse and his team want to change all that. They’ve created three projects that begin to define the new field of interactive biotechnology.

Biotic game playing and design

The team created an arcade-style kiosk that allowed visitors to The Tech Museum in San Jose to interact with Euglena, a freely swimming microorganism that typically lives in ponds. Like plants, Euglena can convert sunlight into sugar through photosynthesis.

A: Biotic games enable human players to interact with cells. B: Conceptual overview of a biotic game setup. C: Students built and played biotic games. Image credits: A C64 joystick by Speed-link. (credit: Nate J. Cira et al./PLOS Biology)

The interactive display capitalized on the organism’s responses to light. In their interactive kiosk, the Euglena inhabited a micro-aquarium that was essentially a specially configured slide mounted between a video microscope and an image projector. This slide, or micro-aquarium, was another instance of what the researchers call a BPU.

This self-contained micro-aquarium was connected to a touch-screen computer display. Museum visitors could use blue, green or red light to draw patterns on the screen and observe how the Euglena reacted. The microorganisms avoided blue light, so drawing a circle around one of the microbes would trap it, which became the name for one of the scientific mini-games the kiosk offered.

Riedel-Kruse also used the light-sensitive Euglena as the model organisms in the class he taught on biotic game design. Nate Cira, the bioengineering doctoral student who led that effort, said the goal was to create a biotech version of popular robotic and video game challenges. He said the team plans to create low-cost kits that would allow hobbyists to construct their own interactive micro-aquariums.

A cloud biology lab

The team also constructed a probiotic biology cloud lab using BPUs capable of carrying out remote-controlled experiments to stimulate biological materials, such as cells, and measure the biological responses. Students and scientists can send instructions to a robotic lab and get back experimental results.

The team constructed this BPU by using LEGO Mindstorms to create a liquid-handling robot. This robot traveled over a flatbed photo scanner. The scanner held petri dishes containing the slime mold Physarum, which eats oatmeal.

The researchers incorporated the BPU as a lab component in a graduate level theory class. Using remote-control interfaces on their smartphones, students ordered the robot to drop oatmeal onto specific petri dishes. The software allowed them to choose different droplet patterns.

The scanner recorded how the Physarum followed each trail of oatmeal dots by “sniffing out” chemotaxis cues in the petri dishes. (Chemotaxis refers to how microorganisms respond to chemical stimuli in their environments.)

The team built three BPUs, each holding six petri dishes. All three units were housed in a server rack typically found in a cloud computer site. “Our prototype BPUs supported 18 users and allowed us to assess the scalability of cloud labs,” said said Zahid Hossain, the Stanford dotoral student who worked with Riedel-Kruse on this third project.  “I want to see advanced BPUs supporting many different types of experiments and thousands of different users.”

“The obvious next application is online education at scale that includes true biology experiments, also opening new opportunities for learning-research. And cloud labs can change how we work as scientists.” Riedel-Kruse said.

Abstract of A Biotic Game Design Project for Integrated Life Science and Engineering Education

Engaging, hands-on design experiences are key for formal and informal Science, Technology, Engineering, and Mathematics (STEM) education. Robotic and video game design challenges have been particularly effective in stimulating student interest, but equivalent experiences for the life sciences are not as developed. Here we present the concept of a “biotic game design project” to motivate student learning at the interface of life sciences and device engineering (as part of a cornerstone bioengineering devices course). We provide all course material and also present efforts in adapting the project’s complexity to serve other time frames, age groups, learning focuses, and budgets. Students self-reported that they found the biotic game project fun and motivating, resulting in increased effort. Hence this type of design project could generate excitement and educational impact similar to robotics and video games.