Bioengineers have created games that allow people to interact with cells, as well as a robotic lab capable of carrying out remote-controlled experiments.
May 1, 2015 - By Tom Abate
In the 1950s, computers were giant machines that filled buildings and served a variety of arcane functions. Today they fit into our pockets or backpacks, and help us work, communicate and play.
“Biotechnology today is very similar to where computing technology used to be,” said Ingmar Riedel-Kruse, PhD, an assistant professor of bioengineering at Stanford.
“Biological labs are housed in big buildings and the technology is hard to access,” he added. “But we are changing that. We are enabling people to interact with biological materials and perform experiments the way they interact with computers today. We call this interactive biotechnology.”
Riedel-Kruse and his team have created three related projects that begin to define this new field of interactive biotechnology.
Two of these projects were unveiled in April at a conference on human-computer interaction in Seoul, South Korea, while the third was recently described in a paper published in PLOS Biology.
In one project, the team created an arcade-style kiosk that allowed visitors to The Tech Museum in San Jose to interact with living cells like fish in an aquarium.
In a second and similar effort, Riedel-Kruse developed a class to teach students how to design bioengineering devices. He taught them by creating so-called biotic games using cells. This class also touched on the ethical principles of interacting with microorganisms for educational or entertainment purposes.
In his third and most far-reaching project, Riedel-Kruse and his team created a robotic biology lab capable of carrying out remote-controlled experiments.
“We call these robots Biotic Processing Units, or BPUs,” said Zahid Hossain, the Stanford doctoral student who worked with Riedel-Kruse on this third project.
Creation of a remote lab
“A BPU is an instrument that can hold and repeatedly stimulate biological materials, such as cells, and measure the biological responses,” Hossain said. “It is the key enabler of interactive biotechnology.”
The remote lab was presented at the conference in South Korea. The intent was to enable students and scientists to send instructions to a robotic lab and get back experimental results — the way people interact with cloud-based data sites today.
Hossain constructed this prototype BPU by using LEGO Mindstorms, a kit for making robots, 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.
We are enabling people to interact with biological materials and perform experiments the way they interact with computers today.
The researchers incorporated this 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 to have the robot drop the oatmeal in different patterns. The scanner recorded how the Physarum followed each trail of oatmeal dots by “sniffing out” chemical cues in the petri dishes. Chemotaxis is the scientific term used to describe how microorganisms respond to chemical stimuli in their environments.
For this project, Riedel-Kruse’s team built three BPUs, each holding six petri dishes. All three units were housed in a server rack typically found in a server farm.
“Our prototype BPUs supported 18 users and allowed us to assess the scalability of cloud labs,” Hossain said. “I want to see advanced BPUs supporting many different types of experiments and thousands of different users.”
This cloud lab project won an honorable mention as a best paper at the computer conference.
The museum kiosk project, led by Seung Ah Lee, a postdoctoral fellow in the Riedel-Kruse lab, was also presented at the conference. Lee explained that the kiosk allowed museum visitors to interact with Euglena, a freely swimming microorganism that typically lives in ponds.
Like plants, Euglena can convert sunlight into sugar through photosynthesis. The interactive display capitalized on the organism’s responses to light. In the 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 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 a class he taught on biotic game design. Nate Cira, the bioengineering doctoral student who worked with that class, said the goal was for students to create a biotech version of popular robotic and video game challenges. He said Riedel-Kruse lab members plan to create low-cost kits that would allow hobbyists to construct their own interactive micro-aquariums.
To assess the educational value of these projects, Riedel-Kruse worked with Paulo Blikstein, PhD, an assistant professor of education at Stanford. The biotic game design class was jointly taught with bioengineering professor Stephen Quake, PhD.
Riedel-Kruse said he thinks that interactive biotechnology is a necessary and inevitable consequence of the maturation of the life sciences that will profoundly affect society, just as computing technology has.
“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. “Ultimately, I hope these interactive media make everyone more understanding and comfortable about what microbiology and biotechnology really is.”
About Stanford Medicine
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