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Molecular Dynamics for the Masses

Interactive Scientific uses Oracle Cloud to bring 3D science to everyone, on everyday devices.

By Mike Faden

September/October 2018

Interactive Scientific Ltd. is on a mission to change the way people experience, research, and learn about science. The company’s simulation platform is designed to bring science to life for everyone from K–12 students to researchers. Students can understand molecules by interacting with 3D models instead of relying on abstract chemical formulas. But it has other uses as well—for example, making it possible for pharmaceutical researchers to build new drug molecules, transform them into different shapes to explore how they work, and investigate ways to design and deliver them.

Because such simulations are highly compute- intensive, they’ve traditionally required substantial onsite computing power delivered by powerful servers or even supercomputers. But by using Oracle Cloud to do the heavy lifting, Interactive Scientific is making its technology available almost anywhere—on everyday devices including smartphones, tablets, and PCs as well as on virtual reality (VR) headsets.

Becky Sage, CEO at Interactive ScientificInteractive Scientific was founded in 2013 with the goal of “taking all the complexity of science and making it simple and accessible using digital tools,” says Becky Sage, CEO at Interactive Scientific.

“We’re on a mission to bring to life the invisible scientific world that exists all around us,” says Becky Sage, CEO at Interactive Scientific. “Oracle opens up new opportunities for us. With compute power and accessibility via the cloud, we are able to scale up this really complex science technology and help solve problems in education and beyond.”

Bringing Science to Life

Based in Bristol, England, Interactive Scientific was founded in 2013 with the goal of “taking all the complexity of science and making it simple and accessible using digital tools,” Sage says.

The company initially focused on education, aiming to make science education fun for kids who are bored by the way it’s currently taught. “We felt that science education wasn’t suited to the world that we live in right now—a lot of people are getting disengaged and switched off,” Sage says. “But science can be extremely exciting, and we can use digital tools to bring science to life.”

Interactive Scientific’s Nano Simbox software turns complex molecular data into interactive models, using a simulation technique known as molecular dynamics. The goal is to make science fun and playful—to make the invisible world of molecules visible and engaging for students.

Designed to support school curricula, the software lets students explore and manipulate molecules while being prompted to discover additional facts for themselves. Although the first products using the platform originally targeted K–12 students, Interactive Scientific is now collaborating with universities to bring it to higher education as well.

With compute power and accessibility via the cloud, we are able to scale up this really complex science technology and help solve problems in education and beyond.”–Becky Sage, CEO, Interactive Scientific

The company is also starting to expand into pharmaceutical research. In the past, researchers painstakingly constructed physical models of molecules to visualize how they work. Today, simulations let researchers assemble and explore new molecules many times as fast. For example, using Nano Simbox VR technology, researchers can play a kind of 3D molecular Tetris—arranging different molecules together, ultimately to discover new drugs, Sage says.

“For researchers, the platform is used more as a toolkit,” she explains. “They want to upload their own simulations and use the platform to manipulate and understand their molecular systems in the way that’s most useful to them.”

The platform could also accelerate research, as demonstrated by a recent VR project involving Interactive Scientific, Oracle, and scientists at Bristol University. In the project, users performed tasks applicable to molecular research—such as retwisting helical molecules and even tying them in knots—significantly faster and more successfully with VR headsets and controls than with a traditional touchscreen or mouse. “As simulations become faster, we can now do this in real time, which will change how drugs are designed and how chemical structures are taught,” says Adrian Mulholland, a Bristol University chemistry professor.

Powering Real-Time Simulations

Making real-time molecular dynamics available on consumer devices such as smartphones and VR headsets is key to Interactive Scientific’s plans to bring the technology to a much bigger audience. “We want to give people access to the same rigorous science that universities and pharma companies run on their supercomputers—and to consume these simulations on a smartphone, regular laptop, or VR headset,” says Phill Tew, Interactive Scientific CTO.

Phill Tew, CTO at Interactive Scientific“We want to give people access to the same rigorous science that universities and pharma companies run on their supercomputers—and to consume these simulations on a smartphone, regular laptop, or VR headset,” says Phill Tew, CTO at Interactive Scientific.

However, this approach also requires a huge amount of back-end processing power to execute the simulations, which are then displayed over the network to users’ devices. Interactive Scientific wanted to make simulations available to a wide range of users, including institutions that didn’t have the wherewithal to invest in supercomputers. So two years ago, the company started to look into how it could use the cloud to provide that back-end processing power. Another big potential advantage of the cloud was that it could support collaborative research, allowing multiple researchers in different locations to work on the same model at the same time.

One big obstacle: at the time, the company had no experience with cloud computing. To help make the leap to the cloud, Interactive Scientific applied to join the Oracle Startup Cloud Accelerator Program, which was just getting off the ground in the UK. Run by Oracle’s research and development staff, the worldwide program aims to help startups by providing technical and business mentoring; coworking space; state-of-the-art technology; free Oracle Cloud credits; and access to Oracle customers, partners, and investors.

Interactive Scientific was one of just 5 companies selected from more than 100 that applied to join the first UK cohort of startups. Tew says that Oracle’s support and expertise proved invaluable. “I had a crash course in cloud computing, and most of the lessons I’ve learned have been through talking to Oracle engineers,” he says. “They really primed us for the problems that we couldn’t foresee at the outset. How do you make something scalable in the cloud? How do you slice up a problem in the correct way, so that when you scale up it doesn’t explode on you?”

The challenge was particularly daunting because the company was trying to achieve something that had never been done. “We had to prove it was even possible to run the simulations in the cloud and stream them to your phone or another device,” Tew says. “It really wasn’t a solved problem at all.”

Oracle’s support helped the company meet the challenges, one step at a time. “We didn’t want to go from zero to autoscaling infrastructure immediately. There are a bunch of steps in between—from the initial prototype implementation to creating a scalable architecture,” says Tew.

Interactive Scientific found that running the simulations on Oracle Cloud Infrastructure Compute bare metal instances provided the performance the company needs to support multiple users in real time. “We get the full power of the compute resources that we need: direct access to the bare metal without the abstraction of virtual machines,” Tew says. “The algorithms used in real-time molecular dynamics are really fast, so we don’t need a GPU. We can just run the simulations on a regular server with a bunch of cores. And we can run them in real time.”

To ensure that the simulation software was both scalable and portable, Interactive Scientific divided it into container-based microservices and migrated it to Linux, Tew adds. Besides ensuring the required performance in the cloud, this approach also meant that universities and pharmaceutical companies that wish to use their existing on-premises infrastructure to run the simulations can continue to do so. “We had to make a product infrastructure that would allow deployment both on premises and in the cloud, to allow seamless access for these simulations,” he says. “We’ve containerized every part of our stack.”

We had to make a product infrastructure that would allow deployment both on premises and in the cloud, to allow seamless access for these simulations. We’ve containerized every part of our stack.”–Phill Tew, CTO, Interactive Scientific

To support real-time simulations, Interactive Scientific aims to refresh the model displayed on users’ devices at 30 frames per second, Tew says. That refresh rate ensures that users don’t experience lags or jerky movements as they manipulate molecular models. To achieve that goal, it’s critical to consistently move data quickly between the cloud and the client device. The broad geographic presence of Oracle Cloud has helped to make that possible; by running the back-end software in a local Oracle Cloud data center, the company is currently able to deliver the required 30-frames-per-second refresh rate when simulating molecules as large as 8,000 atoms. In addition, Interactive Scientific has developed data-compression and other techniques for reducing bandwidth requirements, making it possible to display models even on a smartphone using a 4G connection, Tew says.

From Zero to Cloud in Six Months

With help from Oracle Cloud, Interactive Scientific’s molecular simulations are making science more accessible—and fun—while helping to transform the way researchers discover new medicines. “The best practices shared by the Oracle team have helped us create a scalable solution,” Tew says. “Thanks to our collaboration with Oracle, we were able to go from zero cloud experience to full implementation in six months.”

Next Steps

LEARN about Oracle Cloud Infrastructure Compute.

TRY Oracle Cloud Platform.

WATCH Oracle Cloud Powers Interactive Scientific’s Simulation Engine.

READ about the Oracle Startup Cloud Accelerator program.

Photography by John Blythe