Caleb Goodin has been involved in Folding@home for more than a decade. He remembers having recently arrived at the Army barracks at his first duty station when the platoon sergeant came by for a routine inspection. The sergeant saw his huge gaming PC with all the fans spinning hard and warmth radiating from it and said "Goodin, what the hell is that doing?"
Today, Goodin is a systems engineer with ExtraHop and still folding—with the ExtraHop team. That team got started back in 2019, at the suggestion of software engineer Bryce Handerson. With some organizing by fellow engineer David Monk, the team got rolling.
Now, thanks to all of its members, they've made it into the top 800 in the rankings for F@h, a distributed computing project aiming to better understand diseases like COVID-19.
What Is Protein Folding?
In case you missed a few biology classes, proteins are long chains of amino acids that 'fold' themselves into a particular shape. That shape allows them to serve a specific biological purpose. Hemoglobin, for example, is a protein in red blood cells that can bind to both oxygen and carbon dioxide. That allows it to pick up oxygen in the lungs, carry it to tissues, and bring carbon dioxide back to the lungs to be exhaled. It's the unique structure, the way the long string of amino acids are folded, that allows it to bind to these molecules.
Viruses, like human cells, use proteins. Understanding these proteins could provide a means of stopping them—like preventing their entry into a human cell or destroying their ability to replicate.
Mapping the structure of proteins and understanding their function is complicated. As the Atlantic put it, it's like trying to recreate an origami shape just by looking at the fold lines on a piece of paper. Computers have made it possible to simulate protein folding, but solving these problems require enormous computational resources and a lot of time.
What Is Distributed Computing?
Distributed computing is the practice of yoking multiple computers together over a local or wide area network. They function together as a unified system with greater computing power. As Monk (one of the organizers of the ExtraHop team) explains, one of the key aspects is parallel computing. Mapping proteins serially (one at a time) would take an insane amount of time, but since the calculations don't depend on each other, they can be done in parallel, decreasing the time required as more computers are added to the system.
There are a lot of computers sitting idle at home, and distributed computing can put them to work on important problems. Individuals download a program from F@h which runs on their computer whenever they're not using it.
F@h has put their resources toward a variety of problems, but their focus now is on COVID-19. A better understanding of its structure and function can give insights into how to stop it, including recent breakthroughs that could help researchers develop antivirals.
The potential for impact is huge, given the massive compute power of F@H. Amongst the many challenges of 2020, it means something to be able to contribute. At a time when so much feels outside of our control, Monk is glad to be part of the ExtraHop team. It gives him not just a way to contribute to addressing COVID, but also a way to stay connected in a time of unprecedented isolation.
The ExtraHop team is excited to do their part, and Goodin continues to run F@h on his personal computer, which he's upgraded since his Army days.
So what did Goodin say when his platoon sergeant demanded to know what he was doing? Goodin says he laughed and explained that he was doing science.
Want to do science too? Join the ExtraHop team (just enter team #235547 during installation) or start your own at Folding@home.