Hunting coronavirus protein with the biggest supercomputer on Earth | Upscaled Mini

okay folks welcome to this mini episode of upscaled now this is gonna be a little different from our normal show we produce this a little faster the actual piece is gonna be a little shorter and not go quite as in-depth and also as you may have noticed um this is not our typical set and it’s because I’m filming this from my apartment as we’re all doing our best to stay inside and respect quarantine for our case here I’m actually first and foremost a video producer with Engadget so I already have all the fancy toys we need to make a video here so hopefully this will work alright if you folks are good we’ll even have maybe a guest appearance from my cat and let’s get started steady at home the research project where you could donate your computer’s processing power to help search for aliens announced last month they were going on hiatus after more than 20 years of research now full disclosure I used to work with those folks but before I ever met them I’d run their software for years and I loved the idea that when I wasn’t using my computer it was helping process data from space if like me you are looking for a new project to donate some computing power to or if you’re just stuck inside during these tough times and want to feel like you’re contributing there are other distributed computing projects out there that are trying to understand the coronavirus Rosetta and folding at home are both working to understand the viral proteins that make up the corona virus and so many people are now donating CPU and GPU power that folding at home has become the largest supercomputer on the planet distributed computing works like this researchers who need a lot of processing power to solve a problem can load their data onto a server and then users folks like you and me can download and install a special bit of software that will retrieve a chunk of that data and process and analyze it on your computer when you’re not using it so distributed computing takes a big problem that requires a ton of processing or a huge amount of data and it splits it into a lot of smaller problems and shares it out with a network to work on once your computer has done its part it sends back the result gets a new chunk of data and starts over again SETI at home was one of the first of these types of distributed computing research projects and it launched all the way back in 1999 but folding at home launched only a year later which makes it really one of the pioneers of this type of research and it uses volunteers computers to try to understand how proteins are assembled proteins are the machinery of the cell they are what gets built from DNA and RNA those to form the genome and they’re like the blueprints of a settle but the proteins are what those blueprints can actually build and understanding them tells us a whole lot about how a cell or a virus can function it’s like the difference between looking at a photograph of a helicopter and actually understanding how one works proteins are built from amino acids small molecules that you can link together to form complex structures like hemoglobin or the shell of a virus as you link hundreds or even thousands of amino acids together they form structures like spirals and sheets and these linked together and fold and combine to form even more complex structures understanding the shape of these structures is critical to understanding how the protein works these tiny tiny scales the proteins are actually mechanically grabbing on to other molecules either latching onto them or changing their shape or prying them apart for example the weird knobs on the outside of a corona virus are proteins that actually physically latch on to other receptor proteins in the cells in your lungs if either one of these proteins were a different shape the virus wouldn’t be able to attach and wouldn’t be able to infect the cells antibodies and many medicines actually work by adhering to proteins like this on a virus or bacteria either blocking them up or tearing them apart or marking them for your white blood cells to come and destroy all of this is to say that proteins are incredibly complicated and it takes a lot of processing power to understand how they’re built and how they work since folding at home announced it was working on coronavirus proteins they have seen a surge of new signups and a huge boost in computing power the network has surged over 470 pedo flops as thousands of new computers have signed up to join the network now a flop is a floating-point operation per second it’s essentially the number of math problems with decimal in them that the network can do in a certain amount of time and peda is the prefix that means one quadrillion or a million billion for context summit the most powerful supercomputer in the world at the Oak Ridge National Labs in Tennessee uses about 200,000 CPU cores and 27,000 GPUs

to produce a total sustained output of about a hundred and fifty pedal flops and summit is already 50% faster than its next two competitors Sierra at Lawrence Livermore labs not too far from where we are here and sunway tiny light at China’s national supercomputing Center in fact the combined output of the top seven supercomputers in the world is about 462 peda flops still a bit shy of what the folding at home network is currently processing it’s hard to know exactly how many users the network had but may have had 400,000 new signups so how do you get involved well just head to their website folding at home dot org and click start folding download the software install it and then you are good to go one note the default settings for folding at home can be a little greedy it may use a bit more computing power than you want I would recommend setting it to medium and to only work when idle which will ensure it’s not chugging away while you’re use your computer for something else you can even set a username or join a team and there is a bit of a competition aspect here as teams vie for the top spot in the leaderboard with the most data processed each month one downside of all this increased interest is that the folding at home network has actually been running out of work to distribute and some folks computers have been sitting idle as a result so if you’re looking for another project to support that could really use your processing cycles I’d recommend Rosetta out of the University of Washington this is another protein simulation and research project that runs through the boink interface the software that was actually set up by city at home to get started just download boink add Rosetta as a project make an account and you’re good to go Rosetta is considered extremely accurate at modeling proteins but it’s more concerned with how the final structure works and less about how it’s actually assembled and put together it’s kind of complementary to folding at home and they’ve actually shared research between the two in the past Rosetta can even run on Android – there is a point client in the Play Store so why not run both all of these may increase your electric bill a little bit your computer is working on some hard problems after all but it can also help you feel like you’re making the world a tiny bit better even if you’re stuck inside we heard em catch it are gonna keep working to try to bring you all the best tech news considering the circumstances and we will have more reviews and content for you soon probably also filmed in someone else’s apartment so be sure to LIKE and subscribe and we’ll catch you next time here’s the cat I think at first she didn’t mind me being home but she has slowly grown to resent me