At a time when the ramifications of the coronavirus pandemic are felt in every country, computer chip, and graphics creator Nvidia has urged gamers to share their processing speed to enable researchers working on COVID-19 get a cure faster.
Technology to fight COVID-19
Nvidia is assisting biotechnology by making its Parabricks tool available online to anyone working on COVID-19 for free.
Parabricks Pipeline is a Graphics Processing Unit (GPU) – accelerated germline, or GPU-accelerated genome analysis toolkit. This Genome Assisted Tool Kit (GATK) reduces the time required to analyze a whole human genome from about 30 hours (BWA-GATK4) to 45 minutes on servers with 8 GPUs, while achieving the equivalent result as standard tools. A process that took days can now possibly be completed in a few hours.
The pipeline was built from the ground up for optimizing speed, accuracy, and cost by using the computational power of GPUs.
Nvidia claims that the Parabricks’ pipelines have been engineered to obtain the maximum performance from computing hardware. The toolkits have been tested on Dell, HPE, IBM, and NVIDIA servers at Amazon Web Services, Google Cloud, and Microsoft Azure.
What does a genome accessing toolkit do?
A Genome Analysis Toolkit (GATK) is a structured programming framework designed to ease the development of efficient and robust analysis tools for next-generation DNA sequencers using the functional programming philosophy of MapReduce.
According to the National Center for Biotechnology Information (NCBI) in Maryland, US, the GATK is the industry standard for identifying SNPs and indels in germline DNA and RNA-Seq data. The GATK has been used to implement a range of analysis methods for projects like the Cancer Genome Atlas and the 1000 Genomes Project. The GATK designed originally for human genome and exome analysis can be programmed to handle other organisms. In this case, this technology will help researchers find out how the coronavirus, which originally comes from bats, is rapidly multiplying when in contact with humans with such disastrous consequences.
How NVIDIA is helping
Nvidia has decided to give access to its GATK toolkit Parabricks available to scientists and researchers fighting against COVID-19 for free. They are also providing links to different cloud-based Graphics Processing Unit (GPU) service providers to lower barrier to entry for anyone across the globe. Parabricks, which was acquired by Nvidia late last year, has developed technology that makes it possible to sequence an entire human genome in less than an hour—and that’s using a single server, not an entire server farm.
How will hardware needs be satisfied
At a time when the world is fighting a calamity together, everyone is reaching out to help one another. Sharing has become the mantra to fight this pandemic. Shared computing is helping the scientific community to stay together and search for a cure. Given the alarming rate at which this pandemic is affecting countries across the globe, Nvidia has reached out to the gaming community to share resources with researchers. There are currently eight projects that are using shared computing power to run the complex calculations needed in the search for a COVID-19 vaccine.
Why gaming PCs are ideal for the fight against coronavirus
Gaming PCs come with powerful graphics cards, and these are often ideal to help out with processing huge amounts of data in projects like this. Gamers who join the fight can use the software when their PC is not being used (it needs to be on, though), and they can pause the software when they play games so there’s no impact on performance.
Technology to share
Shared computing software, [email protected] (FAH or [email protected]), allows computer users to download an app on their PCs or laptops that runs in the background. The app lets other users use the processing power of the idle computers.
Nvidia called on the gaming community to share their GPUs by sharing unused power through [email protected] technology.
The initiative drew praise from the online community. Praising Nvidia, processor giant Intel too lent support to the idea of technology sharing. Hardware manufacturer MSI lauded the initiative and called on other hardware manufacturers to come together to defeat the pandemic.
The Daily Mail reported that various researchers have been appreciative of this initiative. Vincent Voelz, a Computational Biophysical Chemistry Group at Temple University, said the support from the PC community had been overwhelming.
“We’re close to releasing the first round of protease inhibitor screening simulations on the CPU client,” he said. Meaning users with better CPUs than GPUs would be able to participate in the experiments, the Daily Mail said. Researchers using the [email protected] servers are trying to understand how viral proteins work and how therapies can be designed to stop them. Those who are sharing their GPU power are helping scientists to run simulations and solve complex calculations.