Cisco aids McMaster Bioinformatics Program That Helps in Tracking COVID-19

Cisco aids McMaster Bioinformatics Program That Helps in Tracking COVID-19

As part of the fight to develop a vaccine for COVID-19, finding out how the virus spreads is a challenge. This requires too much data and too much computing power, as every infected patient adds millions of data points to an already huge database. Yet each bit provides additional information that can point researchers to the locations of transmission events - if it can be analyzed in a timely manner.

McMaster University of Hamilton has partnered with the Ontario Vector Institute in Toronto and Sunnybrook Health Sciences to make this tracking easier. The COVID-19 genotyping tool (CGT) uses big data analytics to help researchers worldwide change the genetic structure of a virus as it moves from one person to another, helping them determine Helps where it came from, and to project where it is. Is it becoming more contagious?

The Cisco High Performance Unified Computing System (UCS) donation of $ 375,000 by the Cisco Foundation reinforces this effort.

“A key element of this research is the COVID-19 Genotyping Tool (CGT), an artificial intelligence / machine learning analytics platform that allows researchers, hospitals, and public agencies around the world to upload their COVID-19 data and provide available sources. Allows to be made relevant with. In the public domain, "explained Rob Barton, the eminent systems engineer at Cisco Canada, in a blog post." By using AI mobility reduction techniques such as UMAP, CGT is able to identify small differences in the virus genome from which it is classified. And can be compared to other known strains. "

But these analyzes cannot find any time as Professor Andrew McArthur, an Associate Professor of Biochemistry and Biomedical Science at McMoster and past Cisco Chair in Bioinformatics, said in an interview. Dr. Andrew McArthur, Associate Professor of Biochemistry and Biomedical Science, McMaster University "The biggest challenge in genomic data is that capacity is growing rapidly," he said. "And during an epidemic when you suddenly want to sequence every positive patient, you're constantly red."

Spiraling with cloud compute costs, the effort was not sustainable on many fronts. This expense also led to concerns about privacy and security. "Because some of the data that comes to us is associated with patient information, we need to build something concrete in the house so that we can protect privacy," he said. Those factors made Cisco's donations highly valuable.

“It was a very important charity, short and long term. MacArthur said it also solves long-term problems. "We are hoping after COVID or during COVID that we are seeing a lot of drug-resistant bacterial infections, using a lot of antibiotics to keep people alive, and this complex biology, how a virus and A human and a bacterium interacts with the community to make people sick, generating huge amounts of data as we begin to prepare and move towards that world with others. And now we really have to do it. This is important for now, medium term and long term.

"The funding of the Cisco device was really for that big picture - there was a difference between people looking at the global scale and people doing sequencing work in your neighborhood," he went on. "We wanted to take data on a global scale, prepare it in advance, and do some really smart machine learning, so that people could take their local data and get it there quickly. And that's really about that machine. Was a big part of it. "