Skip to main content
Premium Trial:

Request an Annual Quote

Washington University Sequencing Center Network Upgrade Eliminates Bottlenecks


ST. LOUIS, Mo.--With a recent upgrade of its enterprise network, North America's fastest sequencing center just got faster. Kelly Carpenter, systems manager at the Washington University Medical Center Genome Sequencing Center here, said the high-performance multilayer switching capabilities installed in the center's four Cisco Cata lyst 5500's have dramatically increased the facility's efficiency. Carpenter spoke with BioInform about the network upgrade and his decision to trade in another manufacturer's system for Cisco hardware.

Demands on the network here are massive: A staff of 225 people transmits 4 trillion bytes of data per day, outputting more sequence data--primarily of the human and 100 million base C. Elegans genomes--than any other sequencing facility on the continent. Two individual researchers at the Washington University facility have produced more sequence than entire operations elsewhere. And Carpenter said the center is in the process of expanding its sequencing power by 50 percent. Only its sister center, the UK's Sanger Centre, has a comparable capacity, he claimed.

Until now, Carpenter said the center's computer network could not handle the amount of data being generated. "The interswitch link between hubs was 10 megabits per second, and each computer was transmitting data at 10 megabits. So 16 or 20 computers would fight trying to transfer data. And since we're on a production schedule, it's all happening at the same time. The connection between the two boxes was completely saturated," he said.

Carpenter explained that the Cisco system has reduced bottlenecks by giving each computer access to the entire 10 or 100 mega bits without interference. "Instead of having hubs, now we have a 100 percent switched network. The backplane of the Cisco Catalyst has the capacity of 3.6 gigabits."

Where once 20 or 30 computers would overload the hubs, Carpenter said now he could "put 360 people on one box and just be at capacity." Plus, Cisco's Fast Ether channel enables four 100Mb lines to be grouped for a 400Mb link.

"In our lab, we have a number of different systems, including workstations, Macintoshes, PC's, etc. By installing route switch modules in the Catalysts, we were able to take advantage of all the multiprotocol benefits of the Cisco IOS software and get the high performance throughput and high densities of ethernet switching," he said.

Carpenter rejected the idea of installing asynchronous transfer mode (ATM) technology at the center. "The Sanger Centre is 100 percent ATM, so a lot of people were expecting me to go with that." A plethora of "totally cool" features, such as video conferencing and good handling of real time data, made ATM a tempting option, he said. In the end, a cost-benefit analysis and Cisco's quality-of-service capability, which offers some of the benefits of ATM, led him to stay with ethernet.

Carpenter said he had an easier time deciding to discontinue the center's relationship with its previous network provider, Bay Net works. "Vapor features are one of the things you're buying when you invest in technology," he acknowledged.

With a previous purchase, Carpenter said the center had been promised v-lan trunking capabilities in the future. But the provider decided later against developing v-lan for the center's model. "It really irritated us. For someone who doesn't mess with computers it doesn't sound like a big deal, but to a person who has to deal with networking things like Windows NT or with moving people around, v-lan trunking makes a difference," Carpenter contended. "Instead of having to configure anything, I type a telnet command and I connect to the switch and it works automatically."

Now Carpenter has only one problem: the accelerated data transfer that the new network allows has "opened up a fire hydrant" to the server. "Before, the performance of the server wasn't getting degraded because the network held it back with so much traffic. Now the server is getting hammered. What it boils down to is that you're moving bottlenecks around."

--Adrienne Burke

Filed under

The Scan

Support for Moderna Booster

An FDA advisory committee supports authorizing a booster for Moderna's SARS-CoV-2 vaccine, CNN reports.

Testing at UK Lab Suspended

SARS-CoV-2 testing at a UK lab has been suspended following a number of false negative results.

J&J CSO to Step Down

The Wall Street Journal reports that Paul Stoffels will be stepping down as chief scientific officer at Johnson & Johnson by the end of the year.

Science Papers Present Proteo-Genomic Map of Human Health, Brain Tumor Target, Tool to Infer CNVs

In Science this week: gene-protein-disease map, epigenomic and transcriptomic approach highlights potential therapeutic target for gliomas, and more