Genome Sciences Information Tech Team
Lead nomination by: Nancy Cameron, Director, Finance and Administration, Genome Sciences
Members of the Genome Sciences Information Tech Team are James Cobb, Dale Hubler, Brian McNally, Roy Obenchain, Alexander Safir, Skylar Thompson, Charles Winston, and Elizabeth Young.
In 2001, the department was formed by the merger of two departments. Since then our tenured positions grew from 12 to 27 currently, and research awards grew from $4.8M to $60M in FY2011 with $36M in equipment. The IT group was established early on to support the faculty and with the move to the Foege Building in 2006, we centralized computing infrastructure. The IT team has supported this phenomenal growth and the move without a hiccup and often invisibly to the labs and staff. Our Foege facility is the fastest growing and now the largest research computing facility on campus.
The IT group supports two distinct departmental needs - research support and technical support. The research computing team, Roy, Skylar, Brian, Dale, and Liz, have dealt creatively and effectively with the rapid growth of systems. For example, the department’s data storage needs have increased twentyfold in just the last three years, while the data processing rate for sequencing has increased thirtyfold in the last 2 years. The research team has managed our exponential growth with technological solutions to the constant pressures on servers, network configurations, firewalls and bandwidth caused by the need to move massive data sets both within the building and across campus. These pressures often require novel solutions. For instance, the department adopted the fastest publicly available networking technology, Quad Data Rate Infiniband at 40 gigabit per second, for a subset of systems that are capable of supporting it. The Infiniband technology had to be incorporated into the existing network.
The research team has also shined in the face of adversity caused by repeated failures in the building’s cooling system—the building’s HVAC is a lemon. These failures occur at all hours and threaten to destroy valuable equipment and invaluable data, but the team responds quickly with minimal loss of data and no loss of equipment. The research computing team (Roy, Skylar, Brian, Dale, and Liz) have been trained by Siemens and UW Facilities on the automated controls for Foege building cooling system. When outages occur, they have to decide within a few minutes whether or not to shutdown hundreds of servers, causing a massive disruption to research. They can now log in remotely to building control system panels and look at exactly what is going on with the mechanical systems to judge the severity of the problem and weigh the risk of overheating $12M in equipment versus turning the power off on hundreds of active systems. They also know who to call based on what is failing (e.g. chillers are maintained by the refer shop, pump problems are routed to the controls shop, etc.). They are on-call; emergencies seem to happen on weekend early mornings. Even though it is not directly his responsibility, Jim has learned how to pause the sequencers so that the hundreds of thousands dollars of reagents, and the experiments underway will not be ruined. Their effort is well beyond expectations normally associated with IT.
The entire IT team is responsible for the support of the several centers in the department that do genome sequencing and genotyping. They maintain 1) the complete pipeline of computers and software that track the human samples, acquire the sequencing data from samples, transfer petabytes of raw data from the sequencers to the mass storage devices; 2) the cluster systems, analysis and job queuing software, required to analyze the raw data; and 3) the Internet and Intranet systems required to disseminate the experimental results. The centers are large operations. Last year, one center alone successfully served 22 UW research labs and 11 external research labs, with $10M in revenue.
The technical support team (Jim, Charles, and Alexander) provide exceptional support to the department, keeping our desktops and systems running, promptly responding to our calls for help, installing the tools we need, considering our schedules and deadlines, and strategically buying the equipment and systems we need. But they do so much more than this, as we describe in a few examples below.
As part of our 10 year celebration, we wanted to tape monthly interviews with distinguished, senior faculty from our formative years. Jim and Alexander agreed to tape these. This required them to quickly learn new skills in videotaping, spending countless hours setting up, taping, and tearing down, until late into the night. When we realized the editing by the consultant was unsatisfactory, Alexander eagerly said he would learn how to do it, better, and on his own time. And he is producing quality videos now available on our web site.
Charles has been referred to as a saint. He ensures that the visiting speakers at our two weekly seminars are able to use their individual, and sometimes idiosyncratic, devices. He supports our July Wednesday Night at the Genome lecture series for the public, our annual symposium and associated evening public event, and our off-campus 3 day retreat for graduate students and research labs. He makes it all happen without a technical glitch.
Jim maintains the hardware and proprietary software for our 11 Illumina sequencers, each costing $750,000. He developed the necessary skills through technical training and extensive Windows systems administration. These sequencers are the heart of the NW Genomics Center and relied on by over 20 UW research labs. Jim has also done cross-platform systems programming in support of our Linux, Mac, and Windows systems as well as our own backbone network. He developed a software package that allows us to manage our inventory, automate cross platform authentication and authorization, and monitor our network infrastructure that has been critical in maintaining a secure and robust environment and allowing us to respond rapidly to the shifting needs of researchers.
The level of support that the IT team provides is so superior to similar departments in other universities, including other top tier institutions, that we use them as a major recruiting tool for faculty, post docs, and graduate students. As a manager in our largest lab said, ‘In discussions with external collaborators about our IT support, I can’t tell you how many times I’ve heard ‘Wow, you’re so lucky, I wish we had that kind of support at our institution.’ The IT group has been instrumental in developing IT solutions to help process the vast quantities of data we generate on a daily basis, and we owe our success in part to their dedication and excellence.’
Genome Sciences would not be what it is today, in the top 5 such departments in the country, without the superior service and innovation that has won the respect of everyone in our department and all those they collaborate with throughout the UW community and outside. We hope you select this team and celebrate their excellence with us. The accompanying support letters are accolades from our faculty, labs, and staff.