UPDATE: See this December 2020 coverage in genomeweb about Biodepot LLC’s “serverless” cloud computing that
accelerates alignment of human RNA sequencing data by more than a thousandfold.
Welcome to our blog series, “UW Researcher Spotlight”. These posts spotlight University of Washington researchers who, as principal investigator—or “PI”—lead their teams on the path from idea to impact with the support of CoMotion. The resulting innovations have been licensed to industry, spun out as a startup or licensed direct to the user from within the UW.
Stay tuned for profiles about UW researchers from computer science & engineering, life sciences, emerging tech, social sciences and more.
What problems do your innovations solve?
“We aim to address three bottlenecks in bioinformatics. First, reproducing bioinformatics analyses results is non-trivial given the rapidly evolving software tools in the field and dependencies between multiple tools. Second, most existing efforts focus on optimizing the processing of thousands of samples or even entire databases while most biomedical scientists want to enhance the efficiency of analyzing their own datasets. Finally, technological advances in cloud technology are generally not accessible to biomedical scientists. Most cloud vendors offer many products, each of which have many options, configurations and parameters. It is unclear what and how to choose between all these offerings. These cloud products are designed for users who are technically trained, and thus, non-trivial to the biomedical community.”
When did you file your first ROI with CoMotion?: May 2019
What can you tell us about your innovations?
“Our latest tool, BioDepot-workflow-builder, was recently published in Cell Systems. Bioinformatics analyses (or workflows) typically consist of a sequence of computational tasks. Each of these computational tasks could potentially be written by different labs and require different computing environments. Our project is supported by an NIH basic science grant in which users can create, share and reproducibly execute modular bioinformatics workflows. Each module (or computational task) is represented by a software container, which encapsulates the entire computing environment, to facilitate reproducibility.”
“Our team has diverse and complementary expertise. Both Wes Lloyd and I have PhDs in computer science while Ling-Hong Hung has a PhD in biochemistry. The primary research area of Hong and I is bioinformatics while Wes’ primary research expertise is in cloud computing. We work closely as a team to develop methods and cloud-enabled tools to facilitate reproducible and efficient analyses of big biomedical data.”
What are the CoMotion services and resources you have used and how did they help?
“We work closely with Ryan who provides us with valuable support and advice. We are currently supported by the STEP fund, and are applying for the CoMotion Innovation Gap Fund. We are also interested in applying for NIH SBIR grants/contracts, and we also received valuable advice and support from Jeanette Ennis. We are very grateful for the support, connections and mentoring provided by CoMotion.”
“Our advice would be to get in touch with CoMotion, attend their events, talk to different people and keep an open mind. There are numerous times that I feel I’m out of my comfort zone. For example, writing a business proposal is quite different than writing a manuscript or an NIH grant proposal. But I have already learned so much in this process. I have to give a pitch soon and I am already nervous!”
What do you like most about working with CoMotion?
“I’d have to say working with Ryan Buckmaster, Senior Innovation Manager in Engineering. It is such a personal experience to have somebody outside your team who believes in your invention and is your advocate.”
Who is your favorite scientist or researcher in your field?
“This is a hard one. There are so many outstanding scientists in bioinformatics. I’d have to say Professor Daphne Koller at Stanford. Not only has she done amazing scholarly work in computer science and bioinformatics, she has founded a company too.”
Background and Bio:
Ka Yee Yeung is a Professor in the School of Engineering and Technology at University of Washington – Tacoma, and an Adjunct Professor in the Department of Microbiology at University of Washington – Seattle. Her research focuses on the development of methods and software tools that leverage cloud and container technology that will allow biomedical researchers to build modular reproducible bioinformatics workflows. She is strongly committed to enhancing the diversity of the STEM workforce.
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About UW CoMotion: CoMotion at the UW is the collaborative innovation hub dedicated to expanding the economic and societal impact of the UW community. By developing and connecting to local and global innovation ecosystems, CoMotion helps innovators achieve the greatest impact from their ideas and discoveries.