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From biochemistry to bioinformatics

As a first-year Ph.D. student in chemistry and biochemistry at the University of Maryland, Yuexi Chen knew that she wanted to spend the summer of 2018 doing something productive and impactful.

She submitted a research proposal that would allow her to increase the accessibility of legacy code for scientific research but was met with disappointment when she didn’t receive funding.

Luckily, Chen’s professor, Dr. David Fushman, had come across a different opportunity that would allow her to work on a project that would make a great impact on research since it would allow more biologists to easily perform experiments.

<strong>Yuexi Chen</strong> presenting “ROTDIF-web and ALTENS: GenApp-based Science Gateways for Biomolecular Nuclear Magnetic Resonance (NMR) Data Analysis and Structure Modeling” at Gateways 2019.The summer internship was organized with collaboration and funding through the Science Gateways Community Institute (SGCI), which offers student-focused programs to give students access to mentoring, career development, workshops, and internships to support growth in the field of gateway development and use.  

Ultimately, Chen’s internship experience opened an unexpected but welcome set of doors. Although she had used online tools for years, she wasn’t familiar with the world of science gateways, let alone the growing community of gateway developers and enthusiasts that she would soon encounter, collaborate with, and learn from through her work with SGCI.  

Although Chen already knew that she wanted to do some type of computational biology-related work, her career goals felt vague in the first year of working toward her Ph.D. The opportunity to work closely with Emre Brookes, professor of research in chemistry and biochemistry at the University of Montana and the creator of the GenApp gateway (an SGCI client), and his team, brought new meaning to her career goals.

From Brookes’ work, Chen learned that gateways such as GenApp allow researchers to create platforms for research through streamlined, user-friendly, web-based interfaces. GenApp, for example, makes it possible to rapidly produce science gateways for research scientists who are not necessarily web developers or computationally savvy but understand their domain and have utilities and code that can be shared with a larger audience.

Her work with Drs. Brookes and Fushman was so eye-opening and inspiring that she realized her thesis should shift from a focus in biochemistry to one in bioinformatics. This change would allow her to develop methods and tools to enable biomedical research, something she’d become passionate about during the summer internship.

Chen would go on to present a poster about her work at the Gateways 2018 Conference in Austin, TX, and then give a talk at Gateways 2019 in San Diego, CA, about her summer work on the GenApp-based gateway called ROTDIF-web and another gateway called ALTENS.

Reflecting on her experience at the Gateways conferences, Chen says, “Usually, academic conferences focus on a specific research area, but the Gateways conferences are very interdisciplinary, and that helps you to communicate better with collaborators with different backgrounds.”

Today, with Chen’s focus shifted to bioinformatics, she is developing machine-learning methods to analyze cancer genomics data. While she isn’t able to develop a science gateway for every single method, she pays close attention to the reusability of her code and aspires to, one day, be known for building a gateway that makes an impact on scientific research.

Learn more about SGCI’s Student-focused Programs here. The Gateways 2020 Conference will be October 19-21 in Bethesda, MD.

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