Hacking is a Broader Impact Activity

Members of Team Supergene, one of the winning teams, discussed their process in a virtual meeting with hackathon organizers. Clockwise from top left: Sherif Negm (team captain, junior); Dr. John Sproul (postdoc); Dr. Lucas Hemmer (postdoc); Xiaolu Wei (graduate student).

Advances in basic biological research methods have generated large amounts of data scattered across divergent datasets and disciplines.

Recognizing this, MCB-funded CAREER-awardee Dr. Amanda Larracuente (MCB-1844693) has developed a broader impact activity to build data literacy, organizing  week-long hackathons open to contestants of any skill level.

The first hackathon, held this past August, was a team effort between Larracuente, Matthew McCall, and Andrew McDavid, her co-chairs on the working group on Life and Biomedical Data Science at the University of Rochester’s Goergen Institute for Data Science. The challenge was to make predictions about a high-dimensional genomic dataset. “For this challenge, it helped to have teams with diverse experiences in computer programming, statistics, and some biology background. It was great to see participants with different backgrounds forming teams!” says Larracuente. Competitors entered the contest either solo or in self-assembled teams of four. Lone entrants who wanted a team experience were assigned to teams based on their self-assessed skills in statistics, programming, and GitHub. Participation was open to anyone enrolled at the University of Rochester, Larracuente’s home institution, and all skill levels and educational background were welcome.

In all, 44 contestants comprised 17 teams, including eight teams of undergraduates. Each day during the five-day contest, teams submitted their predictions to GitHub (a cloud-based hosting service for managing data repositories) and received feedback from the organizers. One important lesson learned, observes Larracuente, is to take advantage of existing campus outreach efforts to broaden recruitment efforts.

Her efforts are motived by her passion for increasing the participation of women and other populations traditionally underrepresented in the field of computational biology. “I really want to help students build confidence in their computational skillset,” says Larracuente.

 She may be succeeding. Khoa Hoang, an undergraduate majoring in microbiology and data science observed, “This has been a cool and beneficial learning experience for many of us…[the hackathon] motivated me a lot to take more data science courses. This is our first time analyzing high dimensional data and it has been a very interesting journey.”

*The division of Molecular and Cellular Bioscience (MCB) recently released a Dear Colleague Letter inviting proposals for conferences focusing on ways to both collate distributed information and synthesize data to advance research. Follow this link for more information on “Conferences to Prepare for the Transformation of Molecular and Cellular Biosciences Research through Information Synthesis and Integration” (NSF 21-017).

DCL 21-017: Conferences to Prepare for the Transformation of Molecular and Cellular Biosciences Research through Information Synthesis and Integration

The field of molecular and cellular biosciences has generated vast amounts of knowledge about cellular parts and processes through advances in biophysical, -omics, and imaging technologies, among others. The work of synthesizing this information, such as harmonizing and collectively interpreting divergent datasets, developing new analytical approaches and tools, building models and theories, and integrating knowledge from within and across various disciplines, can have a transformative impact on all of biology.

NSF has a history of supporting information synthesis through large scale centers, such as the National Evolutionary Synthesis Center (NESCent), that have engaged thousands of investigators over 10-year investment periods and have led to striking advances in their fields.

To begin planning for a synthesis center, the Division of Molecular and Cellular Biosciences has released a Dear Colleague Letter (NSF 21-017) announcing the availability of conference funding to build networks of scientists with diverse perspectives to formulate ideas for a synthesis center in molecular and cellular sciences. To be considered for FY 2021 funding, proposals responsive to this DCL should be received before April 21, 2021. Proposals will be awarded on a rolling basis. Important details about preparing and submitting a competitive conference proposal are included in the announcement.