Advancing Diversity and Inclusion in Scientific Open Source

UC Santa Cruz Genomics Institute Research Mentoring Internship program (RMI) students working together in the lab. Photo courtesy of Jingchun Zhu.

The field of open source as a whole must broaden participation by creating opportunities for developers, maintainers, and contributors of all backgrounds to be active participants in the open source community, but these opportunities need funding and resources.

At CZI, our Essential Open Source Software for Science (EOSS) program supports some of the most widely-used open source software tools in biomedicine. While these are some of the most established and mature projects, their maintainers acknowledge the need for tools and resources to advance diversity and inclusion in their communities.

  • QIIME 2 is a software platform for microbiome analysis. Funding will enable QIIME 2 for use as an on-ramp to scientific computing for Native American students by engaging locally with schools primarily serving Native Americans, while expanding their global user, developer, and educator communities. The team will partner with several Native American groups based out of NAU. (Gregory Caporaso at Northern Arizona University)
  • Common Workflow Language is a standard for describing biomedical analysis workflows and enabling reproducible research. The grant will support hiring a community engineer who will provide software engineering to support community members, mentoring internships via Outreachy, and updating code and documentation to make them more user friendly and accessible. (Sarah Wait Zaranek at the Curii Corporation)
  • UCSC Xena is a visual exploration resource for functional genomics data, with an emphasis on cancer genomics. Funding will support the establishment of a mentored internship program for UCSC students from underrepresented populations to apprentice with UCSC Xena. This program will be in partnership with UC Santa Cruz Genomics Institute’s Research Mentoring Internship Program. (Jingchun Zhu at University of California Santa Cruz)
Greg Caporaso hosting a microbial bioinformatics educational exercise at a K-12 STEM outreach event in Flagstaff, Arizona in 2017. Photo courtesy of Greg Caporaso.

Acknowledgments

We want to acknowledge several advisors and reviewers who, along with CZI staffers, helped us design the EOSS program or participated in the review process for this fourth funding cycle and supplemental D&I funding opportunity: Alberto Bacchelli, Amy Bernard, Abby Cabunoc Mayes, David Feng, Allen Goodman, Casey Greene, Max Haeussler, Mahmoud Hashemi, Kate Hertweck, Kari Jordan, Mike Keiser, Peter Kharchenko, Molly Maleckar, Debbie Marks, Marius Pachitariu, Karthik Ram, Stephan Saalfeld, Nicole Sanchez, Emily Sena, Daniel Standage, Kay Thaney, Gao Wang, Kirstie Whitaker, and Yo Yehudi.

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