Advancing Diversity and Inclusion in Scientific Open Source

While open source software for science aspires to democratize access and reuse of computational methods by all scientists, it is widely known that open source is predominantly created and maintained by a narrowly defined demographic. Open source maintainers are overwhelmingly cisgender white men, and this pattern carries over to most open source projects widely used in science.

Prioritizing diversity and inclusion can help build communities that more accurately represent the people who will ultimately benefit from the work. Having contributions from people of all backgrounds — particularly those who are often underrepresented in biomedical software — can also support maintainers as they identify issues in their projects or communities, such as inherent bias in the software documentation or project roadmap. In short, expanding the makeup and diversity of the teams that build these tools is critical to ensure they can serve everyone, and will inspire the next generation of scientists and developers.

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

As we have learned from other scientific areas that CZI funds, in order to push the bounds of scientific progress, we must deepen our learning of systemic racism and how to address it in biomedicine. We are working to incorporate equity as a key lens in our grantmaking and embed diversity, equity, and inclusion principles at the heart of our strategic priority-setting.

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.

To address this, we launched the first supplemental grant program for current and former EOSS grantees, which provides funding to support the participation, retention, and leadership progression for groups underrepresented in scientific open source. With the help of a slate of external expert reviewers, we identified 14 projects to support for a total of $5 million in funding.

The funded proposals will support a variety of interventions, approaches, and tools for improving diversity and inclusion in open source — including internships, mentoring programs, workshops, and improvements to documentation and accessibility. The proposals also cover a broad range of dimensions in underrepresentation — gender, ethnicity, race, geographic location, and accessibility are all addressed. Funding from these grants will support partnerships between open source maintainers and leading organizations in the DEI space, such as Outreachy, Hack.Diversity, and the Institute for Tribal Environmental Professionals, among others.

A few of the funded projects:

  • 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.

Interventions addressing diversity, equity, and inclusion (DEI) in open source and scientific infrastructure are not widely funded. These grants will not only enable our grantees to implement new programming and improve their communities, but they will also provide us with valuable information about the impact, feasibility, and scalability of these efforts. Given the broad and global adoption of the tools funded through the EOSS program, we hope these DEI investments will have a large impact on open source communities across the globe.

These supplemental grants are announced alongside the newest grantees of the fourth cycle of the EOSS program, which is awarding 35 grants for a total of $11.1 million in funding. Making open source software tools used by scientists globally more scalable, well-documented, maintained, and usable will help us strengthen the computational foundations of biomedical research and support the next scientific breakthroughs. We invite additional funders to join us in investing in open source software — particularly in improving diversity and inclusion in these communities — in order to accelerate science together.

There is still a long way to go to achieve universal and immediate access to all research outputs and knowledge, and most importantly, to make this access equitable and sustainable. This is only the beginning of our explorations in and dedication to DEI in open source, and we know that our work is nowhere near done. We look forward to working with these organizations and project leaders and partnering with other funders in this space.

Learn more about the goals and current initiatives in CZI’s Open Science program.

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.

Carly Strasser, Science Program Manager, Open Science

Carly is an open science advocate and former biology researcher, working at the interface of researchers and those who support them. As Program Manager for Open Science at CZI, she works to support organizations and people that enable open, reproducible, and accessible research. Prior to joining CZI, Carly worked to support researchers at the Fred Hutchinson Cancer Center, the Gordon and Betty Moore Foundation, and the California Digital Library.

Dario Taraborelli, Science Program Officer, Open Science

Dario is a social computing researcher and an open knowledge advocate. As the Science Program Officer for Open Science at CZI, his goal is to build programs and technology to support open, reproducible, and accessible research. Prior to joining CZI, he served as the Director, Head of Research at the Wikimedia Foundation, the non-profit that operates Wikipedia and its sister projects.

Supporting the science and technology that will make it possible to cure, prevent, or manage all diseases by the end of the century.