Enabling Foundational Tools for Scientific Discovery

23 New Grants Support Essential Open Source Tools in Biomedicine

Chan Zuckerberg Initiative Science
The Startup
6 min readMay 27, 2020


We believe in a future where biomedical scientists have access to the most advanced computational tools to conduct research and can build upon, extend, and adapt these tools to meet their needs. With the Essential Open Source Software for Science (EOSS) program, we set out to support the maintenance, development, and community engagement of the most critical open source tools that researchers use on a daily basis — and to make the work of their creators and maintainers visible, recognized, and fundable.

In December 2019, we awarded 32 grants to support some of the most widely used open source software tools across biomedicine, as well as projects that provide foundational capabilities for data analysis, modeling, and data visualization. We’re now expanding our support for scientific open source software with 23 grants from the second funding cycle of the EOSS program. These grants represent a combined $8.8 million in funding and bring the total number of funded proposals to 55.

In the second RFA cycle, we received a total of 194 proposals, which were evaluated by CZI staff and external expert reviewers for their impact, project quality, feasibility, and the value of diversity, equity, and inclusion efforts. We highly value reuse of software as an indicator of impact. Proposals were evaluated for how widely used and useful they are in their relevant communities, as well as the health and maturity of their open source and community engagement practices.

These new grants extend the reach of the EOSS program to now include open source tools used in clinical medicine, two established libraries for biomedical workflows and pipelines, foundational support for real-time collaboration in notebooks, and widely used libraries to accelerate data analysis via parallel computing, graph analysis, and multidimensional data representation. We are also expanding our support to domain-specific open source software by funding widely-used tools in single cell biology, bioinformatics, genomics, imaging, and neuroscience. Read more about the projects we are funding in the second cycle of this program.

“Open source enables the democratization of science, allowing state-of-the-art computational methods to be implemented and extended anywhere in the world.” -Grantee William Noble, University of Washington, Percolator project.

Attendees at CZI’s Essential Open Source Software for Science kickoff meeting in Berkeley, CA. Photos by Scott Murphy/CZI.

Identifying shared needs among maintainers

Moving forward, our goal is to identify the needs of this community of maintainers of critical open source tools and explore successful models to support their work beyond funding. In February, we hosted the EOSS program’s kickoff meeting in Berkeley, CA, bringing together representatives from each of the projects funded in the first cycle, as well as several philanthropic and governmental funders, fiscal sponsors, advocates and researchers studying open source for science. The event was an opportunity to build connections among the maintainers of these projects (many of whom had never been in the same room), foster collaborations, and have an honest discussion about the challenges these projects — and by extension all scientific open source tools — face across their lifecycle.

We learned there’s strong demand for community management, formal governance models, better tools for inclusion and participatory design, and solutions for crediting the invisible work that goes into open source maintenance. Open source maintainers are also calling for better access to funders and for funding informed by and modeled after their needs and pain points. There’s an opportunity for philanthropies, governmental bodies, and industry partners to team up and scale the total amount of funding that can support the scientific open source ecosystem.

Finally, the meeting was a great opportunity for grantees to present their work and explore integrations with other projects. You can check out the slides from the presentations on Zenodo and follow the Twitter conversation from the meeting participants.

Rethinking the architecture of participation

Making open source tools available and accessible to researchers worldwide means ensuring that diversity and inclusion are some of the key principles on which these tools operate when attracting new contributors and serving new audiences. At the EOSS kickoff meeting, we hosted several leaders, including those from The Carpentries and Mozilla, to discuss best practices other organizations have implemented to nurture resilient and diverse leadership in open communities and to expand computational literacy and access to open source tools.

Based on these lessons, we evolved our application process to make diversity, equity, and inclusion statements a requirement of every EOSS application and a key part of our expert review process. Taking it a step further, we required that all funded projects adopt a Code of Conduct during the grant period.

As of today, open source software — and in particular the most established and mature projects the EOSS program supports — is predominantly created and maintained by a narrowly defined demographic. Expanding the makeup and diversity of the teams that build these tools is critical to ensure they can serve everyone. Of all the proposals we funded in this second cycle, 30 percent are led by individuals self-identifying as women or non-binary. The geographical reach of the projects we support in this cycle has also expanded to now include a total of nine countries.

Announcing the third funding cycle

We are proud to partner with the maintainers of numerous tools that scientists all over the world use every day. To expand our support of essential open source software for biomedicine, and to allow existing grantees to request additional funding for their work, we’re launching our third funding cycle, which will officially open for applications on June 16, 2020. Learn more.

Grant proposals funded in EOSS cycle two

  • Open source image registration: the elastix toolbox
  • Computational Biology Software Maintenance Framework
  • Revitalizing NetworkX for Complex Network Analysis
  • Providing a solid foundation for network analysis
  • Real Time Collaboration in Jupyter
  • Bridging The Gap In Medical Image Analysis and Biomechanics with ITK-SNAP
  • Scaling Python with Dask
  • The Percolator analysis engine for tandem mass spectrometry data
  • Rebuilding the community behind VisPy’s fast interactive visualizations
  • Improving usability of core neuroscience analysis tools with MNE-Python
  • HTSJDK: Enhancing the Java toolkit for emerging sequencing technologies
  • OpenMM: Key infrastructure for biomolecular modeling and simulation
  • MACS3: a versatile peak caller for gene regulation studies
  • Improving the User Experience and User Engagement for UCSC Xena
  • OpenCRAVAT community building for integrated variant annotation framework
  • ETE Toolkit: Phylogenomic data analysis and visualization
  • Enabling Biomedical Science with Common Workflow Language
  • Expanding the Open mHealth Platform to Support Digital Biomarker Discovery
  • dynverse: a toolkit for studying cell development with single-cell omics
  • OpenSim: An open source biomechanics simulator to study movement
  • Xarray: N-D labeled arrays and datasets in Python
  • Nextflow and nf-core: Reproducible workflows for the scientific community
  • Open source software for bulk and single-cell RNA-seq

Acknowledging our advisors and partners

We want to acknowledge several advisors and reviewers who helped us design the program or participated in the review process, along with CZI staffers: Alberto Bacchelli, Amy Bernard, Titus Brown, Abigail Cabunoc Mayes, Scott Chamberlain, David Feng, Allen Goodman, Stephanie Hicks, Martin Fenner, Amel Ghouila, Josh Greenberg, Mahmoud Hashemi, Alison Hill, James Howison, Daniel S. Katz, Michael Keiser, Molly Maleckar, Debora Marks, Vilas Menon, Chris Mentzel, Marius Pachitariu, Stephan Preibisch, Jason Priem, Karthik Ram, Danielle Robinson, Stephan Saalfeld, Leah Silen, Arfon Smith, Tracy Teal, Nelle Varoquaux, Luis Villa, Kirstie Whitaker.

To learn more about our work at CZI, visit our website or follow us on Twitter.

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. As a co-author of the Altmetrics Manifesto, a co-founder of the Initiative for Open Citations, and a long-standing open access advocate, he has been designing systems and programs to accelerate the discoverability and reuse of scientific knowledge by scholars, policy makers, and the general public alike.



Chan Zuckerberg Initiative Science
The Startup

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