Researchers awarded for open-source software projects

Lines of code on a computer screen.


3 min read

Three Harvard research teams have been recognized by the Chan Zuckerberg Initiative (CZI) with funding to support their open source software projects, considered to be “essential to biomedical research.” These grants will support software maintenance, growth, development, and community engagement.

Open source software is publicly accessible so that anyone can modify or share it. This approach to building tools for data analysis is widely acknowledged to be crucial to modern scientific research, as it allows scientists worldwide to advance biology and medicine swiftly while providing reproducibility and transparency.

Harvard-led projects include DeepLabCut: An Open Source Toolbox for Robust Animal Pose Estimation, led by Mackenzie Mathis.

“DeepLabCut is an open-source software package that efficiently performs 3D pose estimation on animals from fruit flies to primates,” said Mathis, a Rowland Fellow and a principal investigator at the Harvard Brain Initiative. “We are delighted to receive a grant from CZI to support this software, which is used by hundreds of labs across the world. We are very excited to continue to build new tools, run user training workshops and hackathons, and interface with other open-source modules to aid in developing pipelines for behavior-focused neuroscience and medical research.”

Rory Kirchner, a research scientist in the Department of Biostatistics of the Harvard T.H. Chan School of Public Health, received an award for the bcbio-next project and its work on “Maintenance and Improvement of Validated, Community Developed Next-Generation Sequencing (NGS) Analyses.”

“If you want to be on the cutting edge of genomics, you need to be involved with open source software,” said Kirchner. “Commercial, closed-source solutions exist for many analyses but they are often far behind state of the art, at times lagging by years from what is known to be best. Our goal is to help researchers spend more time thinking about and working on the biology of their experiments and less time struggling with the unimportant and scientifically boring computational processing of their data.”

At the Broad Institute of MIT and Harvard, Bhanu Gandham, senior computational associate, was awarded by CZI for the project GATK (Genome Analysis Toolkit), to further develop GATK Methods for Bacterial Variant Discovery and Evaluation.

“The world’s most pressing needs should be addressed by humanity’s collective scientific talent,” said Gandham. “By providing a platform that improves data sharing and collaboration, we hope to empower researchers with computationally reproducible and interoperable bacterial variant analysis methods.”

In this round of funding, CZI granted $5 million over 32 projects in total. In addition to supporting the improvement of software tools, the organization will offer the awardees opportunities to connect with other open source software developers, technical experts, and members of the broader scientific community.

In an announcement, CZI Head of Science Cori Bargmann said, “Open source software accelerates the work scientists carry out each day, whether it’s searching a genome sequence for a disease gene, tracking a disease outbreak, or counting cells in a microscope image. Scientists are only as good as their tools, and we’re thrilled to support open source projects that will benefit the entire scientific community and help every scientist be a better scientist.”