RNA-Seq bioinformatics among the open source software projects awarded funding from the Chan Zuckerberg Initiative

The Chan Zuckerberg Initiative (CZI) announced $3.8 million in funding for 23 grants to support open source software projects essential to biomedical research, enabling software maintenance, growth, development, and community engagement. As part of CZI’s Essential Open Source Software for Science program, this announcement brings CZI’s total commitment to funding scientific open source to $8.8 million.

Open source software is crucial to modern scientific research, advancing biology and medicine while providing reproducibility and transparency. Yet even the most widely-used research software often lacks dedicated funding. With these grants, awardees will be able to hire additional developers, improve documentation, address usability, improve compatibility, onboard contributors, convene communities, and more.

“Hundreds of thousands of scientists each day use open source software to carry out their research,” said CZI Head of Science Cori Bargmann. “Scientists deserve better tools, and we’re helping to meet that need by supporting open source projects that will advance biomedical science and foster greater access to critical software.”

This new series of grants expands 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. Funds will also support important tools used in single cell biology, bioinformatics, genomics, imaging, and neuroscience.

Maintenance and Improvement of Validated, Community Developed NGS Analyses
bcbio-nextgen – Rory Kirchner (Harvard Chan School of Public Health)
To improve the bcbio-nextgen toolkit, focusing on maintaining existing variant calling functionality and extending support for structural and RNA-seq variant analyses.

Open Source Software for Bulk and Single-Cell RNA-seq
Kallisto – Lior Pachter (California Institute of Technology)
To support development, outreach, and user support for the kallisto RNA-seq and single-cell RNA-seq software project.

View the full list of grantees.

CZI staff will further support awarded projects by convening grantee meetings and connecting open source software developers to technical experts, scientists, and one another, including other CZI-funded grantees and members of the broader scientific community.

CZI supports several areas of basic science and technology with the goal of making it possible to cure, prevent, or manage all diseases by the end of this century. The Essential Open Source Software program aims to support software tools in service of this mission through a series of RFAs. Today’s grant announcement represents the second cycle of the program, and CZI will invite applications for a third distinct cycle opening June 16, 2020.

Applications can request funding between $50,000 and $250,000 total costs. CZI will solicit applications for software projects that are essential to biomedical research, have demonstrated impact, and can show potential for continued improvement. CZI will consider two broad categories of projects:

  • Domain-specific software for analyzing, visualizing, and otherwise working with the specific data types that arise in biomedical science (e.g., genomic sequences, microscopy images, and molecular structures); and
  • Foundational tools and infrastructure that enable a wide variety of downstream software across several domains of science and computational research (e.g. numerical computation, data structures, workflows, and reproducibility). Foundational tools must have demonstrated impact on some area(s) of biomedical research.

Source – Chan Zuckerberg Initiative

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