Chan Zuckerberg Initiative drops $3.8M on 23 biomedical open source projects – TechCrunch


The philanthropic arm of the Zuckerberg fortune is infusing $3.8 million worth of grants into nearly two dozen open source software projects in biomedical research. It’s the second such disbursement of funds, and a third will be open for applications next month.

The grants range in size from $50,000 to $250,000 and any biomed-centric project with impact and room to grow is eligible to apply for them. Of course, they have to be open source as well.

“Hundreds of thousands of scientists each day use open source software to carry out their research. 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,” said Cori Bargmann, head of science at the Chan Zuckerberg Initiative, in a press release.

CZI has supported biomedical software efforts consistently since its foundation, for instance giving the Human Cell Atlas $68M to continue its invaluable work. Its other, larger scale efforts (in the billions over years) aren’t quite so narrowly focused.

Today’s grantees cover a wide variety of applications within biomedical science and research. Here are the very brief summaries; you can find more detail at the CZI announcement.

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

Congratulations to the grantees. If the list above seems like it should include your open source biomedical software project, you can send your application in for the third round starting on June 16.