CZI’s Essential Open Source Software for Science program supports software maintenance, growth, development, and community engagement for open source tools critical to science.
Showing 32 results
To bring the combined power of scikit-image and Dash to a larger number of scientists thanks to increased execution speed, interactive image annotation and processing, and outstanding documentation targeting life sciences practitioners.
Emmanuelle Gouillart (Plotly Technologies, Inc.)
Emmanuelle Gouillart Marianne Corvellec Emmanuelle Gouillart Shammamah Hossain Marianne Corvellec Ryan Kyle Byron Zhu
The project will improve the SciPy library's statistics functionality to better serve biomedical research and downstream projects. In addition, an outreach component will engage female students, inspiring them to participate in open source code development.
Warren Weckesser (University of California, Berkeley; NumFOCUS)
Matt Haberland (California Polytechnic State University, NumFOCUS)
Warren Weckesser Matt Haberland Fletcher Easton
To support the QIIME 2 user and developer communities by enabling sharing of automatically tested third-party content on the QIIME 2 Library, and hosting our first-ever co-convened user and developer workshop and networking event.
Greg Caporaso (Northern Arizona University)
Greg Caporaso Matthew Dillon Evan Bolyen Nick Bokulich
To reengineer the Bioconductor build system for nightly continuous integration, production, and distribution of tarballs and binaries for over 1,700 user-contributed software packages.
Vincent Carey (Brigham and Women's Hospital)
Vincent Carey Shweta Gopaulakrishnan Benjamin Stubbs Kimberly Glass
To develop extensive functionality, expand user support, and initiate new modes of community outreach for Seurat, an open-source R toolkit for integrative single-cell analysis.
Rahul Satija (New York Genome Center)
Rahul Satija Tim Stuart Paul Hoffman
To maintain BWA and improve the performance and robustness of BWA and its next major version BWA-MEM2.
Heng Li (Dana-Farber Cancer Institute)
To build Cytoscape Explore, a web-based biological network viewer and editor that will make key aspects of the widely used Cytoscape application accessible to new audiences as part of its evolution from a desktop application to a cloud ecosystem.
Dexter Pratt (University of California, San Diego)
Dexter Pratt Gary Bader Keiichiro Ono Sophie Liu Max Franz
To support the maintenance, new extensions, and education of users of the DeepLabCut software community.
Mackenzie Mathis (Harvard University & Swiss Federal Institute of Technology Lausanne (2020))
Mackenzie Mathis Alexander Mathis
To improve ease of use and interoperability of these packages, make methodological responses to new data challenges, refresh the documentation and structure of these packages, and prepare training materials.
Gordon Smyth (Walter and Eliza Hall Institute of Medical Research)
Gordon Smyth Charity Law Yunshun Chen Gordon Smyth Yunshun Chen Charity Law Göknur Giner Gordon Smyth Charity Law
To enhance bedtools’ functionality, documentation, and access to data, which will empower and expand the user community.
Aaron Quinlan (University of Utah)
Aaron Quinlan Brent Pedersen Hao Hou Aaron Quinlan Michael Cormier Joe Brown
To support continued maintenance and development of pandas, an open source, BSD-licensed library providing high-performance, easy-to-use data structures and data analysis tools for the Python programming language.
Tom Augspurger (NumFOCUS)
To complete the design, implementation, and rollout of pip's next-generation dependency resolver, and permanently improve pip's maintainer capacity and user experience.
Ernest W. Durbin III (Python Software Foundation)
Ernest W. Durbin III Sumana Harihareswara
To develop an open standard and API for phylogenetic models and improve the speed and scalability of the IQ-TREE software for phylogenetic inference from ultra-large genomic data.
Minh Bui (Australian National University)
Minh Bui Robert Lanfear
To improve community support and technical maintenance across the JupyterHub repositories.
Chris Holdgraf (University of California, Berkeley; NumFOCUS)
Chris Holdgraf Tim Head Georgiana Dolocan
To put Rocker, the de facto standard for reproducible, containerized R analyses, on a path to sustainable maintenance through refactoring, improving the quality of documentation, expanding the community, and targeting new hardware platforms.
Carl Boettiger (University of California, Berkeley)
Carl Boettiger Noam Ross Dirk Eddelbuettel
To improve the bcbio-nextgen toolkit, focusing on maintaining existing variant calling functionality and extending support for structural and RNA-seq variant analyses.
Rory Kirchner (Harvard Chan School of Public Health)
Rory Kirchner Sergey Naumenko
To enable Matplotlib to continue as the core plotting library of the scientific Python ecosystem by addressing the maintenance backlog and planning Matplotlib's evolution to meet the community’s visualization challenges for the next decade.
Thomas A. Caswell (Brookhaven National Laboratory, NumFOCUS)
Thomas A. Caswell Hannah Aizenman Michael Grossberg
To support the open source µManager optical microscopy acquisition platform to improve its architecture, infrastructure, and support to ensure many years of growth, both in user base and capabilities.
Kevin Eliceiri (University of Wisconsin, Madison)
Kevin Eliceiri Mark Tsuchida Nico Stuurman Bing Dai Kevin Eliceiri Mark Tsuchida Bing Dai
To construct a solid foundation for the next generation of Protege using a modern web stack that will make Protege easier to maintain, extend, and — crucially — make it easier for third parties to contribute to the code base.
Mark Musen (Stanford University)
Mark Musen Matthew Horridge Josef Hardi
To provide open-source, interoperable, and extensible statistical software for quantitative mass spectrometry, which enables experimentalists and developers of statistical methods to rapidly respond to changes in the evolving biotechnological landscape.
Olga Vitek (Northeastern University)
Olga Vitek Meena Choi Olga Vitek Kylie Bemis
To support the Bio-Formats user community and develop new formats to make proprietary file formats obsolete.
Jason Swedlow (University of Dundee)
Jason Swedlow David Gault Sebastien Besson Petr Walczysko Jean-Marie Burel
To enable the analysis of thousands of next generation data-independent acquisition (DIA) mass spectrometry measurements by implementing algorithms, visualization tools, and cloud containers based on OpenMS and the OpenSWATH algorithm.
Hannes Rost (University of Toronto)
Hannes Rost Timo Sachsenberg
To hire an outreach coordinator and (part of) a software developer for the Apollo genome annotation editor, provide developer- and user-oriented workshops and training, develop a plugin framework, and integrate protein visualizations.
Ian Holmes (University of California, Berkeley)
Ian Holmes Nathan Dunn Ian Holmes Rob Buels
To create a smoother experience for PsychoPy users by detecting potential problems in user-created experiments before they are launched, and by increasing the test coverage within the application code itself.
Jonathan Peirce (University of Nottingham)
Jonathan Peirce David Bridges Alain Pitiot Jonathan Peirce Alain Pitiot
To accelerate biomedical research, biomarker discovery, and the translation of artificial intelligence into clinical practice by enhancing the QuPath open source platform and by integrating it with other CZI-funded software.
Peter Bankhead (University of Edinburgh)
To establish teaching material, improve documentation, and minimize maintenance effort of the Bioconda project by extending automation of code review, testing, and building.
Johannes Köster (University of Duisburg-Essen, Bioconda Core Team)
To establish Zarr as a foundation for scientific data storage, with clear data format and protocol specifications, implementations in multiple programming languages, and a community process for evolving to support new scientific applications.
Ryan Williams (Mount Sinai School of Medicine)
Ryan Williams Alistair Miles John Kirkham Josh Moore
To attract new contributors by improving OpenRefine's documentation, and implement a new data model to improve the scalability, transparency, and reproducibility of OpenRefine workflows.
Antonin Delpeuch (Code for Science and Society)
Antonin Delpeuch Owen Stephens
To expand Scanpy’s core infrastructure and community platforms for stability, versatility, and sharing knowledge.
Fabian Theis (Helmholtz Zentrum Munich)
Fabian Theis Alex Wolf Phillipp Angerer
To improve the open-source machine learning library scikit-learn and aid in maintaining the project, while considering the new implementation of Gradient boosting.
Andreas Mueller (Columbia University)
Andreas Mueller Nicolas Hug
To grow the maturity of the NumPy project through governance, documentation, and website work by improving the robustness of its links with OpenBLAS, and through diversifying the core team beyond the developer role.
Ralf Gommers (Quansight, NumFOCUS)
Ralf Gommers Martin Kroeker
To develop GATK methods for variant discovery and evaluation in bacteria, resolve inconsistent and diverse results from different research groups, and allow for the sharing of data and analysis globally to control bacterial transmission and antibiotic resistance.
Bhanu Gandham (Broad Institute of MIT and Harvard)
Bhanu Gandham David Benjamin
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