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 55 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
This grant supports implementation of biomechanical analysis features in ITK-SNAP, an open source application for medical image segmentation, with the goal of streamlining image processing, anatomical modeling, and tissue mechanics analysis from clinical image data.
Alison Pouch (University of Pennsylvania)
Alison Pouch Ankush Aggarwal Lukasz Kaczmarczyk Paul Yushkevich
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 reorganize the libSBML and Deviser code bases for better community involvement, spin out part of libSBML as a reusable component for Deviser and other projects, and establish protocols for long-term sustainability of these important resources.
Sarah Keating (University College London)
Sarah Keating Frank Bergmann Brett Olivier Sarah Keating Frank Bergmann Brett Olivier
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
Single-cell biology is the application of technologies that enable multi-omics investigation at the level of a single cell. This project will streamline trajectory inference from single-cell omics data by improving integration with upstream and downstream analysis pipelines.
Yvan Saeys (Vlaams Instituut voor Biotechnologie)
Yvan Saeys Robrecht Cannoodt Wouter Saelens
To enable portability of complex biomedical workflows across different clouds and on-premise environments via better documentation, community support, and tooling for Common Workflow Language (CWL) with examples using Arvados and from the Personal Genome Project.
Sarah Wait Zaranek (Curii Corporation)
Sarah Wait Zaranek Peter Amstutz
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 support the release and maintenance of a new version of the ETE toolkit including updated documentation and new features such as tree diff, tree-like regular expression searches, and large tree visualization.
Jaime Huerta Cepas (Centro de Biotecnología y Genómica de Plantas)
Jaime Huerta Cepas Renato Alves Ziqi Deng Ana Hernández Francois Serra
Open mHealth created an open data standard and community for patient-generated data, and the Digital Biomarker Discovery Pipeline will enable transformation of that data into indicators of health outcomes and evaluation of novel digital biomarkers.
Jessilyn Dunn (Duke University)
Jessilyn Dunn Brinnae Bent Ida Sim Karnika Singh Will (Ke) Wang
To enhance the HTSJDK Java toolkit for genomics with an extensible plugin framework that will enable support for emerging technologies required by contemporary analysis methods, such as long reads, graph/circular references, and epigenetic modifications.
Eric Banks (Broad Institute of MIT and Harvard)
Eric Banks Louis Bergelson Christopher Norman
To enhance usability of MNE-Python through improvements to its computational efficiency, API, interactive visualization capabilities, and the clarity and consistency of documentation.
Daniel McCloy (University of Washington)
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 improve the user experience of UCSC Xena and better engage users by implementing the redesign of two core features using UX principles, standardizing training materials, and publishing a blog highlighting research use cases.
Jingchun Zhu (University of California, Santa Cruz)
Jingchun Zhu Brian Craft Mary Goldman
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 enhance the infrastructure to support the continuous development and growing community of the popular algorithm MACS for gene regulation studies, in order to expand its features and adapt to new technologies such as single-cell ATAC-seq.
Tao Liu (Roswell Park Alliance Foundation)
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 support a fast-growing, community-building software for infrastructure agnostic, open source biomedical pipelines.
Ellen Sherwood (KTH Royal Institute of Technology)
Evan Floden Paolo Di Tommaso Ellen Sherwood Philip Ewels Gisela Gabernet Harshil Patel Alexander Peltzer
This project will improve accessibility, interoperability, efficiency, and sustainability of the biomedical image registration software Elastix by providing complete support of Python, better integration with other software, code improvements, and a focus on community.
Marius Staring (Leiden University Medical Center)
Marius Staring Niels Dekker
To support development, outreach, and user support for the kallisto RNA-seq and single-cell RNA-seq software project.
Lior Pachter (California Institute of Technology)
To create a sustainable open-source community resource for deep annotation of genetic variants.
Rachel Karchin (Johns Hopkins University)
Rachel Karchin Kymberleigh Pagel
This team will support the continued development of OpenMM to better serve its broad biomolecular modeling community, as well as support its extension to integrate machine learning that will enable genomic-scale biomolecular modeling, simulation, and prediction.
Thomas Markland (Stanford University)
Thomas Markland John Chodera Peter Eastman Gianni De Fabritiis Raimondas Galvelis Karmen Condic-Jurkic Ana Silveira
To improve the usability, computational performance, maintenance and outreach of the open source software OpenSim and to support the education and training of its users around the world.
Ajay Seth (Delft University of Technology)
Ajay Seth Jennifer Hicks Adam Kewley Thomas Uchida
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
This project will solidify the use and future development of the cross-language igraph package to support network analysis in all scientific domains, including biomedical and life sciences.
Vincent Traag (Leiden University)
Vincent Traag Gábor Csárdi Szabolcs Horvát Tamás Nepusz Fabio Zanini
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)
This team will build a real-time data model for Jupyter to lay the foundation for real-time collaboration on notebooks.
Saul Shanabrook (Quansight)
Saul Shanabrook Eric Charles Mars Lee Athan Reines
To attract new users and contributors to the VisPy project through software improvements, community outreach, and instructional materials.
David Hoese (University of Wisconsin - Madison)
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 meet the needs of the scientific community over the next decade, this team will revitalize NetworkX — the fundamental network analysis tool in Python — by growing its developer community, refactoring code, improving performance, and making a major release.
Stefan van der Walt (University of California, Berkeley)
Stefan van der Walt Jarrod Millman Dan Schult
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 provide dedicated community support and maintenance for the Dask project and support growth in the biological sciences field.
Matthew Rocklin (NumFOCUS)
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
To improve Percolator, the dominant software for analyzing spectrum identifications produced by protein tandem mass spectrometry, by making the software faster, more robust, and applicable to more types of mass spectrometry data.
William Noble (University of Washington)
William Noble Markus Ekvall Lukas Kall
To grow the use of Xarray in the biosciences as a foundational data model and computational toolkit for multidimensional labeled arrays.
Joseph Hamman (NumFOCUS)
Joseph Hamman Ryan Abernathey Benoît Bovy Deepak Cherian Stephan Hoyer
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