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 72 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.)
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)
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)
To support the growth, sustainability, and diversity of the Apache Arrow project by expanding an apprenticeship program, which recruits developers from underrepresented groups and trains them to be open source software maintainers.
Wes McKinney (Ursa Labs)
To develop an automated tool that uses optimization to calibrate models of the musculoskeletal system and improve simulation results, and disseminate the tool to the OpenSim community with documentation, examples, case studies, and outreach events.
Thomas Uchida (University of Ottawa)
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)
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)
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)
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)
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)
To support code maintenance, a new code cookbook, and user education for the DeepLabCut software community and set the foundation towards becoming a sustainable software package for years to come.
Mackenzie Mathis (Harvard University & Swiss Federal Institute of Technology Lausanne)
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))
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)
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)
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)
To develop training materials, perform software maintenance, expand outreach, and provide community support for the Open Health Imaging Foundation (OHIF) web-based medical imaging framework including its underlying libraries (e.g., Cornerstone).
Gordon Harris (Massachusetts General Hospital)
To enhance bedtools’ functionality, documentation, and access to data, which will empower and expand the user community.
Aaron Quinlan (University of Utah)
To provide significant modernization and enhanced usability of the R packages mixtools and tolerance for improved utilization and accessibility within the biomedical and health research communities.
Derek Young (University of Kentucky Research Foundation)
To extend DESeq2 functions to develop interfaces with Bioconductor’s rich experiment and annotation data, including single-cell datasets and genomic annotations, all leveraging tximeta’s metadata functionality for computational reproducibility.
Michael Love (The University of North Carolina at Chapel Hill)
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)
To make scientific Python documentation more valuable by improving the user experience of linking between projects, and promote this ability within the scientific Python community.
Eric Holscher (Read the Docs, Inc)
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)
To extend Galaxy, a web-based computational workbench used by thousands of scientists across the world, so that it can analyze large datasets and connect with other analysis tools.
Jeremy Goecks (Oregon Health & Science University)
To maintain the popular scikit-image Python library for microscopy and medical imaging data and bring significant improvements via development of a backend system enabling multi-threading and GPU acceleration, an improved release process for more rapid cycles, and expanded biomedical examples.
Gregory Lee (Quansight)
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)
To integrate ilastik with napari and Dask, replacing the outdated internal viewer and task scheduler by modern, community-supported alternatives with the aim to reduce technical debt, engage with the community, and deliver a superior user experience for the bioimage analysis community.
Anna Kreshuk (European Molecular Biology Laboratory)
To improve Bokeh in key areas that are relevant to bioscience research and to secure a solid foundation for long-term project health and sustainability by engaging in important maintenance and fostering new contributors.
Bryan Van de Ven (Nvidia)
To improve the robustness and usability of NumPy by continuing to work in documentation and community building, modernizing its integration with Fortran tools via numpy.f2py, and ensuring the sustainability of both NumPy and OpenBLAS.
Melissa Mendonça (Quansight)
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)
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)
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)
To improve community support and technical maintenance across the JupyterHub repositories.
Chris Holdgraf (University of California, Berkeley; NumFOCUS)
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)
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)
To enable Matplotlib to continue as the core plotting library of the scientific Python ecosystem for researchers in biomedical imaging, microscopy, and genomics by addressing the maintenance backlog and beginning Matplotlib's evolution to meet the community’s visualization challenges for the next decade.
Thomas A. Caswell (Brookhaven National Laboratory, NumFOCUS)
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)
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)
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)
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)
To support the Bio-Formats user community and develop new formats to make proprietary file formats obsolete.
Jason Swedlow (University of Dundee)
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)
To support a fast-growing, community-building software for infrastructure agnostic, open source biomedical pipelines.
Ellen Sherwood (KTH Royal Institute of Technology)
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)
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)
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)
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)
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)
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)
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)
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)
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)
To advance support and development of the open source Salmon and Alevin software for gene expression quantification of single-cell and bulk RNA-seq.
Carl Kingsford (Ocean Genomics)
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)
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)
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)
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)
To strengthen the social and code foundations of the Nibabel library by extending the API and input/output to better support metadata, supporting outputs from image registration, and through educational outreach.
Matthew Brett (NumFOCUS)
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)
To improve Monocle with algorithms, statistical methods, and web-based visualization tools that will enable biologists using single-cell genomics to extract and disseminate new insights from their experiments.
Cole Trapnell (University of Washington)
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)
To ensure the continued health of the pandas library by dedicating resources specifically to maintenance and implementing consistent missing data handling for all data types.
Tom Augspurger (NumFOCUS)
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)
To grow the use of Xarray in the biosciences as a foundational data model and computational toolkit for multidimensional labeled arrays.
Joseph Hamman (NumFOCUS)
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