Essential Open Source Software for Science

CZI’s Essential Open Source Software for Science program supports software maintenance, growth, development, and community engagement for open source tools critical to science.

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3D Slicer for African Scientists: Enabling AI for Health

To empower African scientists to develop 3D Slicer AI-based extensions for health priorities and enable their deployment to global communities through customized AI models for multilingual translation. Note: This proposal was funded by Wellcome Trust as part of our co-funded EOSS Cycle 6.

Project 3D Slicer
Lead

Sonia Pujol (Brigham and Women's Hospital, Harvard Medical School)

Funding Cycle 6
3D Slicer for Latin America: Localization and Outreach

To empower the biomedical research community in Latin America by localizing 3D Slicer to Spanish and Portuguese, improving tutorial localization infrastructure, and holding outreach events.

Project 3D Slicer
Lead

Sonia Pujol (Brigham and Women’s Hospital, Harvard Medical School)

Funding Cycle 5
3D Slicer in My Language: Internationalization and Usability Improvements

To increase the accessibility of the 3D Slicer open source platform for biomedical research to clinicians and scientists in non-English speaking countries.

Project 3D Slicer
Lead

Sonia Pujol (Brigham and Women's Hospital, Harvard Medical School)

Funding Cycle 4
A Hub for Probabilistic Analysis for Single-Cell Genomics

To develop scvi-tools 2.0: an accessible and scalable environment for probabilistic modeling for single-cell genomics that enables the next generation of massive-scale studies.

Project scvi-tools
Lead

Nir Yosef (Weizmann Institute of Science)

Funding Cycle 6
A Modular Suite of Advanced Bioimaging Tools with scikit-image and Dash

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.

Projects scikit-image, Dash
Lead

Emmanuelle Gouillart (Plotly Technologies, Inc.)

Funding Cycle 1
A Solid Foundation for Statistics in Python with SciPy

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.

Project SciPy
Leads

Warren Weckesser (University of California, Berkeley; NumFOCUS)

Matt Haberland (California Polytechnic State University, NumFOCUS)

Funding Cycle 1
A Unified Framework for Cell-Cell Communication Modeling

To develop an open source, unified framework for cell-cell communication modeling and exploration that is available to the entire scientific community.

Project NicheNet
Lead

Yvan Saeys (VIB-Ghent University)

Funding Cycle 6
Accessible Interactive Data Visualizations in Python with Bokeh

To address accessibility gaps in Bokeh, Panel, and Holoviz by incorporating accessibility affordances to ensure everyone can benefit from their powerful data visualization capabilities.

Project Bokeh
Lead

Tania Allard (Quansight Labs)

Funding Cycle 6
Achieving Accessibility for UpSet Plots

To make UpSet plots accessible to low-vision and blind users, and to simplify authoring UpSet plots.

Project UpSet
Lead

Alexander Lex (University of Utah)

Funding Cycle 5
Adapting limma and edgeR for Single-cell and Proteomics

To address new challenges posed by replicated single-cell RNA-seq data and by mass spectrometry proteomics.

Projects limma, edgeR
Lead

Gordon Smyth (Walter & Eliza Hall Institute of Medical Research)

Funding Cycle 4
Advancing an Inclusive Culture in the Scientific Python Ecosystem

To support the onboarding, inclusion, and retention of people from historically marginalized groups on scientific Python projects and structurally improve the community dynamics of NumPy, SciPy, Matplotlib, and pandas.

Project NumPy, SciPy, Matplotlib, and pandas
Lead

Melissa Mendonça (Quansight, NumFOCUS)

Funding Cycle D&I
Advancing Array Interoperability Within the PyData Ecosystem

To advance array interoperability within the PyData Ecosystem by accelerating Array API adoption in key libraries used in biomedical research and building infrastructure for measuring API compliance.

Project Data APIs
Lead

Athan Reines (Quansight)

Funding Cycle 6
Advancing Microbiome Research Through QIIME 2 Community Development

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.

Project QIIME 2
Lead

Greg Caporaso (Northern Arizona University)

Funding Cycle 1
AnnData for R

To enhance the anndataR package for improved interoperability and functionality in handling single-cell data within the R programming environment.

Project anndataR
Lead

Robrecht Cannoodt (Open Collective Europe Foundation)

Funding Cycle 6
Apache Arrow Apprenticeship Program for OSS Maintenance and Community

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.

Project Apache Arrow
Lead

Wes McKinney (Ursa Labs)

Funding Cycle 3
Automated Generation of Galaxy Tools

To develop software that is able to automatically integrate existing open source software into the Galaxy platform. Note: This proposal was funded by Wellcome Trust as part of our co-funded EOSS Cycle 6.

Project Galaxy
Lead

Daniel Blankenberg (The Cleveland Clinic)

Funding Cycle 6
Automated Optimal Model Calibration for the OpenSim Biomechanics Simulator

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.

Project OpenSim
Lead

Thomas Uchida (University of Ottawa)

Funding Cycle 3
Bacterial Variant Calling with Snippy

To develop a modular and extensible variant caller for microbial genome data that is sequencing technology agnostic and underpinned by an extensive validation and test suite.

Project Snippy
Lead

Torsten Seemann (The University of Melbourne)

Funding Cycle 6
Bayesian Open Source Software for Biomedicine: Stan, ArviZ and PyMC3

To develop key infrastructure updates and collaboration resources for state-of-the-art Bayesian modeling software libraries.

Projects PyMC, ArviZ, Stan
Lead

Christopher Fonnesbeck (NumFOCUS)

Funding Cycle 4
bcbio-nextgen: Reproducible, Community Developed Analysis Pipelines

To provide ongoing maintenance and community support for the bcbio-nextgen toolkit, focusing on existing variant calling functionality and improving the epigenomic pipelines.

Project bcbio-nextgen
Lead

Shannan Ho Sui (Harvard T.H. Chan School of Public Health)

Funding Cycle 5
Bioconductor Build System: Continuous Integration and Developer Feedback

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.

Project Bioconductor Build System
Lead

Vincent Carey (Brigham and Women's Hospital)

Funding Cycle 1
Bioconductor: High Quality Training and Support for a Worldwide Community

To provide Bioconductor training globally by redeveloping the website and developing infrastructure to deliver high quality community-led training in local languages.

Project Bioconductor
Lead

Aedin Culhane (Dana-Farber Cancer Institute, Harvard University)

Funding Cycle 4
Bioconductor: Sustaining a Worldwide Community of Genome Data Scientists

To increase participation of underrepresented groups in genome data science research through alliances with organizations advancing diversity in science, increased mentoring activities for developers, and enhanced governance of Bioconductor.

Project Bioconductor
Lead

Vincent Carey (The Brigham and Women's Hospital)

Funding Cycle D&I
Bokeh Raster Image and Time Series Improvements for Biomedical Applications

To extend the open source Bokeh library to cover streaming gridded visualizations for bioscience applications that currently require expensive proprietary tools.

Project Bokeh
Lead

Bryan Van de Ven (NumFOCUS)

Funding Cycle 5
Bridging the Gap In Medical Image Analysis and Biomechanics with ITK-SNAP

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.

Project ITK-SNAP
Lead

Alison Pouch (University of Pennsylvania)

Funding Cycle 2
Bringing GPU Scientific Visualization to the Web with VisPy 2.0

To bridge the gap between the desktop and the web for large-scale GPU scientific visualization by developing a web version of VisPy 2.0 based on Python, WebAssembly, WebGPU, and Datoviz.

Project VisPy
Lead

Cyrille Rossant (NumFOCUS)

Funding Cycle 6
Bringing Micro-Manager to Classrooms and the Cutting-Edge

To create a versatile, inclusive, open source microscopy platform for diverse global educational and research communities by modernizing and extending Micro-Manager.

Project Micro-Manager
Lead

Henry Pinkard (NumFOCUS)

Funding Cycle 6
Building Pediatric and Clinical Data Pipelines for MNE-Python

To enhance MNE-Python for clinical neuroscience uses by improving spectral and spectro-temporal data handling, and by providing standardized preprocessing pipelines for data.

Project MNE-Python
Lead

Daniel McCloy (University of Washington)

Funding Cycle 4
Code Contribution for Women in Network Science

To develop tools, training materials, and mentorship opportunities to help women and nonbinary people in network science to use and contribute code to the igraph open source network analysis library.

Project igraph
Lead

Brooke Foucault Welles (Northeastern University)

Funding Cycle D&I
cogent3 Python APIs for IQ-TREE and GraphBin via a Plug-In Architecture

To enhance metagenomic analysis by integrating cogent3, GraphBin and IQ-TREE to support innovative genomic technologies for monitoring the impact of viral and bacterial diversity on human health.

Project cogent3 Python APIs
Lead

Gavin Huttley (Australian National University)

Funding Cycle 5
Comprehensive, Scalable, and Collaborative Single-Cell Analysis with Seurat

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.

Project Seurat
Lead

Rahul Satija (New York Genome Center)

Funding Cycle 1
Comprehensive, Scalable, and Collaborative Single-Cell Analysis with Seurat

To develop extensive functionality, expand user support, and facilitate interoperability for Seurat, an open source R toolkit for integrative single-cell analysis.

Project Seurat
Lead

Rahul Satija (New York Genome Center)

Funding Cycle 5
Computational Biology Software Maintenance Framework

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.

Projects libSBML, Deviser
Lead

Sarah Keating (University College London)

Funding Cycle 2
Computational Tools for Population-Scale Single Cell Genomics

To develop statistically robust, computationally efficient, and maximally compatible open source software for the design and analyses of multiplexed single-cell sequencing experiments.

Project Demuxlet, Freemuxlet, Memento
Lead

Jimmie Ye (University of California, San Francisco)

Funding Cycle 5
Connecting Open Source Biomolecular Software Communities

To effectively support community building efforts across open source ecosystems in molecular sciences, improve contributor pipelines, and seek synergies and collaboration opportunities in this space.

Project Open Molecular Software Foundation
Lead

Karmen Condic-Jurkic (Open Molecular Software Foundation)

Funding Cycle 5
Continuous Improvement to Essential High-Throughput Bio-Sequence Aligners

To maintain BWA and improve the performance and robustness of BWA and its next major version BWA-MEM2.

Project BWA
Lead

Heng Li (Dana-Farber Cancer Institute)

Funding Cycle 1
Cytoscape Explore for Biological Networks Brings Cytoscape to the Cloud

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.

Project Cytoscape
Lead

Dexter Pratt (University of California, San Diego)

Funding Cycle 1
Deep Probabilistic Programming for Biology with Pyro

To accelerate single-cell biology methods research and empower their developers with foundational probabilistic AI software.

Project Pyro
Lead

Eli Bingham (Broad Institute of MIT and Harvard)

Funding Cycle 5
DeepGaitLab: Reconciling Vision-Based Motion Tracking with ISB Standards

To interface recently developed computer vision tools with an open-source biomechanical modeling software, which should facilitate the uptake of markerless motion tracking in biomedicine.

Project DeepGaitLab
Lead

Eni Halilaj (Carnegie Mellon University)

Funding Cycle 4
DeepLabCut AI Residents for Next-Gen Animal Behavior

To develop a DeepLabCut AI Residency Program for underrepresented groups in machine learning and computer science in order to recruit, fund, and nurture the next generation of open source leaders.

Project DeepLabCut
Lead

Mackenzie Mathis & Alexander Mathis (École Polytechnique Fédérale de Lausanne (EPFL))

Funding Cycle D&I
DeepLabCut: A Software Package for Animal Pose Estimation

To provide maintenance, user-focused extensions, education, and support of the growing DeepLabCut software community.

Project DeepLabCut
Lead

Mackenzie Mathis (École Polytechnique Fédérale de Lausanne (EPFL))

Funding Cycle 4
DeepLabCut: An Open Source Toolbox for Robust Animal Pose Estimation

To support the maintenance, new extensions, and education of users of the DeepLabCut software community.

Project DeepLabCut
Lead

Mackenzie Mathis (Harvard University & Swiss Federal Institute of Technology Lausanne (2020))

Funding Cycle 1
DeepLabCut: An Open Source Toolbox for Robust Animal Pose Estimation

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.

Project DeepLabCut
Lead

Mackenzie Mathis (Harvard University & Swiss Federal Institute of Technology Lausanne)

Funding Cycle 3
Delivering High-Quality Bioconductor Training for a Worldwide Community

To expand the global Bioconductor-Carpentries training program, increase equity and accessibility using culturally sensitive AI translation, and build capacity for workshops in Africa

Project Bioconductor
Lead

Aedin Culhane (University of Limerick)

Funding Cycle 6
Democratizing Deep Learning for Microscopists with DL4MicEverywhere

To establish DL4MicEverywhere, a containerized deep learning for microscopy toolkit extending the easy-to-use ZeroCostDL4Mic, with interactive notebooks for training and deployment across platforms. Note: This proposal was funded by Wellcome Trust as part of our co-funded EOSS Cycle 6.

Project DL4MicEverywhere
Lead

Ricardo Henriques (Instituto Gulbenkian de Ciência)

Funding Cycle 6
dynverse: A Toolkit for Studying Cell Development with Single-Cell Omics

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.

Project dynverse
Lead

Yvan Saeys (Vlaams Instituut voor Biotechnologie)

Funding Cycle 2
Enabling Biomedical Science with Common Workflow Language

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.

Project Common Workflow Language (CWL)
Lead

Sarah Wait Zaranek (Curii Corporation)

Funding Cycle 2
Enabling Differential Analyses of Genomic Data with limma, edgeR and Glimma

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.

Projects limma, edgeR, Glimma
Lead

Gordon Smyth (Walter and Eliza Hall Institute of Medical Research)

Funding Cycle 1
Engaging Native American Students in Scientific Computing with QIIME 2

To use QIIME 2 as an on-ramp to scientific computing for Native American students by engaging locally with schools primarily serving Native Americans, while expanding the global QIIME2 user, developer, and educator communities.

Project QIIME 2
Lead

Greg Caporaso (Northern Arizona University)

Funding Cycle D&I
Enhancing Diversity in Computational Mass Spectrometry

To increase diversity in computational mass spectrometry through teaching and mentoring with the open-source framework OpenMS.

Project OpenMS
Lead

Hannes Rost (University of Toronto)

Funding Cycle D&I
Enhancing Giotto for Spatial Multi-Resolution Technologies

To enhance Giotto by implementing a novel data structure and framework for the abstract representation and analysis of emerging datasets from multi-modal and multi-resolution spatial technologies.

Project Giotto
Lead

Ruben Dries (Boston Medical Center Corporation / Boston University)

Funding Cycle 5
Enhancing High-Level Scientific Computing Support in CuPy

To provide a series of GPU accelerated routines for signal processing and interpolation in CuPy to be a foundation for the research community.

Project Enhancing High-Level Scientific Computing Support in CuPy
Lead

Kenichi Maehashi (NumFOCUS)

Funding Cycle 5
Enhancing Interoperability, UI, and Documentation of MOOSE

To enhance the Multiscale Object-Oriented Simulation Environment software package through development of new GUIs, data and model import tools, and tutorials for computational modeling in neuroscience and systems biology. Note: This proposal was funded by The Kavli Foundation as part of our co-funded EOSS Cycle 6.

Project moose
Lead

Upinder Bhalla (National Centre for Biological Sciences)

Funding Cycle 6
Enhancing Spyder IDE Remote Support for Scientific Research in Python

To improve Spyder support for connecting to a remote machine to develop, execute, and debug Python code, as well as installing packages, managing environments and interacting with the remote filesystem.

Project Spyder
Lead

Carlos Cordoba (Quansight, LLC)

Funding Cycle 5
Enhancing the Bactopia Ecosystem with Trainings and Visual Reports

To ensure ongoing maintenance and community growth of Bactopia, focusing on integrating visual reports and comprehensive training materials.

Project Bactopia
Lead

Robert Petit (NumFOCUS)

Funding Cycle 6
Enhancing the Open Health Imaging Foundation Web Medical Imaging Framework

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).

Projects Open Health Imaging Foundation (OHIF) Viewer, Cornerstone
Lead

Gordon Harris (Massachusetts General Hospital)

Funding Cycle 3
Enhancing the Open Source SciML Stack for Clinical Trial Simulations

To make significant improvements to the SciML project, which is leveraged by pharmacologists in academia and industry for simulation of virtual clinical trials, drug design, and systems biology modeling.

Project SciML
Lead

Samuel Isaacson (Boston University, NumFOCUS)

Funding Cycle 4
Enhancing the Performance, Documentation, and Data Ecosystem for bedtools

To enhance bedtools’ functionality, documentation, and access to data, which will empower and expand the user community.

Projects bedtools, Go Get Data (GGD)
Lead

Aaron Quinlan (University of Utah)

Funding Cycle 1
Enhancing Usability of mixtools and tolerance for the Biomedical Community

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.

Projects mixtools, tolerance
Lead

Derek Young (University of Kentucky Research Foundation)

Funding Cycle 3
Ensuring Reproducible Transcriptomic Analysis with DESeq2 and tximeta

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.

Project DESeq2
Lead

Michael Love (The University of North Carolina at Chapel Hill)

Funding Cycle 3
Ensuring the Continued Growth of pandas

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.

Project Pandas
Lead

Tom Augspurger (NumFOCUS)

Funding Cycle 1
Ensuring the Continued Growth of pandas

To support the growth and health of pandas, the foundational library for tabular data structures in the Scientific Python Ecosystem, by funding continued maintenance and community building efforts.

Project pandas
Lead

Joris Van den Bossche (NumFOCUS)

Funding Cycle 4
EpiStan: Notebooks and Methods for Disease Modeling in Stan

To build a repository of infectious disease models in Stan that will provide researchers with in-depth examples, helping them to draw sound conclusions and make better predictions from their data.

Project EpiStan
Lead

Mitzi Morris (Columbia University)

Funding Cycle 5
ETE Toolkit - Enabling Large Scale Phylogenomic Analysis and Visualization

To enable interactive analysis and exploration of phylogenetic data at the genomics and metagenomics scale.

Project ETE
Lead

Jaime Huerta-Cepas (Centro de Biotecnología y Genómica de Plantas (CBGP, UPM/INIA-CSIC))

Funding Cycle 5
ETE Toolkit: Phylogenomic Data Analysis and Visualization

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.

Project ETE Toolkit
Lead

Jaime Huerta Cepas (Centro de Biotecnología y Genómica de Plantas)

Funding Cycle 2
Expand Interoperability of Hosted Scientific Documentation

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.

Project Read the Docs
Lead

Eric Holscher (Read the Docs, Inc)

Funding Cycle 3
Expanding and Deploying Data Visualization Tools for Mining Metagenomes

To expand on existing web infrastructure by building highly intuitive and responsive data visualization tools for mining ‘shotgun’ metagenomic data.

Project MicrobiomeDB.org
Lead

Daniel Beiting (University of Pennsylvania)

Funding Cycle 5
Expanding and Modernizing the Salmon Ecosystem

To expand the capabilities and improve the robustness and maintainability of the salmon software ecosystem, further widening its scope of applicability and improving the user and developer experience.

Project Salmon Ecosystem
Lead

Robert Patro (University of Maryland)

Funding Cycle 5
Expanding the Open mHealth Platform to Support Digital Biomarker Discovery

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.

Project Open DBDP
Lead

Jessilyn Dunn (Duke University)

Funding Cycle 2
Extending Galaxy for Large-Scale and Integrative Biomedical Analyses

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.

Project Galaxy
Lead

Jeremy Goecks (Oregon Health & Science University)

Funding Cycle 3
Fast Software Package Management for Bio and Data Science

To improve the tooling around the conda ecosystem to better serve the millions of users in biological sciences, data sciences, physics, robotics and other scientific disciplines.

Projects conda-forge, mamba
Lead

Wolf Vollprecht (conda-forge core, QuantStack, NumFOCUS)

Funding Cycle 4
FastSurfer - AI-Based NeuroImage Analysis Package

To provide an efficient neuroimage analysis pipeline for the medical imaging communities by consolidating advanced DL-methods into a single user-friendly, maintainable, open source software framework.

Project FastSurfer
Lead

Martin Reuter (German Center for Neurodegenerative Diseases)

Funding Cycle 5
Flexible, Modular and Extensible Pipelines for Integrative Neuro-Histology

To develop an easy-to-use and validated neuroanatomical framework for the multidimensional image viewer napari, bringing state-of-the-art image analysis plugins to neuroscience.

Project BrainGlobe
Lead

Adam Tyson (Sainsbury Wellcome Centre & Gatsby Computational Neuroscience Unit, University College London)

Funding Cycle 5
From Library to Protocol: scikit-image as an API Reference

To create a consistent, type-annotated, discoverable, and extensible API for scikit-image and facilitate interoperability in the broader image analysis ecosystem.

Project scikit-image
Lead

Juan Nunez-Iglesias (Monash University / NumFOCUS)

Funding Cycle 5
Future: Simple, Scalable Parallelization in R for the Biomedical Community

To sustain maintenance, improve community support, enhance usability and robustness, and add improvements for the future framework.

Project Future
Lead

Henrik Bengtsson (University of California, San Francisco)

Funding Cycle 4
Globalization of CGAP to Advance Genome Medicine

To inspire a diverse global community to collaborate in genome medicine, research, and education by packaging CGAP’s portal and cloud infrastructure as self-serve, orchestrated, open source software.

Project CGAP
Lead

Dana Vuzman (Harvard Medical School)

Funding Cycle 5
GPU Acceleration, Rapid Releases, and Biomedical Examples for scikit-image

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.

Project scikit-image
Lead

Gregory Lee (Quansight)

Funding Cycle 3
GPU-accelerated Computing in Bioconductor

To support GPU-accelerated Bioconductor packages through continuous integration, user-friendly packaging of system-level dependencies, and foundational packages for Bioconductor GPU programming.

Project Bioconductor
Lead

Levi Waldron (CUNY Graduate School of Public Health and Health Policy)

Funding Cycle 6
GPU-accelerating Fiji and Friends Using Distributed CLIJ, NEUBIAS-style

To enable end-users of ImageJ/Fiji, Icy and napari to process biological imaging time-lapses or large-scale image data tile-by-tile on multiple graphics processing units (GPUs) using CLIJ.

Project CLIJ
Lead

Robert Haase (Cluster of Excellence “Physics of Life”, Technische Universität Dresden)

Funding Cycle 4
Growing a Diverse and Inclusive Workflow Ecosystem with CWL

To expand our community so new individuals can meaningfully contribute code, documentation, workflows and other software artifacts by hiring a dedicated software engineer.

Project CWL
Lead

Sarah Wait Zaranek (Curii Corporation)

Funding Cycle D&I
GSVA: Optimizing Gene Set Variation Analysis for Single-Cell Data

To optimize GSVA functionality to analyze single-cell and spatial transcriptomic data sets, increasing its robustness and scalability and improving user interface and documentation.

Project GSVA
Lead

Robert Castelo (Universitat Pompeu Fabra)

Funding Cycle 5
HTSJDK: Enhancing the Java Toolkit for Emerging Sequencing Technologies

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.

Project HTSJDK
Lead

Eric Banks (Broad Institute of MIT and Harvard)

Funding Cycle 2
ilastik and Scientific Python Ecosystem: Deep Integration with Other Tools

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.

Project ilastik
Lead

Anna Kreshuk (European Molecular Biology Laboratory)

Funding Cycle 3
ilastik: Faster and More User-Friendly Through Full Pyramid Support

To enable multi-scale interactive machine learning on large datasets in ilastik through full exploitation of state-of-the-art pyramidal file formats and viewers, and extend functionality to other bioimage analysis tools.

Project ilastik
Lead

Anna Kreshuk (European Molecular Biology Laboratory)

Funding Cycle 4
ilastik: Future-Proof Through Stable APIs and Interoperability

To make ilastik more interoperable and its results more reusable and reproducible through the development of Python APIs and general improvement of the third-party developer experience.

Project ilastik
Lead

Anna Kreshuk (European Molecular Biology Laboratory)

Funding Cycle 6
Improving Bokeh Figure Publication: SVG, LaTeX, and Maintenance

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.

Project Bokeh
Lead

Bryan Van de Ven (Nvidia)

Funding Cycle 3
Improving Computational Methods for High-throughput Sequence Data Analysis

To maintain and improve the three proposed software projects: minimap2, BWA and hifiasm, and extend them to new architectures and new data types.

Projects minimap2, BWA, hifiasm
Lead

Heng Li (Dana-Farber Cancer Institute)

Funding Cycle 4
Improving OpenRefine’s Reproducibility

To improve OpenRefine to empower users without programming experience to publish research datasets along with verifiable and reproducible workflows, and to automate such workflows.

Project OpenRefine
Lead

Antonin Delpeuch (Code for Science & Society)

Funding Cycle 5
Improving QIIME 2 pathogen identification and developer community tools

To facilitate the detection and characterization of pathogens in microbiome data, while supporting community development and dissemination of accessible and reproducible bioinformatics applications.

Project QIIME 2
Leads

J. Gregory Caporaso (Northern Arizona University)

Nicholas Bokulich (ETH Zurich)

Funding Cycle 5
Improving Standard Practice for Neuroimaging Analyses with Nilearn

To scale technical and social support for new analyses in Nilearn including the general linear model, giving access to a broad statistical framework for neuroimagers within the open source Python ecosystem.

Project Nilearn
Lead

Jean-Baptiste Poline (McGill University)

Funding Cycle 5
Improving the Analytical Flexibility of bedtools

To improve the flexibility and utility of bedtools for large-scale genomic analyses.

Project bedtools
Lead

Aaron Quinlan (University of Utah)

Funding Cycle 4
Improving Usability and Sustainability for NumPy and OpenBLAS

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.

Projects NumPy, OpenBLAS
Lead

Melissa Mendonça (Quansight)

Funding Cycle 3
Improving Usability of Core Neuroscience Analysis Tools with MNE-Python

To enhance usability of MNE-Python through improvements to its computational efficiency, API, interactive visualization capabilities, and the clarity and consistency of documentation.

Project MNE-Python
Lead

Daniel McCloy (University of Washington)

Funding Cycle 2
Improving User Experience and Debuggability of pip For All Python Users

To complete the design, implementation, and rollout of pip's next-generation dependency resolver, and permanently improve pip's maintainer capacity and user experience.

Project pip
Lead

Ernest W. Durbin III (Python Software Foundation)

Funding Cycle 1
Improving User Experience and Engagement for UCSC Xena

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.

Project UCSC Xena
Lead

Jingchun Zhu (University of California, Santa Cruz)

Funding Cycle 2
Inclusive and Accessible Scientific Computing in the Jupyter Ecosystem

To bring systematically marginalized voices of disabled scientists into scientific computing communities via building and applying accessibility tools, standards, and community contribution practices in the Jupyter ecosystem.

Project JupyterLab
Lead

Tania Allard (Quansight LLC)

Funding Cycle 4
Industry Open Source Diversity Genomics Internship Program

To improve diversity of computational biology and open source development, providing professional industry opportunities for talent underrepresented within the field of genomics.

Project Salmon
Lead

Carl Kingsford (Ocean Genomics)

Funding Cycle D&I
Integrating the Software Toolkit for Protein Structure Modeling

To build a new class of macromolecular modeling methods to study the interplay of structure, dynamics, cellular assemblies, and disease from the subatomic to nanometer scale.

Project CCTBX, Integrative Modeling Platform (IMP), and qFit
Lead

James Fraser (University of California, San Francisco)

Funding Cycle 5
Integration of Protégé with Other Open Tools for Ontology Engineering

To integrate the WebProtégé ontology editor with other open source tools that together constitute an ecosystem that is used widely to develop and manage biomedical ontologies.

Project WebProtégé
Lead

Mark Musen (Stanford University)

Funding Cycle 5
IQ-TREE for Ultra-Large Genomic Data

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.

Project IQ-TREE
Lead

Minh Bui (Australian National University)

Funding Cycle 1
JupyterHub Community Strategic Lead

To broaden participation in the JupyterHub community by establishing a role dedicated to strategy and stewardship for pathways into and throughout the community, as well as programs that provide onboarding and mentorship for historically underrepresented groups.

Project JupyterHub
Lead

Chris Holdgraf (NumFOCUS)

Funding Cycle D&I
JupyterHub Contributor in Residence Program

To improve community support and technical maintenance across the JupyterHub repositories.

Project Project Jupyter (JupyterHub, The Binder Project)
Lead

Chris Holdgraf (University of California, Berkeley; NumFOCUS)

Funding Cycle 1
MACS3, Peak Caller with Single-Cell Resolution

To maintain the established infrastructure and optimize the current features of the popular peak caller MACS for gene regulation studies, while focusing on building the data structure and features for single-cell data analysis.

Project MACS3
Lead

Tao Liu (Roswell Park Alliance Foundation)

Funding Cycle 4
MACS3: A Versatile Peak Caller for Gene Regulation Studies

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.

Project MACS
Lead

Tao Liu (Roswell Park Alliance Foundation)

Funding Cycle 2
Maintaining Rocker: Sustainability for Containerized Reproducible Analyses

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.

Project The Rocker Project
Lead

Carl Boettiger (University of California, Berkeley)

Funding Cycle 1
Maintenance & Extension of scikit-learn: Machine Learning in Python

To further the sustainability and usability of scikit-learn by reducing the maintenance backlog and extending its machine learning models and pipelines to support more complex datasets.

Project scikit-learn
Lead

Thomas Fan (Quansight)

Funding Cycle 4
Maintenance and Improvement of Validated, Community Developed NGS Analyses

To improve the bcbio-nextgen toolkit, focusing on maintaining existing variant calling functionality and extending support for structural and RNA-seq variant analyses.

Project bcbio-nextgen
Lead

Rory Kirchner (Harvard Chan School of Public Health)

Funding Cycle 1
Matplotlib: Foundation of Scientific Visualization in Python

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.

Project Matplotlib
Lead

Thomas A. Caswell (Brookhaven National Laboratory, NumFOCUS)

Funding Cycle 1
Matplotlib: Foundation of Scientific Visualization in Python

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.

Project Matplotlib
Lead

Thomas A. Caswell (Brookhaven National Laboratory, NumFOCUS)

Funding Cycle 3
Matplotlib: Foundation of Scientific Visualization in Python

To support the continued maintenance, growth, development, and community engagement of Matplotlib, the foundational plotting library of the Scientific Python Ecosystem.

Project Matplotlib
Lead

Thomas Caswell (Brookhaven National Laboratory, NumFOCUS)

Funding Cycle 4
MDAnalysis: Faster, Extensible Molecular Analysis for Reproducible Science

To improve and maintain high-performance tools for analysis of biological systems at the molecular scale and incentivize scientists to drive transparent and reproducible research.

Project MDAnalysis
Lead

Oliver Beckstein (Arizona State University, NumFOCUS)

Funding Cycle 4
MDAnalysis: Outreach and Project Manager

To grow the MDAnalysis community sustainably.

Project MDAnalysis
Lead

Richard Gowers (Open Molecular Software Foundation)

Funding Cycle 5
MicroManager 2.0: An Open Platform for Microscopy Image Acquisition

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.

Projects MicroManager, ImageJ
Lead

Kevin Eliceiri (University of Wisconsin, Madison)

Funding Cycle 1
Migrating Protege to a Modern Web Stack

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.

Project Protege
Lead

Mark Musen (Stanford University)

Funding Cycle 1
Modernizing the igraph Interfaces

To modernize the igraph interfaces to make network analysis easier.

Project igraph
Lead

Vincent Traag (Leiden University)

Funding Cycle 4
Molecular Visualization: Transitioning Chimera to ChimeraX

To keep ChimeraX molecular and microscopy analysis software current with the latest technology and facilitate the migration of tens of thousands of Chimera users to ChimeraX.

Project ChimeraX
Lead

John Morris (University of California, San Francisco)

Funding Cycle 4
MSstats and Cardinal: Next Generation Statistical Mass Spectrometry in R

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.

Projects MSstats, Cardinal
Lead

Olga Vitek (Northeastern University)

Funding Cycle 1
Neurodesk: a platform for reproducible neuroimaging

To develop features for an improved user and developer experience in the Neurodesk platform allowing for easier, portable, scalable, and reproducible neuroscience and biomedical imaging analysis. Note: This proposal was funded by Wellcome Trust as part of our co-funded EOSS Cycle 6.

Project Neurodesk
Lead

Steffen Bollmann (The University of Queensland)

Funding Cycle 6
Next Generation File Formats for BioImaging

To support the Bio-Formats user community and develop new formats to make proprietary file formats obsolete.

Project Open Microscopy Environment
Lead

Jason Swedlow (University of Dundee)

Funding Cycle 1
Next Generation Mass Spectrometry with OpenMS

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.

Project OpenMS
Lead

Hannes Rost (University of Toronto)

Funding Cycle 1
Next-Generation Movement Monitoring with the DeepLabCut Ecosystem

To enhance the DeepLabCut ecosystem with a new 3D pose module, integration with generative AI (AmadeusGPT), providing codebase and DLC-Live! code upkeep, and continuing our DEI AI Residency Program. Note: This proposal was funded by The Kavli Foundation as part of our co-funded EOSS Cycle 6.

Project DeepLabCut
Lead

Mackenzie Mathis (Swiss Federal Institute of Technology, Lausanne)

Funding Cycle 6
Next-Generation Simulation and Learning in Imaging-Based Biomedicine

To develop and integrate open computational geometry and simulation technology enabling digital twins in biomedicine – next-generation imaging-based modeling, simulation, optimization, and learning. Note: This proposal was funded by Wellcome Trust as part of our co-funded EOSS Cycle 6.

Projects wildmeshing, FEniCS Project
Lead

Marie E. Rognes (Simula Research Laboratory)

Funding Cycle 6
Nextflow and nf-core

To keep the current momentum of initiatives and push forward with new actions for accessibility, internationalization, mentorships and ambassadors.

Project Nextflow, nf-core
Lead

Ellen Sherwood (KTH Royal Institute of Technology)

Funding Cycle D&I
Nextflow and nf-core: Reproducible Workflows for the Scientific Community

To support a fast-growing, community-building software for infrastructure agnostic, open source biomedical pipelines.

Projects Nextflow, nf-core
Lead

Ellen Sherwood (KTH Royal Institute of Technology)

Funding Cycle 2
Nextflow and nf-core: Reproducible Workflows for the Scientific Community

To continue support for a fast-growing community, building open source software for infrastructure agnostic, open source biomedical analysis workflows.

Projects Nextflow, nf-core
Lead

Ellen Sherwood (KTH Royal Institute of Technology)

Funding Cycle 4
NGFF: Democratize Access to Next-Generation Bioimaging Data

To coordinate and foster next-generation file formats while increasing community access to public imaging data.

Project Open Microscopy Environment Consortium
Lead

Josh Moore (German BioImaging Society)

Funding Cycle 5
NiPreps - a Community Framework for Reproducible Neuroimaging

To solidify NiPreps by boosting community growth, securing maintenance, and developing new components to expand the diversity of supported data such as imaging parameters, modalities, populations, and species.

Project NiPreps
Lead

Oscar Esteban (Lausanne University Hospital and University of Lausanne)

Funding Cycle 5
OME-Zarr Support for Java/Fiji

To develop a general-purpose Java library for the community standard image file format OME-Zarr, and robustly integrate it into the widespread image processing and analysis software Fiji.

Project Fiji
Lead

Pavel Tomancak (Max Planck Institute of Molecular Cell Biology and Genetics)

Funding Cycle 6
Ontological Resource Tagging and Discovery for Bioconductor

To enhance discoverability and use of Bioconductor packages and data and teaching resources by tagging them with formal vocabulary and concept relations in ontologies like EDAM.

Project Bioconductor
Lead

Vincent Carey (Harvard Medical School)

Funding Cycle 6
Open Health Imaging Foundation (OHIF) and Cornerstone Medical Web Viewer

To partner with hack.diversity to serve as curriculum designers and mentors, equipping their Fellows to contribute to open source web-based medical imaging, as well as mentor existing global OHIF contributors.

Project OHIF, Cornerstone
Lead

Gordon Harris (Massachusetts General Hospital)

Funding Cycle D&I
Open Health Imaging Foundation Web Medical Imaging Framework

To develop, upgrade, and migrate documentation; perform software maintenance; and provide community support for the Open Health Imaging Foundation web-based medical imaging framework.

Project Open Health Imaging Foundation
Lead

Gordon Harris (Massachusetts General Hospital)

Funding Cycle 5
Open Source Image Registration: The elastix Toolbox

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.

Project elastix
Lead

Marius Staring (Leiden University Medical Center)

Funding Cycle 2
Open Source Image Registration: The elastix Toolbox

To improve accessibility, interoperability, efficiency, and sustainability of the biomedical image registration software elastix, by making it a library-first package, allowing integration with other software and improving its performance.

Project elastix
Lead

Marius Staring (Leiden University Medical Center)

Funding Cycle 4
Open Source Image Registration: the Elastix Toolbox

To improve accessibility, efficiency, and sustainability of the biomedical image registration software Elastix, by improving interaction possibilities, speed, and accessibility via a web browser. Note: This proposal was funded by Wellcome Trust as part of our co-funded EOSS Cycle 6.

Project Elastix
Lead

Marius Staring (Leiden University Medical Center)

Funding Cycle 6
Open Source Ontologies to Power an Open Science Community

To develop open medical ontologies and analytics that enable large-scale generation of real-world evidence on disease and the effects of medical interventions across the world’s electronic health data.

Project Observational Health Data Sciences and Informatics
Lead

George Hripcsak (Columbia University)

Funding Cycle 5
Open Source Software for Bulk and Single-Cell RNA-seq

To support development, outreach, and user support for the kallisto RNA-seq and single-cell RNA-seq software project.

Project kallisto
Lead

Lior Pachter (California Institute of Technology)

Funding Cycle 2
OpenCRAVAT Community Building for Integrated Variant Annotation Framework

To create a sustainable open-source community resource for deep annotation of genetic variants.

Project OpenCRAVAT
Lead

Rachel Karchin (Johns Hopkins University)

Funding Cycle 2
Opening Omics Data Science to All with Tidyomics

To administer and expand the scope of the Tidyomics Project, enabling computational biologists to employ a user-friendly grammar to manipulate rich biological datasets across omics and platforms. Note: This proposal was funded by Wellcome Trust as part of our co-funded EOSS Cycle 6.

Project tidyomics
Lead

Michael Love (University of North Carolina Chapel Hill)

Funding Cycle 6
OpenMM: A Toolkit for Biomolecular Modeling and Simulation

To grow the OpenMM development community and expand the OpenMM software ecosystem to better serve user needs. Note: This proposal was funded by Wellcome Trust as part of our co-funded EOSS Cycle 6.

Project OpenMM
Lead

Thomas Markland (Stanford University)

Funding Cycle 6
OpenMM: Key Infrastructure for Biomolecular Modeling and Simulation

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.

Project OpenMM: A high performance toolkit for molecular simulation
Lead

Thomas Markland (Stanford University)

Funding Cycle 2
OpenRefine for Everyone

To continue to diversify contributors by building capacity in project management, as well as offering internships and eliminating cultural or linguistic biases in the Open Refine tool.

Project OpenRefine
Lead

Antonin Delpeuch (Code for Science & Society)

Funding Cycle D&I
OpenSim Creator: Empowering Biomedical Research with Biomechanical Models

To develop accurate, fast, and researcher-friendly open tools for creating and simulating neuromuscular and musculoskeletal models to address biomedical questions in human and animal mobility.

Project OpenSim Creator
Lead

Ajay Seth and Adam Kewley (Delft University of Technology)

Funding Cycle 5
OpenSim: An Open Source Biomechanics Simulator to Study Movement

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.

Project OpenSim
Lead

Ajay Seth (Delft University of Technology)

Funding Cycle 2
Outreach and Software Development for the Apollo Genome Annotation Editor

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.

Projects Apollo, JBrowse
Lead

Ian Holmes (University of California, Berkeley)

Funding Cycle 1
Papyri: Better Documentation for the Scientific Ecosystem in Jupyter

To upgrade the interactive documentation experience of IPython and Jupyter to allow inline graphs, navigation, and indexing, and to support features currently only available on hosted websites.

Project Papyri
Lead

Matthias Bussonnier (NumFOCUS, Quansight Labs)

Funding Cycle 4
Performance Boosts and Updated Algorithms in NetworkX

To update NetworkX algorithms, increase performance of key biomedically related tools such as community detection (CD) and subgraph-isomorphism (SI), and develop a roadmap for improved visualization. Note: This proposal was funded by Wellcome Trust as part of our co-funded EOSS Cycle 6.

Project NetworkX
Lead

Daniel Schult (Colgate University)

Funding Cycle 6
PhasorPy: A Python Library for Phasor Analysis of FLIM and Spectral Imaging

To develop an open Python library and community between spectroscopy and fluorescence microscopy users that is both accessible and self-sustainable in the long term.

Project PhasorPy
Lead

Leonel Malacrida (Institut Pasteur Montevideo)

Funding Cycle 5
Predictive Modeling of Single-Cell Multiomics Over Time and Space

To develop an end-to-end, predictive computational ecosystem for quantitative spatiotemporal modeling of spatial and single-cell multiomics.

Project Aristotle
Lead

Jonathan Weissman (Whitehead Institute for Biomedical Research)

Funding Cycle 5
Predictive Models Evaluation & Inspection in Scikit-learn

To sustain the scikit-learn library through maintenance, improvement, and extension, notably in the domain of predictive model evaluation and inspection. Note: This proposal was funded by Wellcome Trust as part of our co-funded EOSS Cycle 6.

Project scikit-learn
Lead

Guillaume Lemaitre (Inria Foundation)

Funding Cycle 6
Processing of Large Image Data in Fiji: ImgLib2/BigDataViewer Ecosystem

To support the maintenance, development and dissemination of ImgLib2 and BigDataViewer, key infrastructural software components for visualization and analysis of large image data on the Java-based platforms Fiji, KNIME, and Icy.

Projects ImgLib2, BigDataViewer
Lead

Pavel Tomancak (Central European Institute of Technology)

Funding Cycle 4
Providing a Solid Foundation for Network Analysis

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.

Project igraph
Lead

Vincent Traag (Leiden University)

Funding Cycle 2
PsychoPy3: Essential Open Source Software for Neuroscience and Psychology

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.

Projects PsychoPy, PsychoJS
Lead

Jonathan Peirce (University of Nottingham)

Funding Cycle 1
QuPath: Boosting Bioimage Analysis for Users & Developers

To enable researchers to more deeply interrogate complex biomedical images by improving the extensibility, robustness, and interoperability of QuPath.

Project QuPath
Lead

Peter Bankhead (University of Edinburgh)

Funding Cycle 4
QuPath: Open Source Bioimage Analysis and Quantitative Pathology

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.

Project QuPath
Lead

Peter Bankhead (University of Edinburgh)

Funding Cycle 1
Raising Diversity and Internationalization in PsychoPy

To hire a dedicated Communities Champion, running code-sprints and contributor workshops and translating our desktop app into additional languages.

Project PsychoPy
Lead

Jonathan Peirce (University of Nottingham)

Funding Cycle D&I
Real-Time Collaboration in Jupyter

This team will build a real-time data model for Jupyter to lay the foundation for real-time collaboration on notebooks.

Project JupyterLab
Lead

Saul Shanabrook (Quansight)

Funding Cycle 2
Real-Time Genomic Epidemiology with IQ-TREE

To significantly speed up IQ-TREE to enable real-time genomic epidemiology during ongoing outbreaks such as COVID-19, and to introduce continuous integration and a testing framework to ease software maintenance for all developers.

Project IQ-TREE
Lead

Minh Bui (Australian National University)

Funding Cycle 4
Rebuilding the Community Behind VisPy's Fast, Interactive Visualizations

To attract new users and contributors to the VisPy project through software improvements, community outreach, and instructional materials.

Project VisPy
Lead

David Hoese (University of Wisconsin - Madison)

Funding Cycle 2
Reproducibility in Bioinformatics by Sustaining Bioconda Development

To establish teaching material, improve documentation, and minimize maintenance effort of the Bioconda project by extending automation of code review, testing, and building.

Project Bioconda
Lead

Johannes Köster (University of Duisburg-Essen, Bioconda Core Team)

Funding Cycle 1
Revitalizing NetworkX for Complex Network Analysis

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.

Project NetworkX
Lead

Stefan van der Walt (University of California, Berkeley)

Funding Cycle 2
Salmon: Improving RNA-seq Quantification & Building an Inclusive Community

To advance support and development of the open source Salmon and Alevin software for gene expression quantification of single-cell and bulk RNA-seq.

Project Salmon
Lead

Carl Kingsford (Ocean Genomics)

Funding Cycle 3
Scalable Storage of Tensor Data for Scientific Computing

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.

Project Zarr
Lead

Ryan Williams (Mount Sinai School of Medicine)

Funding Cycle 1
Scalable Visual Data Analytics with Orange Data Mining Toolbox

To refactor Orange Data Mining toolbox to include the latest Python libraries for parallel, server-based data analysis, allowing it to scale to large biomedical datasets.

Project Orange Data Mining
Lead

Blaž Zupan (University of Ljubljana)

Funding Cycle 4
Scaling OpenRefine

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.

Project OpenRefine
Lead

Antonin Delpeuch (Code for Science and Society)

Funding Cycle 1
Scaling Python with Dask

To provide dedicated community support and maintenance for the Dask project and support growth in the biological sciences field.

Project Dask
Lead

Matthew Rocklin (NumFOCUS)

Funding Cycle 2
Scaling the Foundations of scverse

To scale the core scverse data structures (AnnData, MuData, and SpatialData) for out-of-core/cloud-based analysis to accelerate everything from common analysis tasks to foundational model training. Note: This proposal was funded by Wellcome Trust as part of our co-funded EOSS Cycle 6.

Project AnnData
Lead

Fabian Theis (Helmholtz Munich)

Funding Cycle 6
Scanpy 2.0

To expand Scanpy’s core infrastructure and community platforms for stability, versatility, and sharing knowledge.

Project Scanpy
Lead

Fabian Theis (Helmholtz Zentrum Munich)

Funding Cycle 1
Scikit-learn Maintenance and Enhancement for Gradient Boosting

To improve the open-source machine learning library scikit-learn and aid in maintaining the project, while considering the new implementation of Gradient boosting.

Project scikit-learn
Lead

Andreas Mueller (Columbia University)

Funding Cycle 1
SciPy: Fundamental Tools for Biomedical Research

To better serve biomedical applications, SciPy will add important new features, perform essential maintenance, and disseminate the work to biomedical researchers and software developers.

Project SciPy
Lead

Matt Haberland (California Polytechnic State University, San Luis Obispo)

Funding Cycle 5
scvi-tools: Enabling Probabilistic Analysis for Single-Cell Genomics

To maintain and further develop a community resource for probabilistic analysis of single-cell omics data, including an application interface for rapid development of new probabilistic models.

Project scvi-tools
Lead

Nir Yosef (University of California, Berkeley)

Funding Cycle 4
Seamless Integration of Ad-hoc Analysis into Snakemake Workflows

To enhance Snakemake accessibility with open source tools and engage the community to reduce ad-hoc unstructured code and promote a culture of sustainability in data analysis beyond reproducibility.

Project snakemake
Lead

Ivan Molineris (University of Turin)

Funding Cycle 6
SPAdes and QUAST Toolkits For Genome Sequence Assembly and Analysis

To turn SPAdes and QUAST codebases into scalable, modular, extensible and user-friendly frameworks that will streamline future research and development in genome assembly, analysis and quality assessment.

Projects SPAdes, QUAST
Lead

Anton Korobeynikov (Saint Petersburg State University)

Funding Cycle 4
Sparse Arrays for Scientific Python

To improve sparse structures in SciPy so they support array semantics, to deprecate SciPy’s sparse metrics, and to assist with sparse array adoption in downstream ecosystem packages.

Project Scientific Python
Lead

Stéfan van der Walt (University of California, Berkeley)

Funding Cycle 5
Strengthening Community and Code Foundations for Brain Imaging

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.

Project Nibabel
Lead

Matthew Brett (NumFOCUS)

Funding Cycle 3
Strengthening Computational Neuroanatomy Using DIPY

To extend DIPY’s registration framework for generic use in biomedical research, add parallel computing, strengthen maintenance, expand documentation, and improve educational capabilities.

Project DIPY
Lead

Serge Koudoro (Indiana University - DIPY)

Funding Cycle 5
Strengthening NumPy’s Foundations: Growing Beyond Code

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.

Projects NumPy, OpenBLAS
Lead

Ralf Gommers (Quansight, NumFOCUS)

Funding Cycle 1
Supporting and Sustaining Bioconductor Developers

To champion Bioconductor developers through better community and technical infrastructure, accessibility of documentation, support for developer working groups, and cross-community collaborations.

Project Bioconductor
Lead

Maria Doyle (University of Limerick)

Funding Cycle 6
Supporting Next Generation Single-Cell Genomics Experiments with Monocle

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.

Project Monocle
Lead

Cole Trapnell (University of Washington)

Funding Cycle 3
Supporting the adoption of Xarray in the biomedical research community

To accelerate the adoption of Xarray in the biomedical research community.

Project Xarray
Lead

Joe Hamman (Earthmover PBC)

Funding Cycle 6
Sustained Code and Community Development for NetworkX

To expand and strengthen the NetworkX developer community, reinforce connections with the scientific Python ecosystem, improve documentation and training materials for users, and refine development infrastructure and process.

Project NetworkX
Lead

Daniel Schult (NumFOCUS)

Funding Cycle 4
Sustaining Parsl: Enabling Extreme-Scale Biomedicine

To enable the biomedical community to more easily use large-scale computing to efficiently run complex workflows via Parsl.

Project Parsl
Lead

Kyle Chard (University of Chicago)

Funding Cycle 5
SymPy: Improving Foundational Open Source Symbolic Mathematics for Science

To improve the SymPy Python symbolic mathematics library in the key areas of performance, code generation, and documentation.

Project SymPy
Lead

Aaron Meurer (Quansight)

Funding Cycle 4
The GATK Methods for Bacterial Variant Discovery and Evaluation

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.

Project GATK
Lead

Bhanu Gandham (Broad Institute of MIT and Harvard)

Funding Cycle 1
The Health of pandas

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.

Project pandas
Lead

Tom Augspurger (NumFOCUS)

Funding Cycle 3
The Percolator Analysis Engine for Tandem Mass Spectrometry Data

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.

Project Percolator
Lead

William Noble (University of Washington)

Funding Cycle 2
Transparent, Open & Sustainable Infrastructure for conda-forge and bioconda

To improve conda-forge and bioconda’s sustainability and transparency by adopting vendor-agnostic and secure infrastructure practices and develop comprehensive maintenance metrics and dashboards.

Project conda-forge & bioconda
Lead

Jaime Rodríguez-Guerra (Quansight)

Funding Cycle 5
UCSC Xena Mentorship Program

To cultivate the next generation of biomedical open source software data scientists through recruitment, mentorship, and training of underrepresented students.

Project UCSC Xena
Lead

Jingchun Zhu (University of California, Santa Cruz)

Funding Cycle D&I
Unifying and Enhancing Open Source Transcriptomics Analysis

To improve the interoperability, efficiency, and robustness of popular bulk and single-cell transcriptomics analysis tools, and to add important new capabilities to the open source ecosystem.

Project STAR
Lead

Robert Patro (University of Maryland)

Funding Cycle 6
Unlocking Clinical Data for Biomedical Research in LMICs

To support biomedical research in low-resource settings with open tools for extracting, normalizing, and de-identifying patient-level clinical data from widely adopted OpenMRS Electronic Medical Records.

Project OpenMRS
Lead

Jan Flowers (University of Washington)

Funding Cycle 6
VisPy 2.0: Next-Generation Interactive Scientific Visualization in Python

To support and further develop a library for high-performance scientific visualization in Python by maintaining the VisPy package and improving documentation within the community.

Project VisPy
Lead

Kenneth Harris (University College London)

Funding Cycle 4
Web-Based Analysis and Collaboration Tool, seqr, for Rare Disease Genomics

To maintain and enhance seqr, a high quality rare disease genomic analysis platform, for usage across the global scientific community, enabling collaboration for rare disease diagnosis and gene discovery.

Project seqr
Lead

Heidi Rehm (Massachusetts General Hospital and Broad Institute of MIT and Harvard)

Funding Cycle 5
Xarray: Multidimensional Labeled Arrays and Datasets in Python

To grow the use of Xarray in the biosciences as a foundational data model and computational toolkit for multidimensional labeled arrays.

Project Xarray
Lead

Joseph Hamman (NumFOCUS)

Funding Cycle 2
Zarr: A Common Backbone for the Scalable Storage of Annotated Tensor Data

To establish Zarr as a common, cross-community mechanism for storing collections of annotated tensors with consistent access for both local and large-scale cloud data.

Project Zarr
Lead

Josh Moore (German BioImaging)

Funding Cycle 4

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