Essential Open Source Software for Science (EOSS) Grants

Essential Open Source Software for Science (EOSS) Grants is sponsored by Chan Zuckerberg Initiative (CZI). CZI's Open Science program invests in tools, platforms, and organizations that promote the universal and immediate open sharing of scientific knowledge, processes, and outputs. This includes supporting open-source software development for science.

Essential Open Source Software for Science (EOSS) Proposals - Chan Zuckerberg Initiative 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.

Search the Essential Open Source Software for Science Grants 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.

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

Sonia Pujol (Brigham and Women’s Hospital, Harvard Medical School) Sonia Pujol Steve Pieper Andras Lasso Adriana Herlinda Vilchis González Luiz Otavio Murta Junior 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.

Sonia Pujol (Brigham and Women's Hospital, Harvard Medical School) Sonia Pujol Steve Pieper Andras Lasso Mamadou Camara Ibrahima Fall Samba Diaw 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.

Nir Yosef (Weizmann Institute of Science) 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.

Emmanuelle Gouillart (Plotly Technologies, Inc.) Emmanuelle Gouillart Marianne Corvellec Emmanuelle Gouillart Shammamah Hossain Marianne Corvellec Ryan Kyle Byron Zhu 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.

Warren Weckesser (University of California, Berkeley; NumFOCUS) Matt Haberland (California Polytechnic State University, NumFOCUS) Warren Weckesser Matt Haberland Fletcher Easton 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.

Yvan Saeys (VIB-Ghent University) 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.

Tania Allard (Quansight Labs) Achieving Accessibility for UpSet Plots To make UpSet plots accessible to low-vision and blind users, and to simplify authoring UpSet plots. Alexander Lex (University of Utah) 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.

Gordon Smyth (Walter & Eliza Hall Institute of Medical Research) Gordon Smyth Mengbo Li Pedro Baldoni Gordon Smyth Yunshun Chen Mengbo Li Ilariya Tarasova 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.

NumPy, SciPy, Matplotlib, and pandas Melissa Mendonça (Quansight, NumFOCUS) 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.

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.

Greg Caporaso (Northern Arizona University) Greg Caporaso Matthew Dillon Evan Bolyen Nick Bokulich To enhance the anndataR package for improved interoperability and functionality in handling single-cell data within the R programming environment.

Robrecht Cannoodt (Open Collective Europe Foundation) 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.

Wes McKinney Neal Richardson 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.

Daniel Blankenberg (The Cleveland Clinic) 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.

Thomas Uchida (University of Ottawa) Thomas Uchida Jennifer Hicks Carmichael Ong Ajay Seth 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.

Torsten Seemann (The University of Melbourne) 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.

Christopher Fonnesbeck (NumFOCUS) Christopher Fonnesbeck Thomas Wiecki Ravin Kumar Oriol Abril Breck Baldwin Andrew Gelman 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. Shannan Ho Sui (Harvard T. H.

Chan School of Public Health) Shannan Ho Sui Sergey Naumenko 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.

Bioconductor Build System Vincent Carey (Brigham and Women's Hospital) Vincent Carey Shweta Gopaulakrishnan Benjamin Stubbs Kimberly Glass 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.

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

Vincent Carey (The Brigham and Women's Hospital) 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. Bryan Van de Ven (NumFOCUS) Bryan Van de Ven James A.

Bednar 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.

Alison Pouch (University of Pennsylvania) Alison Pouch Ankush Aggarwal Lukasz Kaczmarczyk Paul Yushkevich 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.

Cyrille Rossant (NumFOCUS) 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.

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.

Daniel McCloy (University of Washington) Daniel McCloy Eric Larson 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.

Brooke Foucault Welles (Northeastern University) 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.

Gavin Huttley (Australian National University) 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.

Rahul Satija (New York Genome Center) Rahul Satija Tim Stuart Paul Hoffman 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.

Rahul Satija (New York Genome Center) 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.

Sarah Keating (University College London) Sarah Keating Frank Bergmann Brett Olivier Sarah Keating Frank Bergmann Brett Olivier 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.

Demuxlet, Freemuxlet, Memento Jimmie Ye (University of California, San Francisco) 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.

Open Molecular Software Foundation Karmen Condic-Jurkic (Open Molecular Software Foundation) 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.

Heng Li (Dana-Farber Cancer Institute) 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.

Dexter Pratt (University of California, San Diego) Dexter Pratt Gary Bader Keiichiro Ono Sophie Liu Max Franz Deep Probabilistic Programming for Biology with Pyro To accelerate single-cell biology methods research and empower their developers with foundational probabilistic AI software.

Eli Bingham (Broad Institute of MIT and Harvard) 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.

Eni Halilaj (Carnegie Mellon University) Eni Halilaj Jennifer Hicks Silvia Zuffi 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.

Mackenzie Mathis & Alexander Mathis (École Polytechnique Fédérale de Lausanne (EPFL)) DeepLabCut: A Software Package for Animal Pose Estimation To provide maintenance, user-focused extensions, education, and support of the growing DeepLabCut software community.

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

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

Mackenzie Mathis (Harvard University & Swiss Federal Institute of Technology Lausanne) Mackenzie Mathis Alexander Mathis 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 Aedin Culhane (University of Limerick) 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. Ricardo Henriques (Instituto Gulbenkian de Ciência) 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.

Yvan Saeys (Vlaams Instituut voor Biotechnologie) Yvan Saeys Robrecht Cannoodt Wouter Saelens 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.

Common Workflow Language (CWL) Sarah Wait Zaranek (Curii Corporation) Sarah Wait Zaranek Peter Amstutz 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.

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 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.

Greg Caporaso (Northern Arizona University) Enhancing Diversity in Computational Mass Spectrometry To increase diversity in computational mass spectrometry through teaching and mentoring with the open-source framework OpenMS.

Hannes Rost (University of Toronto) 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. Ruben Dries (Boston Medical Center Corporation / Boston University) Ruben Dries Jiaji George Chen Joselyn C.

Chávez-Fuentes Guo-Cheng Yuan 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.

Enhancing High-Level Scientific Computing Support in CuPy Kenichi Maehashi (NumFOCUS) 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. Upinder Bhalla (National Centre for Biological Sciences) 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.

Carlos Cordoba (Quansight, LLC) 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.

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).

Open Health Imaging Foundation (OHIF) Viewer, Cornerstone Gordon Harris (Massachusetts General Hospital) Gordon Harris James Hanks Dan Rukas Erik Ziegler Danny Brown Gordon Harris James Hanks Dan Rukas Erik Ziegler Danny Brown 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.

Samuel Isaacson (Boston University, NumFOCUS) Samuel Isaacson Chris Rackauckas Viral Shah 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.

bedtools, Go Get Data (GGD) Aaron Quinlan (University of Utah) Aaron Quinlan Brent Pedersen Hao Hou Aaron Quinlan Michael Cormier Joe Brown 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.

Derek Young (University of Kentucky Research Foundation) 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.

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

Tom Augspurger (NumFOCUS) 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.

Joris Van den Bossche (NumFOCUS) 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.

Mitzi Morris (Columbia University) ETE Toolkit - Enabling Large Scale Phylogenomic Analysis and Visualization To enable interactive analysis and exploration of phylogenetic data at the genomics and metagenomics scale.

Jaime Huerta-Cepas (Centro de Biotecnología y Genómica de Plantas (CBGP, UPM/INIA-CSIC)) Jaime Huerta-Cepas Jorge Botas Miret Ziqi Deng Jordi Burguet Castell 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.

Jaime Huerta Cepas (Centro de Biotecnología y Genómica de Plantas) Jaime Huerta Cepas Renato Alves Ziqi Deng Ana Hernández Francois Serra 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.

Eric Holscher (Read the Docs, Inc) 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.

Daniel Beiting (University of Pennsylvania) 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.

Robert Patro (University of Maryland) Robert Patro Jason Fan Jamshed Khan 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.

Jessilyn Dunn (Duke University) Jessilyn Dunn Brinnae Bent Ida Sim Karnika Singh Will (Ke) Wang 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.

Jeremy Goecks (Oregon Health & Science University) Jeremy Goecks Enis Afgan Nuwan Goonasekera 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.

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

Martin Reuter (German Center for Neurodegenerative Diseases) 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.

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

Juan Nunez-Iglesias (Monash University / NumFOCUS) Juan Nunez-Iglesias Lars Grüter Marianne Corvellec 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.

Henrik Bengtsson (University of California, San Francisco) 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.

Dana Vuzman (Harvard Medical School) Dana Vuzman Dominik Glodzik William Ronchetti Kent Pitman 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.

Gregory Lee Marianne Corvellec Emmanuelle Gouillart Juan Nunez-Iglesias 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.

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

Robert Haase (Cluster of Excellence “Physics of Life”, Technische Universität Dresden) Robert Haase Stéphane Rigaud Martin Jones Lucy Collinson Amy Strange 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.

Sarah Wait Zaranek (Curii Corporation) 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.

Robert Castelo (Universitat Pompeu Fabra) Robert Castelo Justin Guinney Beatriz Calvo 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.

Eric Banks (Broad Institute of MIT and Harvard) Eric Banks Louis Bergelson Christopher Norman 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.

Anna Kreshuk (European Molecular Biology Laboratory) 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.

Anna Kreshuk (European Molecular Biology Laboratory) Anna Kreshuk Dominik Kutra 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.

Anna Kreshuk (European Molecular Biology Laboratory) 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.

Bryan Van de Ven (Nvidia) Bryan Van de Ven Carolyn Hulsey Pavithra Eswaramoorthy Brendan Collins 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.

Heng Li (Dana-Farber Cancer Institute) Heng Li Haoyu Cheng Heng Li Heng Li Haoyu Cheng 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.

Antonin Delpeuch (Code for Science & Society) 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. J. Gregory Caporaso (Northern Arizona University) Nicholas Bokulich (ETH Zurich) J.

Gregory Caporaso Nicholas Bokulich 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.

Jean-Baptiste Poline (McGill University) Jean-Baptiste Poline, Jerome Dockès, and the Nilearn core developer team Improving the Analytical Flexibility of bedtools To improve the flexibility and utility of bedtools for large-scale genomic analyses.

Aaron Quinlan (University of Utah) Aaron Quinlan Hao Hou Joe Brown 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.

Melissa Mendonça (Quansight) Melissa Mendonça Pearu Peterson Martin Kroeker 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.

Daniel McCloy (University of Washington) 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. Ernest W. Durbin III (Python Software Foundation) Ernest W.

Durbin III Sumana Harihareswara 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.

Jingchun Zhu (University of California, Santa Cruz) Jingchun Zhu Brian Craft Mary Goldman 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.

Tania Allard (Quansight LLC) Tania Allard Isabela Presedo-Floyd 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.

Carl Kingsford (Ocean Genomics) 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.

CCTBX, Integrative Modeling Platform (IMP), and qFit James Fraser (University of California, San Francisco) 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.

Mark Musen (Stanford University) Mark Musen Matthew Horridge 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.

Minh Bui (Australian National University) 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.

Chris Holdgraf (NumFOCUS) JupyterHub Contributor in Residence Program To improve community support and technical maintenance across the JupyterHub repositories.

Project Jupyter (JupyterHub, The Binder Project) Chris Holdgraf (University of California, Berkeley; NumFOCUS) Chris Holdgraf Tim Head Georgiana Dolocan LinkML: An Open Data Modeling Framework to increase usability of LinkML (Linked data Modeling Language), an open, extensible framework for modeling, validating, and distributing data that is reusable and interoperable.

Note: This proposal was funded by Wellcome Trust as part of our co-funded EOSS Cycle 6. Sierra Moxon (Lawrence Berkeley National Laboratory) 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.

Tao Liu (Roswell Park Alliance Foundation) 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.

Tao Liu (Roswell Park Alliance Foundation) 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.

Carl Boettiger (University of California, Berkeley) Carl Boettiger Noam Ross Dirk Eddelbuettel 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.

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.

Rory Kirchner (Harvard Chan School of Public Health) Rory Kirchner Sergey Naumenko 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. Thomas A.

Caswell (Brookhaven National Laboratory, NumFOCUS) Thomas A. Caswell Hannah Aizenman Michael Grossberg 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