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 Lead: Fabian Theis (Helmholtz Munich)
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 Lead: Ivan Molineris (University of Turin)
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 Lead: Maria Doyle (University of Limerick)
Supporting the adoption of Xarray in the biomedical research community
To accelerate the adoption of Xarray in the biomedical research community.
Project Lead: Joe Hamman (Earthmover PBC)
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 Lead: Robert Patro (University of Maryland)
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 Lead: Jan Flowers (University of Washington)
Achieving Accessibility for UpSet Plots
To make UpSet plots accessible to low-vision and blind users, and to simplify authoring UpSet plots.
Project Lead: Alexander Lex (University of Utah)
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 Lead: Gavin Huttley (Australian National University)
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 Lead: Rahul Satija (New York Genome Center)