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 Lead: Lior Pachter (California Institute of Technology)
OpenCRAVAT Community Building for Integrated Variant Annotation Framework
To create a sustainable open-source community resource for deep annotation of genetic variants.
Project Lead: Rachel Karchin (Johns Hopkins University)
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 Lead: Thomas Markland (Stanford University)
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 Lead: Ajay Seth (Delft University of Technology)
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 Lead: Vincent Traag (Leiden University)
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 Lead: Saul Shanabrook (Quansight)
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 Lead: David Hoese (University of Wisconsin – Madison)
Scaling Python with Dask
To provide dedicated community support and maintenance for the Dask project and support growth in the biological sciences field.
Project Lead: Matthew Rocklin (NumFOCUS)
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 Lead: William Noble (University of Washington)