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Bioconductor Build System: Continuous Integration and Developer Feedback

Project Bioconductor Build System

Vincent Carey (Brigham and Women's Hospital)

Funding Cycle 1

Proposal Summary

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

The Bioconductor mission is to promote the statistical analysis and comprehension of current and emerging high-throughput biological assays. Bioconductor is based on packages written primarily in the R programming language. Bioconductor is committed to open source, collaborative, distributed software development and literate, reproducible research. Enabling user and developer communities is an essential part of our mission. Scientific and Technical Advisory Boards provide project oversight. This proposal enhances the Bioconductor project by re-engineering the (currently bespoke) continuous integration and package distribution system to be more scalable, robust, maintainable, and independently deployable. The build system is a fundamental vehicle for coordinating and improving the reliability of work of hundreds of developers of components of a widely-used and interoperable genome analysis software ecosystem. Bioconductor is already closely involved with multiple communities and large-scale projects such as Human Cell Atlas and NHGRI AnVIL.

Key Personnel

Vincent Carey
Shweta Gopaulakrishnan
Benjamin Stubbs
Kimberly Glass