Maintaining and documenting seven Bioconductor services after sudden relocation of core engineer #74
Description
Project
Bioconductor
Summary
In the fall of 2025, one of Bioconductor's five core engineers suddenly relocated out of the United States due to immigration concerns, leaving some public infrastructure services developed by this team member without a viable maintainer. This proposal requests funding to create comprehensive public documentation for these services, which address common challenges (for some across any open-source scientific project, others specifically relating to R-based scientific projects), as well as maintain them for one year while exploring long-term funding solutions post-relocation from the United States to Europe.
submitter
Alexandru Mahmoud
project lead
Community benefit
Impact on Bioconductor Community
The sudden departure of a core engineer has created an immediate need for Bioconductor users who depend on several services that have become integral to their workflows and expectations. These services were developed organically during previous years in response to emerging community needs, despite not being part of original project plans. Their discontinuation would represent a significant regression in user experience, and potentially undermine community trust in the project's reliability.
Without this funding, essential services may gradually degrade and fail. Namely, the Dev Status Page (https://dev.status.bioconductor.org/) provides transparency about system health. The Identity Management System enables seamless authentication for Bioconductor users, especially for the workshop cloud infrastructure. The Hubs Ingestion Platform securely processes community data contributions that enrich the Bioconductor ecosystem. The bioc2u and webR/RWASM binaries have transformed how users deploy Bioconductor in Ubuntu-based environments and browser-based educational settings. Losing these capabilities would force users to implement complex workarounds or abandon Bioconductor-related products.
Broader Scientific Computing Ecosystem Impact
This project delivers significant value beyond Bioconductor by thoroughly documenting reusable infrastructure patterns that address common challenges faced by open-source scientific computing projects, particularly R-based projects. The comprehensive public documentation will serve as templates and reference implementations that other projects can adapt, reducing duplicated effort across the Open Source Open Science ecosystem.
The Dev Status Page (https://dev.status.bioconductor.org/) provides an open-source solution for automated service monitoring with user-facing transparency, a need shared by any project managing distributed infrastructure. The Keycloak-based Identity Management System offers a production-ready complete implementation for projects requiring centralized authentication across multiple services, particularly valuable for communities running workshops or multi-tool ecosystems where user login is useful. The Hubs Ingestion Platform addresses the universal challenge of securely accepting, validating, and publishing community data contributions while maintaining security and quality standards. The simple redirect endpoints (https://slack.bioconductor.org) provide elegant and user-friendly solutions for service migrations that maintain user trust through transparent communication.
For R-ecosystem projects specifically, the bioc2u infrastructure demonstrates how to deliver system-integrated package installation via Debian’s native apt package manager widely used in Ubuntu systems, and the webR/RWasm binaries enable modern browser-based R experiences without any backend server. These patterns are directly applicable to other R-based projects.
By maintaining and documenting these services thoroughly, this grant transforms project-specific solutions into reusable community resources, while maintaining continuity of services for the Bioconductor community.
Amount requested (USD)
10000
Execution plan
Implementation Details
The relocated core engineer who designed and maintained all these services will execute this project on a part-time basis over 1 year. As one of Bioconductor's five core engineers, this individual possesses irreplaceable institutional knowledge and technical expertise spanning identity management, cloud infrastructure, containerization, binary compilation, and web services. No other team member has equivalent familiarity with these systems, making knowledge transfer through comprehensive documentation essential. Bioconductor project leadership and the Core Team as a whole will provide oversight, strategic guidance on priorities, and facilitate knowledge sharing with other team members during the SDG period.
Timeline and Milestones
Months 1-2: Infrastructure Assessment and Framework (15 hours)
- Ensure services are still running and perform critical updates to maintain continuity
- Establish documentation structure and templates
- Set up public GitHub repositories for documentation for services lacking existing repos
Deliverable: Updated production services running as expected, and documentation repositories created
Months 3-6: Primary Documentation Phase (105 hours)
- Continue maintaining services infrastructure and performing minor updates as needed
- Produce comprehensive documentation for all six services
- Develop deployment guides with infrastructure-as-code templates where appropriate
- Write troubleshooting and maintenance procedures
- Document security considerations and best practices
- Build example configurations for production deployments
Deliverable: Complete draft documentation for all six services ready for review by other team members
Months 7-9: Refinement and Maintenance (40 hours)
- Continue monitoring service health and apply future-proof updates (eg: updating to latest OS/Kubernetes versions)
- Incorporate feedback from Bioconductor team and any early adopters
- Provide user/admin support for documentation-related questions, establishing one-on-one meetings with other team members as needed to ensure adequate knowledge transfer
- Refine documentation based on operational learnings
Deliverable: Refined deployment documentation and addition of update procedures documentation
Months 10-12: Sustainability Transition (40 hours)
- Perform final service maintenance and security updates
- Finalize all documentation with lessons learned
- Complete knowledge transfer materials for future maintainers after attempted use by other team members
- Document long-term sustainability recommendations and expected update cadence
Final Deliverable: Complete public documentation suite and validated transferred knowledge
Budget Allocation
The $10,000 budget covers 200 hours at $50/hour roughly divided across the 1-year project as described above, with maintenance tasks throughout the period, and a clear timeline for the creation of public documentation. All work will be tracked transparently through GitHub activity, monthly progress reports to Bioconductor leadership, and publicly visible documentation commits. The final deliverable will be up-to-date services in production and a comprehensive, publicly accessible documentation suite that enables both continued operation of these services and adaptation by other projects in the scientific computing ecosystem.