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BiocCommits: Bioconductor centric hackathons

Bioconductor is a mature, diverse, and well-maintained project that performs and facilitates research across a variety of medical and natural science fields. One of the strengths of the project over its history has been the Bioconductor community. These hackathon events are intended to bring that community together to tackle project-wide problems and opportunities, from simple bug fixes to maintenance of core packages, to construction and publication of new packages or workflows.

Who can contribute

Participation is open to anyone with experience with Bioconductor software. Though many projects may be deeply technical, the most important qualities needed for participation are a willingness to learn and a commitment to being a good team player. New or early career contributors to Bioconductor are encouraged to participate in person or virtually.

How to contribute

For BiocCommits events attached to conferences, in-person participation is encouraged, but not required. Virtual contributions are welcomed. Most contributions, particularly those to R packages will be expected to be R centric in terms of code actually written. However, some projects focusing on code infrastructure may require fluency in C, Fortran, or other lower level languages. Also, projects focusing on workflows or other themes may require fluency in bash, Docker, specific workflow languages, or 4GLs besides R.

Bioconductor is a diverse and complex project with many ways to contribute.

Project types

BiocCommits events will feature a small array of proposed or solicited project ideas, but participants are welcome to bring their own as long as they’ve been discussed with event organisers beforehand. Generally projects will fall into, but are not limited to, one of three general categories.

Micro Contributions

General bug fixes and feature additions. These are contributions that can be bottled up into a single or a few github pull requests. If you’ve encountered a bug, aberrant behavior, or lack of a useful feature in a core or popular package that is accepting pull requests, these events can provide expertise or guidance for submitting those fixes or feature additions. These can be a great way for new contributors to learn about the internals of Bioconductor and R, good software development practices, version control and management, and team coding environments. Tangible outcomes from these contributions may be (but are not strictly) limited to tracked github activity.

General Contributions

Package or workflow sized team projects. Complete a full and complex package or workflow across the entire event. These contributions will be great for ideas that require diverse scientific or technical backgrounds.

Major Contributions

Complex and thoughtful contributions to existing or planned Bioconductor or R infrastructure. These will typically require considerable fluency with Bioconductor and R internals, C/C++, and good software development practices.

Expected outcomes

There will be an emphasis on generating tangible and public work products from BiocCommits events. Functional and tested R packages and general workflows are ideal, though not required. Participants should be able to point to a professional and accessible github repository at the end of the event that can lead to further projects or collaborations, and serve as a clear resume line representing a work product.

Project scope and goals will be discussed at the beginning of the event.

Planned BiocCommit events

Hackathon on spatial omics and image-derived data

This event is planned for 19-22 April 2026 and will take place at the San Servolo Conference Centre of Venice International University on San Servolo, Italy (an island in front of Venice’s San Marco square).

Topics of interest will include spatial omics and other bioimaging data, with a focus on data representation, interoperable serialization, scalability data handling, Python interoperability, interactive visualization, etc.

We expect both remote and in-person participants from the Bioconductor and scverse communities – across Europe, the USA and Australia – who are working in this field and have a background in software development.

Contributions during and following the event will be coordinated through GitHub, here.

Organizers: * Prof Dr. Davide Risso, Professor of Statistics, University of Padova, Italy * Dr. Wolfgang Huber, Research Group Leader & Senior Scientist, EMBL, Germany * Dr. Helena L. Crowell, SNSF Postdoctoral Fellow, CNAG, Barcelona

The event is funded in part by the European Research Council (ERC) Grant CoG 101171662.

EuroBioc2026 General Hackathon

A general bioconductor-centric hackathon is being planned for the two days preceding EuroBioc2026 in Turku, Finland. A few projects are already planned, but participants are welcome to bring their own as long as those ideas have been communicated to organisers beforehand. General bug hunting or feature additions in existing packages that are willing to accept pull requests will also be supported!

In person participation is encouraged, and virtual participation will be supported on a project by project basis.

Current projects include:

  • An R package for CUDA API bindings, to facilitate development and access to CUDA natively in R, package name TBD
  • A tool for building minimal, lightweight containers for bioconductor packages on the fly, from the package dependency graph
  • A package or function for converting R scripts into commandline executables, with an emphasis on robust and reliable deployment
  • A tidy / spatial -omics project, TBD (this was a generally solicited project, if you are interested in leading or organising it, please reach out!)

If you’re interested please complete our participant form!

Bioconductor is a mature, diverse, and well-maintained project with many different ways to contribute. Participants from all career stages and technical backgrounds are welcome, with the only requirements being a willingness to learn and work well in a collaborative environment.

We will be in contact about a month before the conference to confirm participation, plan out teams for projects, and ensure any questions or concerns are addressed.

Hackathon goals can vary widely depending on project complexity, but in general working and tested R packages are the goal where applicable. Tangible contributions to repositories that can be clearly professionally communicated by participants will be the goal otherwise.

Please direct questions to Nicholas(dot)Cooley(at)ul(dot)ie.

Products and Projects from previous BiocCommits events

Coming soon!